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Learning Objectives After studying this chapter, you should be able to: • Explain why plants are important for humans and the environment. • Understand the process of scientific inquiry and follow the steps of the scientific method. • Describe the difference between basic and applied science • List some examples of what a botanist does and explain why it is important to learn about plants. 01: Introduction To Plants Plants are a common sight in our daily lives, the grass in the park, the flowers in our neighborhood, the shade trees in the streets, the palm trees on the beach, the green on the mountains, or even the leaves on our salad. However, we usually do not stop to think about the crucial role of plants in our ecosystems, their importance in our lives, or the basics of how they function. For starters, plants provide us with food and oxygen. They belong to a group of organisms that are able to produce their own food (autotrophs) through a process called photosynthesis, and since they also produce the food for most animals, including humans, they are the basis (producers) for all terrestrial ecosystems (Figure $1$). Besides food (in the form of sugars), photosynthesis also produces oxygen, which is required for all animals, fungi, and most bacteria in order to survive. As the producers in terrestrial ecosystems, plants are found on all of the continents of Earth, in all types of ecosystems, like forests, deserts, and savannas. They provide not only food for animals, but also shelter and nesting materials, among other things. Over millions of years of evolution, plants and other organisms, like insects, have created relationships that make them indispensable for each other's survival (Figure $2$). Just think about bees and flowers, you cannot remove either from the equation without having dire consequences on the ecosystem. In the case of Hawai‘i, these relationships are truly unique, given that the Hawaiian archipelago is one of the most isolated places on Earth. With over 47 million years of evolution in isolation from people and large terrestrial mammals, Hawaiian plants and animals have forged unique relationships, creating a delicate balance on the Hawaiian ecosystems. The majority of native Hawaiian plants are unique and cannot be found anywhere else on Earth. Hawaiʻi’s climate and landscape play an important role in the diversity of native plants that can be found here. For example, 90% of native plants are endemic therefore can only be found in Hawai‘i. Not only do we need plants for food and oxygen, but our lives are intertwined with plants. We use plants for a variety of things: raw materials for paper, building materials, solvents and adhesives, fabrics, medicines, biofuels (i.e. biodiesels and ethanol), and many other products. Plants also play a crucial role in most cultures. If you think of a wedding or graduation, very likely plants are involved. Ceremonial uses of plants can be found in most cultures around the world. Hawai‘i is a special place due to people’s cultural connection to plants. Once humans arrived in the islands, many new plant species were introduced eventually creating the collection of plants we find in Hawai‘i today. The strong connection of Native Hawaiians to plants can be seen in hula, medicine, and agriculture (Abbott, 1992; Lincoln and Vitousek, 2017; Figure $3$). It can also be seen in inclusion of kalo as an intrinsic part of their genealogy. As Kalei Laimana articulated “the strongest evidence that Hawaiians sought to solidify their connection to plants occurred when they included the kalo plant into their genealogy as a Kaikuaʻana (elder sibling) to the Hawaiian people. No other plant has ever been given such a place of honor and reverence. Such familial relationships set up the proper relationship of respect and endearment for future generations” (pers. communication).	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/01%3A_Introduction_To_Plants/1.01%3A_Why_are_plants_important.txt
The science that studies plants is called Botany. All natural sciences, including botany, aim to understand how the natural world functions. To be able to do this we need to make observations, run experiments, generate and test hypotheses, record data, and report results. In Western science, people use a series of steps, called the scientific method, that helps to answer a question in an unbiased way. It is important to notice that indigenous peoples across the globe have their own knowledge systems that are different from the Western science approach, where “...knowledge for observing, collecting, categorizing, recording, using, disseminating and revising information and concepts that explain how the world works…” (Whyte et al., 2016). Indigenous knowledge often takes place at a much longer time scale with knowledge and observations passed on from generation to generation. The two systems do not need to be isolated and sometimes are used together to answer questions. “Hawaiians like many indigenous people were careful observers of nature. They observed closely, developed possible explanations for what they observed, conducted experiments to either confirm or refine their understanding until they were confident in their understanding. Once their understanding was perfected, they then committed it to memory using such mnemonic devices as the mele (song), oli (chant) or moʻolelo (story) which was then passed on to the next generation. We only have to look at Hawaiian fishponds to realize how many observations, experiments, refinements that must have taken place before they made the immensely huge labor intensive commitment to build a fishpond. One thing we can be sure of, the perfection of the Hawaiian fishpond did not occur in one generation; it was a deliberate process. The western "Scientific Method" operates in much the same way, observations are made, hypotheses presented, experiments conducted to refine the observation, the main difference is that in the west every step is carefully written down and documented.” (Kalei Laimana, pers. communication). The Scientific Method Botanists and other scientists learn about the natural world by asking questions about it and using a systematic approach, known as the scientific method, to find answers. It might surprise you to learn that even you use this method in your life to solve everyday problems or answer questions that are apparently not related to science. The first step of the scientific method is an observation, which usually leads to a question. Imagine you have some beautiful puakenikeni plants in your garden and you notice their leaves start to turn yellow (Figure $1$). This is an observation that can lead you to the question: “why are the leaves of my plants turning yellow?” Since you are not a plant expert, you turn to the internet or a member of the family that has a green thumb to try to answer the question and ultimately solve the problem. Scientists follow a similar process; they research information relevant to the question to try to find the answer to it, see if other scientists already tried to answer the question or came across a similar problem and how they solved it. Going back to our example, after you search the internet for “plant leaves turning yellow” you find several potential reasons for the leaves of your plants turning yellow. Which one is the correct one? After reading more details about some of the causes you decide it must be lack of water, the soil around your plants seems dry so your plants are probably not getting enough water. Now you have a likely answer for your question, or a hypothesis. A hypothesis is a potential explanation for the question that can be tested. Hypotheses usually follow an “if … then” format, that represents the question and the proposed solution. In this case your hypothesis could be: “If I water my puakenikeni plant more often, then the leaves won’t turn yellow.” In our example, there are different reasons that can cause the leaves on your plants to turn yellow, so there are several hypotheses that could be tested, and this is true for most questions in science. Take a look at the scientific method flow chart presented in Figure $2$. You can see that we have already followed several of the steps that compose the scientific method in our example: observation, question, and hypothesis/prediction. The following step is to run an experiment to test your hypothesis. Now, how would you test your hypothesis? Sometimes we imagine that scientific experiments are complex and advanced processes that need to be carried out in a super fancy and high-tech facility, but that is not always the case. To a certain extent, we all can run experiments in an easy and accurate way. After determining that your plants have been underwatered, the most logical experiment would be to add more water than normal to your plants to see if this solves the yellowing of the leaves. An experiment can be as simple as that; however, scientists need to be sure of exactly what is affecting the results. In order to do this scientific experiments have one or several experimental variables, which is (are) the part(s) of the experiment that can be changed. In our case the amount of water provided to the plants would be the experimental variable. Experiments also need a control group, which is a group that has all the same characteristics as the experimental group (the one in which you are changing the variable), but in which we do not change the variable. By having a control group, we are making sure that the lack of water is the variable (characteristic) that is causing the yellowing of the leaves in your plants and that there is not another reason. In your garden a simple way to test this hypothesis accurately would be to set up an experiment that includes an experimental group and a control group. In the experimental group you are going to have at least one puakenikeni plant that you are going to water more frequently, so the variable you are changing is the water frequency. On the other hand, the control group will be at least one puakenikeni plant to which you will continue to water with the same frequency as you have done until now. You will continue to do this for several weeks, and then you can record your results. If a scientist wanted to run a similar experiment, she/he would probably run it in a greenhouse or nursery, to be able to regulate all other environmental conditions and any other variables, so that nothing else affects the results of the experiment. A scientist would also have several replicas or repetitions of the experiment, to ensure that the results are unbiased. For example, instead of increasing the watering on just one plant, a scientist might have a group of 30 plants that are watered more frequently as the experimental group and a group of 30 plants that are kept in the same watering regime as the control group. The next step in the process is to analyze the results. For several weeks you have been watering at least one of your puakenikeni plants more frequently (experimental group) and kept watering at least one puakenikeni plant as before (control group), so it is time to analyze the results of your experiment. You take a good look at the leaves of both plants and to your dismay the leaves of both plants look similarly yellow. At this point you can conclude that it was not the water that was causing the yellowing of the leaves in your plants, therefore your initial hypothesis was incorrect. What do you do next to save your plants? If you look at the flowchart of the scientific method (Figure $2$), you see that if your hypothesis was not supported by your experiment then you need to try again. Do you remember that there were other causes you found on the internet that could be causing the yellowing of the leaves in your plants? Well, you can now test another hypothesis: maybe your plant is suffering from a lack of nutrients in the soil. You need to run a new experiment to test this new hypothesis in a similar way you tested for the water hypothesis. So let’s imagine you add fertilizer to at least one of your puakenikeni plants to increase the nutrients available in the soil (experimental group) and leave at least one puakenikeni plant without fertilizer (control group). After several weeks you analyze the results, and you see that the plant that had fertilizer added now has beautiful green leaves and looks healthy, while your control plant has yellow leaves. Congratulations, you have cracked the case and now you can help your plants live long and healthy lives by adding fertilizer to all of your puakenikeni plants! Normally, an experiment requires replication, so it would require that you had several plants in your control group and several in your experimental group. That’s not always possible if you are doing that in your backyard, but it is important to know that researchers do that to make sure that the results are not the influence of a random variable (for example, the influence of the location of the plant). The last step in the scientific method is to report or disseminate the results, which in the scientific community is usually done by publishing a scientific paper or report, doing a public presentation in a scientific meeting, or even publishing an article in a newspaper if the issue is of interest to the community. This last step is important, because it helps to build knowledge and advance science, so that we do not get stuck trying to solve the same issue over and over again. In our example, you could also share the results of your experiment with your family and friends to help somebody facing the same issue. Experiments are not the only way to answer a question in science. Sometimes we use descriptive methods when an experimental approach is not feasible. For example, if you wanted to determine how many individuals of an endangered Hawaiian plant are left in the wild in Mount Ka‘ala on O‘ahu, the best approach would be to do a survey or record all the plants of that species in that mountain, instead of running an experiment. Basic and applied science There are two main types of science: basic and applied. Basic science aims to broaden knowledge; not seeking to find a practical utilization or creating a product, just the spread of knowledge in the subject. An example of basic science would be to record all the different species of plants that are present in Hawai‘i. This does not seem to have any practical application, but we could actually use the knowledge gathered in basic science for applied science. Applied science aims to use science to create a product or solve a real-life problem. For example, if we recorded all the individuals of an endangered Hawaiian plant that are left in the wild in Mount Ka‘ala on O‘ahu, we could use this information to create a conservation plan to save this species from extinction by growing it in the lab and then planting it in the wild to restore native ecosystems. A great example of applied plant science is agriculture, because it uses the plant knowledge to create and improve plant varieties that are adapted to local environments, produce more fruit or yield, or increase resistance to drought. An example is tomato varieties that were developed by University of Hawai‘i plant breeders that were resistant to several tropical diseases. This effort not only helped local food production from 1950-1980s, but helped breeding programs in many countries. The tomato varieties developed here were then used by other research programs to breed other varieties (Teves, 2017). Why is Botany important? Botany is a broad science with many different sub-disciplines that encompass different aspects of plant sciences. Some botanists work on biotechnology, like people extracting compounds from plants to create medicines or studying the chemicals produced by different plants to find new uses for them. For example, we use some plant chemicals to treat certain types of cancer. One of these compounds is taxol, which is extracted from the Pacific yew (Taxus brevifolia) and is used to treat ovarian cancer. Botanists in the field of conservation, seek to preserve plant species and restore damaged ecosystems. They can also use biotechnology and grow a whole plant out of a single cell (tissue culture). Other botanists are interested in understanding how plants function (plant physiology), so they focus on studying things like photosynthesis, transportation of nutrients, and the movement of water in plants. Other botanists are more interested in exploring how plants have traditionally been used by people in cultural practices, medicine, or cooking (ethnobotany). Other botanists are interested in studying fossil plants and understanding how plants have evolved over time (paleobotany and plant evolution). These are just a few examples to illustrate the diversity of the botanical field. Learning about plants is not only useful for botanists, but to all people. For example, learning about plants can help you grow and maintain healthy plants in your house and garden. In some booming businesses, like natural products and hemp/marijuana products, there is always the need for people with plant knowledge and, in some cases, lab experience, as the extraction of plant compounds can require the use of specific lab techniques. Learning about plants that have traditionally been used in your culture can also help you to connect with your family and community (Figure $4$). And of course, you cannot pass up the opportunity to answer some of the burning questions that you always had: Why are plants green? What is that smell when I cut grass? How do some plants move? What are those sticky things that attach to my socks? Do carnivorous plants eat human flesh?	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/01%3A_Introduction_To_Plants/1.02%3A_The_science_of_Botany.txt
Plant cells Let’s start with the most basic unit of life: cells. All living organisms are composed of cells, and are called unicellular when they are composed of a single cell or multicellular, when they have more than one cell. A plant is composed of millions of cells, organized into tissues (similar cells grouped together) and organs (different tissues grouped together). All living cells have common structures like the cell membrane, cytoplasm or ribosomes. Some groups of organisms have certain characteristics in their cells that are unique. Plant cells, for example, are different from animal, fungi, and bacteria cells. They have cell walls, a central vacuole, and chloroplasts. Cell walls in plants are made of cellulose, hemicellulose, and pectin, organic compounds called polysaccharides. The function of the cell wall is to protect the cell and provide mechanical support. A thicker cell wall provides more mechanical support and a thinner cell wall provides flexibility. The central vacuole is essential in the regulation of the turgor pressure, which is the pressure that liquid exerts against the cell wall (Figure $1$). This internal pressure is important for the physiology of plants because that’s how they are able to remain upright and not wilt. Plants also have unique organelles, called plastids, that have different functions: photosynthesis (chloroplasts), synthesis and storage of starches (amyloplasts), and synthesis of special pigments (chromoplasts). Plant tissues Plants are composed of different types of cells, which have different functions. The cells group together into tissues, which in plants can be simple (one type of cell) or complex (more than one type of cell). Simple plant tissues are parenchyma, collenchyma and sclerenchyma. • Parenchyma cells are the least specialized type of plant cell and the most abundant in plants. They are usually rounded and can be found in all plant organs. In leaves they make up the mesophyll, where photosynthesis takes place (Chapter 4). In stems and roots they make up the cortex, which is responsible for storing carbohydrates and other substances needed for plants to function (Chapters 2 and 3). Parenchyma cells also participate in plant support and the transfer of nutrients in the phloem. Parenchyma cells are the cells that divide and produce new cells when plants are growing. Parenchyma cells make up the parenchyma tissue. • Collenchyma cells are elongated and provide support to growing plant organs, like leaves. Their primary cell wall is thick, but lacks lignin, making them flexible. Collenchyma cells group into a tissue of the same name. • Sclerenchyma cells are thick as their cell walls contain lignin, a rigid polysaccharide. They are mostly dead when mature, and their main function is to provide mechanical support, for example in the stem. Complex plant tissues are xylem, phloem, epidermis and periderm: • Xylem is the tissue that transports water and nutrients from the roots to the leaves. It is composed of specialized parenchyma cells, tube shaped cells called vessels and tracheids, form long tubes for longitudinal transportation and are usually dead at maturity, and ray cells for lateral conduction. • Phloem is the tissue that transports the sugars produced in photosynthesis. Unlike xylem, it is composed of live cells called sieve tube members (tube shaped cells) and companion cells, which help control the flow of liquid on the sieve tube members. • Epidermis is usually a one cell layer on the outside of the plant tissues for protection, and secretes a protective layer called cuticle. Different cells can be found here: parenchyma cells, guard cells in the stomata (openings for gas exchange on leaves), trichomes (hairs), root hairs in the roots, and glands (production of substances). • Periderm is the outermost layer of woody plants, or outer bark. It is composed of cork cells and lenticels, which are clusters of parenchyma cells that help bring more oxygen into the stem.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/01%3A_Introduction_To_Plants/1.03%3A_Plant_cells_and_tissues.txt
Learning Objectives After studying this chapter, you should be able to: • State the primary functions of roots. • Distinguish the two types of root systems. • Identify the different root regions and their corresponding function: root cap, region of cell division, region of elongation, and region of maturation. • List the name and function of the main root tissues: epidermis, cortex, endodermis, pericycle, xylem, and phloem. • Describe how water absorption happens in roots. • List and describe the various types of specialized roots and provide examples of each. • List economically important root crops. 02: Roots Roots are the plant tissue that we see less often because they are usually found underground, making them the plant tissue that we know the least about (Figure $1$). Roots come in all sizes and lengths, being deeper for trees and more shallow for herbs. Some trees in arid places can grow very deep root systems in search of underground water. Kiawe (mesquite, Prosopis pallida), which is an introduced species in Hawai‘i, can grow a root system as deep as 55 meters (180 feet). In contrast, some plants like giant redwoods have a widespread but relatively shallow root system. The giant redwood tree (Sequoiadendron giganteum) can be as tall as 75 meters (245 feet) with roots reaching only 12 -14 meters (39 - 46 feet) into the ground, but extending for over 4,000 square meters (1 acre). Roots have three main functions in plants. First, they anchor the plant to the soil, providing mechanical stability and support. Second, they absorb water and dissolved minerals from the soil and transport them upward to be used by the plant. Third, roots store the carbohydrates produced in photosynthesis. Besides these basic functions, roots also produce and export the plant hormones cytokinins and gibberellins, which are involved in promoting cell division and plant growth respectively. Finally, in addition to their basic functions, some roots also have specialized functions which we will discuss later in this chapter. There are two types of root systems: taproots and fibrous roots (also known as adventitious roots; Figure $2$). Tap roots have a prominent primary root that develops when the seed germinates and the radicle emerges. From there, secondary or lateral roots grow. As the secondary roots grow they can also get thicker and develop further secondary roots, ending in a highly ramified root system. Taproots are characteristic of eudicots (Chapter 9), such as beans and carrots. Fibrous roots, as the name suggests, look like fibers, with all the roots being of similar length and diameter. Fibrous roots usually form a dense superficial root system. Fibrous roots are also known as adventitious roots because the primary root that forms when a seedling germinates does not remain. Instead, roots grow out of the stem of the plant and are called adventitious. Fibrous roots are characteristic of monocots (Chapter 9), such as corn and grass (Figure $2$). 2.02: The regions of the root When a seed is germinating, one of the first things to emerge from the seed coat is the root. This initial “root” is called a radicle and as it grows it gives origin to the root system. To understand how roots grow, we need to take a peek inside of a growing root. If we look at a root tip, we can recognize four root regions: the root cap, the region of cell division, the region of elongation and the region of maturation (Figure $1$). All of these regions are usually found within the first few centimeters of the root tip, so we are talking about a very small area. Root Cap A root growing into the soil faces physical challenges, like friction and potential damage from rock particles present in the soil. The root cap is a mass of cells (parenchyma cells) located at the tip of the root that protects it from mechanical damage. It also secretes a slimy substance called mucilage to help the root grow more smoothly into the soil. The root cap also plays a role in the plant perception of gravity (gravitropism), which makes plant roots always grow downward (Figure $2$). The region of cell division The region of cell division is found just under the root cap. In this region, cells are perpetually dividing (mitosis), meaning there is a constant generation of new cells, causing the root to grow in length (primary growth). These regions of active cell division in plants are found in the growing tips of roots and stems, and they are called apical meristems. The region of elongation Following the region of cell division is the region of elongation. When new cells are created in the apical meristem of the root they are small and rounded. In this region they grow in size, lengthening the root as they grow. The cells in this region are still undifferentiated; therefore they do not have a specific function yet. The Region of Maturation Following the region of elongation comes the final one, the region of maturation, where cells differentiate and become a specific type of cell. It is here that cells get their final function assigned depending on where they are located in the root. For example, cells in the center of the root will become specialized in transport (xylem and phloem), while the cells towards the periphery (outside) of the root will become specialized in protecting the root (epidermis). In this region of maturation is also where root hairs are formed. Root hairs are extensions of some epidermal cells in the region of maturation (Figure $2$). They extend the surface area of each cell, increasing their absorption capacity. In fact, most of the water and mineral absorption happens in the root hairs; therefore plants have massive amounts of them (in the range of several billion in a mature plant). Root hairs are delicate and only survive for several days, but as the root grows, new root hairs are formed in the region of maturation. Root hairs can be easily damaged if you are transplanting seedlings to a new pot, which may limit the seedling’s ability to absorb water and nutrients.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/02%3A_Roots/2.01%3A_Types_of_root_systems.txt
The main function of roots is the absorption of water and dissolved nutrients. To understand how water moves from the soil to the root and from there to the stems and leaves, we need to look at the different internal layers (tissues) that are inside of the root. If you take a carrot root and lay it flat on a cutting board, then cut it into thin slices, in each slice, you are able to see different concentric areas or tissues (Figure $1$). A tissue is defined as a group of specialized cells that have a common function. This type of cut in botany is called a cross-section, and it allows us to have a top view of the tissues inside of a plant; in this case, a top view of the root tissues. Starting from the outermost layer in a root the first thing we find is the cuticle, which is not a tissue, but a waxy substance that covers all external parts of a plant. Its main function is to protect the plant from water loss and bacterial or fungal infection. In the roots, the cuticle is thin to allow water absorption. After the cuticle we find the true tissues of the root, starting on the outside of the cross-section to the inside we find: epidermis, cortex, endodermis with Casparian strips, and the stele or vascular cylinder which is composed of pericycle, xylem and phloem (Figure $2$). Root tissues Epidermis (epi = outside; dermis = skin) literally translates as outer skin, and it delimits the root, protecting the inner tissues from the outer environment and physical damage.It usually is one cell layer thick. Cortex is the tissue just underneath the epidermis and it is several cell layers thick. The function of the cortex is to store food and water. Endodermis (endo = inner; demis = skin) literally means the inner skin. It delimits the inner cylinder of the root and it is one single layer of cells. The cells of the endodermis are thicker than those in the cortex because the cell walls of the endodermal cells have lignin and suberin (structural plant compounds) that form bands called Casparian trips. These waterproof strips play an important role in the absorption of water in the roots, by not allowing the water and dissolved substances to pass in through the porous cell wall of the endodermal cells, but instead forcing the water to move to the inside of the endodermal cell to be transferred from there to the vascular cylinder. We will review this in more detail in the section below: Absorption of water and dissolved substances. Pericycle is the tissue found just inside of the endodermis, commonly one cell thick and it is the first one found on the stele or vascular cylinder. Its main function is to produce lateral roots. Xylem is the tissue in the middle of the root, usually looking as an X in young eudicots, and arranged in a ring around a central pith in monocots (Figure $3$). The xylem is responsible for water and dissolved nutrient transportation. It transports water upward from the roots to the leaves. Phloem is the tissue that transports the carbohydrates (sugars) produced in photosynthesis throughout the plant. In roots it is usually found in between the xylem in the vascular cylinder. In Biology all transport tissues are referred to as vascular tissues. For example, when we talk about vascular diseases in humans, we are referring to a disease that affects our vascular tissues: arteries and veins. In plants we also use the term vascular when referring to the plant transportation system. Instead of arteries and veins, plants have xylem and phloem. As we just learned, roots have a vascular cylinder, which in simple terms is a cylinder in the middle of the roots that has xylem and phloem. These two tissues are found in all plant organs: roots, stems, leaves, and reproductive organs. Absorption of water and dissolved nutrients Plants need water for several physiological processes required for their survival, such as photosynthesis and transpiration. The water in soil is absorbed by the roots and transferred to the xylem to be transported to other parts of the plant. Water moves from the soil to the root hairs through a process called osmosis. In osmosis, water moves through a plasma membrane from a place with more water to a place with less water. Because of the presence of salts and other minerals inside of the root hairs, water is less abundant inside of the cells than on the outside in the soil, where there are less salts and minerals: therefore the water present in the soil moves to the inside of the root hairs. If you remember, water is transported by the xylem. Do you remember where the xylem is located in a root? It is the innermost tissue, found in the middle of the vascular cylinder. This means that the water that is absorbed by the root hairs has to be moved through every single tissue of the root until it finally reaches the xylem, where it will be transported upward to the plant. After water is absorbed by the root hairs it can move through the root tissues using two different routes: between the porous cell walls of the cells (apoplastic transport) or directly from cell to cell (symplastic transport), through tiny pores that join the cells called plasmodesmata. We can trace the water movement from the root hairs to the cortex and then to the endodermis. But here water finds an impenetrable barrier, the Casparian strips, that impede the water and dissolved substances from moving in between the cell walls, forcing them to go inside of the cell instead. Through this process the plants are able to control which dissolved substances will be transferred to the vascular cylinder for further transportation. In the process of water absorption, the roots also absorb other substances, like minerals and nutrients, that are dissolved in the water. As with any other organism, plants require certain nutrients to be able to grow and survive. We can divide them into macro and micronutrients. Macronutrients (macro = big) are essential components of plants and they are available in large quantities. Examples of macronutrients are phosphorus (P), nitrogen (N) and Potassium (K). Micronutrients are also needed by plants, but they are available in small quantities. Examples of micronutrients are iron (Fe), copper (Cu) and manganese (Mn).	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/02%3A_Roots/2.03%3A_Root_Anatomy.txt
Some plant roots may be modified for special purposes in addition to accomplishing the root’s basic functions. Storage roots Some plants store carbohydrates in the roots for use in case of emergency or in preparation for the winter months, as some plants lose their leaves and are unable to perform photosynthesis. Most of this storage in plants happens in the roots, where it can be safe from animals and be preserved better than aboveground. We are familiar with this strategy of food storage, as we animals also store extra food as fat in our bodies to use in case of food scarcity. For example, animals that hibernate accumulate fat to be able to survive the winter. Plants do not use fat to store food, instead they use mainly starch, which is more stable and lasts for longer periods of time. Roots have been sources of food for humans since the dawn of our species. Examples of economically important root crops are cassava, sweet potatoes (Figure $1$), carrots, beets, sugar beets, turnips, radishes, parsnips, and horseradishes. Currently, the most important root crop in the world is cassava (Manihot esculenta, Figure $2$). There are dozens of common names for this crop. In Hawaiʻi, it can be known as tapioca. This plant is also originally from South America, but now it is widely cultivated in most tropical and subtropical regions including many Pacific islands. It is the third most important source of carbohydrates in the tropics, behind rice and corn. Cassava can grow in poor soils and in places with low rainfall. Proper cooking and preparation are important, as some varieties contain cyanide that needs to be removed before consumption. Cassava is a versatile crop and can be used in many ways: fried as in french fries, mashed as in mashed potatoes, fermented and made into an alcoholic beverage, and dried into different types of flour with long shelf life (e.g. tapioca flour). The tapioca balls in bubble tea are made of starches extracted from this root. Another important root is ʻuala or sweet potato (Ipomea batatas). They have been cultivated by Native Hawaiians since prior to European contact and were a very important source of carbohydrates for the population in the islands (Figure $1$). Sweet potatoes are a very convenient crop as they grow in all kinds of environments: wet, dry, near sea level, and higher elevations. However, it was extensively cultivated in the Kohala agricultural system on Hawai‘i Island (Lincoln and Vitousek, 2017). Many different varieties of sweet potatoes were grown in the past and this crop still is an important component of the diet today, although the majority of varieties grown locally are recent introductions to Hawai‘i. Sweet potatoes are native to South America, where they were first domesticated. They were cultivated in Hawaiʻi prior to European contact with Hawaiʻi and even the Americas. But how did they travel from South America to Hawaiʻi? There are a few hypotheses that try to explain this. One explanation is that the plant arrived by rafting, or getting a ride on oceanic currents (Montenegro et al., 2008). However, there are linguistic similarities to the names used for sweet potato in Polynesia and the coast of Ecuador. The word for sweet potato in Polynesia is “kumala” which is similar to the original Ecuadorian Quechua word for sweet potato “kumara”. In Hawai‘i the sweet potato is known as ‘uala (Adelaar, 2011). Therefore, it is plausible that Polynesians traveled by canoes as far as South America, traded with the native populations there and brought the sweet potato back home (Roullier et al., 2013). Adventitious roots Roots usually grow underground, but some modified roots can grow above ground from the stem and they are called adventitious roots. We will subdivide adventitious roots into prop, buttress, and aerial roots. Prop roots Prop roots extend from the stem to the soil and provide extra mechanical support to the plant and an increased absorption capacity after they reach the soil. Hala (Pandanus sp.) is a great example of a plant with prop roots (Figure $2$E). In this plant prop roots can grow 3- 4 meters (10-13 feet) long. Another good example is red mangrove (Rhizophora mangle) which is native to tropical and subtropical places; however, this species is not native to Hawai‘i. The prop roots help to support branches, allowing the tree top to extend laterally, creating a beautiful maze of roots. This also helps the tree to withstand tidal changes and storm surges while creating habitat for fish and other aquatic organisms. Buttress roots These modified wall-like roots are characteristic of some large trees growing in the tropics, usually in shallow soils, providing the tree extra mechanical support. Ceibas are great examples of trees with buttress roots (Figure $2$D). Aerial roots Most orchids are epiphytic, meaning they grow on top of other plants, like trees, and not in the soil. This means that their roots are not underground, but grow along the surface of the bark. However, this does not mean they are parasitic, as they are only using the tree as a place to grow and they still gather the water and nutrients from the environment to be able to carry on their photosynthesis. Orchid roots are covered in a thick layer of dead cells called velamen, which looks whitish, that helps to retain water (Figure $2$B). Parasitic roots Some plants have specialized roots, called haustoria, that penetrate other plants to steal water and nutrients. These plants are called parasitic, but the level of parasitism differs among parasitic species. Some parasitic plants steal water and are still capable of undergoing photosynthesis to produce their own food, like the mistletoe plant. Other parasitic plants are absolute parasites that do not even have chlorophyll to be able to carry on the process of photosynthesis, meaning they must obtain water and food from the host plant in order to survive. An example of a fully parasitic plant is dodder. The Kauna'oa kahakai (Cuscuta sandwichiana) is an example of a Hawaiian endemic plant that is fully parasitic (Figure $2$C). Reproductive Roots Roots from certain species can produce new plants via asexual reproduction. This is very common in stems and relatively rare in roots. This type of modification allows the plant to grow a new individual from their root systems. This is the case of breadfruit. If the main breadfruit tree gets damaged by animals like pigs, the tree will send out new shoots from its root system. If the main tree dies, this new plant can grow and become a new tree. Even if the tree is only damaged, the new plant can grow and become its own individual. People all over the Pacific take advantage of this reproductive strategy to propagate breadfruit. Since many varieties do not produce seeds due to human domestication, the roots are used to propagate existing trees (Figure $2$F). Mycorrhizae Mycorrhiza (myco = fungus; rhiza = root) is a symbiotic relationship that most plants have with fungi in their roots (Figure $3$; mycorrhizae is the plural form of mycorrhiza). Symbiosis means “relationship” which can be mutualistic, commensalistic, or parasitic. Sometimes both partners get something from this relationship (mutualism), other times, the fungus or the plant may not get anything in return (commensalism; Pringle et al., 2011). The fungal body is called mycelium (plural mycelia) and it is composed of root-like extensions called hyphae that absorb water and scavenge the soil for nutrients like phosphorus or nitrogen and give it to the host plant, increasing the total absorptive capacity of the plant. In exchange, the plant may give the fungus carbon (normally in the form of glucose) produced in photosynthesis. There are two types of mycorrhizae: ectomycorrhizae (Figure $3$A) where the fungi grows its hyphae (root-like fungi body) in the outermost layers of the cortex cells of the root. This type of mycorrhiza is commonly found in trees. Endomycorrhiza (Figure $3$B) is when the hyphae penetrates the cortex cells, all the way to the endodermis. Sometimes the hyphae will swell up and form vesicles which store nutrients derived from the plant-fungus interaction (Figure $3$B). The fungi does not damage the plant cells. Endomycorrhiza is found in woody as well as herbaceous plants. Root nodules Nitrogen is one of the macronutrients plants need in order to grow. Although it comprises 79% of the air, plants cannot absorb it directly from the atmosphere. In fact, most organisms, including animals, cannot absorb nitrogen in its gaseous form. Fortunately, some nitrogen-fixing bacteria are capable of fixing or changing nitrogen into a usable form (i.e. nitrates). Some plants have the capability of forming a symbiotic relationship with some species of these bacteria in their roots, increasing nitrogen absorption. The plant forms a rounded structure in their roots called nodules that host and protects the nitrogen-fixing bacteria (Figure $4$). Plants with this mutualistic association include plants in the legume family (Fabaceae) like beans, peas, and peanuts. Other families of plants are also able to have this kind of relationship with bacteria.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/02%3A_Roots/2.04%3A_Modified_roots.txt
Learning Objectives After studying this chapter, you should be able to: • Describe the parts of the stem and its main function. • Describe the differences between the monocot and eudicot stems. • List the name and function of the main woody stem tissues: bark, epidermis, phloem, vascular cambium, and xylem. • Distinguish between primary growth and secondary growth in stems. • Describe the composition of wood and its annual rings, sapwood, heartwood, and bark. • List the main uses of stems. • Describe the differences among modified stems: rhizomes, tubers, bulbs, stolons/runners, corms, and cladophylls. 03: Stems Stems play a huge role in our life, as they have a vast range of uses, such as food, fuel, shelter, construction materials, furniture, light poles, musical instruments, and raw materials for a vast variety of paper products (paper towels, toilet paper, writing paper). One of the most important sources of carbohydrates worldwide are potatoes (Solanum tuberosum), which are a type of modified stem (tuber). Potatoes were first domesticated in South America about 8,000 -10,000 years ago and were taken to Europe in the 16th century. It is now cultivated worldwide and many cultures have incorporated it into their cuisines. In the Pacific many island nations cultivate taro/kalo (Colocasia esculenta), a modified stem called corm, which originated in China and migrated with people throughout the Pacific. Stem anatomy Stems are the vertical structures of plants where leaves attach. They are usually found above ground, providing mechanical support, conducting water and nutrients, and sometimes storing food. Stems can be woody (e.g. koa tree) or herbaceous (e.g. tomato), they can be tall as in sequoias (75 meters or 245 feet) or short as in ʻilima papa (12 cm or 5 inches); wide as in some cypress trees (11.5 meters or 36 feet) or thin as in sunflowers (2 meters or 6 feet). In most woody flowering plants we can recognize nodes and internodes as the basic parts of the stem (Figure $1$). The nodes are the place where leaves attach to the stem, while internodes are the spaces between the nodes. Internal parts of the stem Some stems are woody and some stems are herbaceous, which will define the type of tissues present inside of them. Monocots always have herbaceous stems, while eudicots can have herbaceous or woody stems. In both groups the vascular tissue is arranged in bundles (vascular bundles), a region where you have both xylem and phloem grouped next to each other, and these bundles are surrounded by ground tissue, which is composed of cells called parenchyma. The organization of the vascular bundles is an identifying characteristic in monocots and eudicots. In monocots, like corn, these vascular bundles are scattered throughout the stem tissue. If you were to take a closer look at each individual vascular bundle in monocots, you will see alien faces, with big eyes (Figure $2$). So if you are in the microscope and you find cute alien faces staring back, you know you are looking at a monocot stem. Eudicots, like beans and mango trees, are a little more complex. Eudicot stems can be herbaceous or woody. In herbaceous or young woody eudicots the vascular bundles are arranged in a ring fashion around the stem (Figure $2$) and there are not cute alien faces on them. In older stems these bundles tend to fuse to each other to form concentric rings. Primary growth Stems grow vertically and, similarly to roots, they have meristematic tissue on their tips, where cells are constantly dividing through mitosis, allowing the stem to elongate. This growth in length is called primary growth. Some plants can grow indefinitely for their entire lives, even for thousands of years. However, the rate of growth varies from plant to plant and it also depends on the environmental conditions where the plant is growing. Some plants can grow really fast, like albizia (Falcataria moluccana), an invasive species in Hawai‘i, which can grow 4.5 meters (15 feet) per year (Little and Skolmen, 1989). Other plants grow very slowly, like the bristlecone pine trees in California, where a 5,000 old tree can measure just 18 meters (60 feet). Similarly, in Hawai‘i there are some oʻhiʻa lehua (Metrosideros polymorpha) trees that are very short (30 centimeters or 12 inches), but can be as old as 300 years. The meristem found on the tip of a stem is called the apical or terminal meristem, and it receives this name because it is located at the apex or end of the stem. In the stem we also find meristematic tissue in the nodes, specifically in a little rounded bump found above the place of leaf attachment. They are called axillary buds and are found in the angle formed between the leaf stalk (petiole) and the stem (Figure $1$). These buds are protected by bud scales, and they can become branches, flowers, or new leaves. Each new branch will develop their own apical meristem, ensuring that each branch can grow independently.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/03%3A_Stems/3.01%3A_Parts_of_the_stem_and_primary_growth.txt
Besides growing vertically, some plants also have secondary growth, meaning they also grow in diameter. This is especially true for plants that grow for several growing seasons (perennial), like woody plants (i.e. eudicots and gymnosperms). Herbaceous plants, like monocots and herbaceous eudicots, only grow for one growing season (annuals) and they do not present secondary growth. The tissues in woody stems, starting from the outer layer are: bark, vascular cambium, sapwood and heartwood (Figure $1$). The bark consists of cork, cork cambium and phloem. Vascular cambium is a layer of meristematic tissue that produces secondary xylem to the inside and phloem to the outside. This is the reason why woody plants can grow in diameter. The tissue responsible for the secondary growth in woody stems is the vascular cambium. Vascular cambium is found in between the xylem and phloem in woody stems, it produces xylem to the inside of the stem and phloem to the outside of the stem. Because we are considering the secondary growth, we refer to the xylem produced by the vascular cambium as secondary xylem (wood). As the secondary xylem accumulates from one growing season to the next, the stem grows in diameter (this is called girth). In temperate climates plants grow according to the seasons, growing mainly during the spring and summer, resulting in clearly defined growth rings visible on woody stems (Figure $2$). These growth rings provide information about the age of the tree, as usually one growing season represents one year. Each ring consists of an area of light-colored wood (spring wood) that is formed during the spring, when water is readily available for plant growth, and an area of dark wood (summer wood) that is formed late in the growing season when water availability is starting to decrease. Spring wood consists of xylem cells that are larger in diameter (vessel elements), while the xylem cells in the summer wood are smaller in diameter. The amount of water available during the growing season is correlated to the amount of spring wood produced in each ring; therefore, growth rings also provide insights into the climatic conditions prevalent during the growing season. For example, a thicker growth ring indicates a year with more precipitation/water availability than a thinner growth ring. Xylem in woody stems is what is called wood, and its main function is to transport water and nutrients. Functioning xylem (sapwood) is lighter in color and is found closest to the vascular cambium. Older xylem (heartwood) can be recognized because of its darker color, and it is found towards the center of the stem (Figure 5). This older xylem is no longer functional, however both sapwood and heartwood provide mechanical support for the plant. Many trees are able to survive and function normally after losing the heartwood, either to rotting or fire, as in the case of giant sequoias. Some trees in the tropics never stop growing because they may exist in a place without well developed seasons. In this case, the tree may not produce rings (Figure $3$). Wood or not wood? It is important to note that not all woody stems are the same. The wood that is produced by eudicots is commonly called hardwood, while the wood produced by conifers, like pine trees is called softwood. The main difference between the wood from these two groups of plants is that wood from eudicots is composed of cells called vessel elements, fibers and tracheids, while in conifers the wood is composed only of cells called tracheids. Other plants, like coconut or hala (Pandanus sp., Figure $4$), appear woody but they are not. Monocots are unable to produce wood, so they are mostly herbaceous, but that does not mean some species cannot grow tall. Some monocots are able to grow long stems by having thicker parenchyma cells in between the scattered vascular bundles (e.g. coconut and hala), other monocots have overlapping leaves with thick petioles wrapped around the stem that provide mechanical support (e.g. some palm trees), and other monocots have prop roots to increase the mechanical support of the stem (e.g. hala). Putting this knowledge into practice: How to kill an invasive tree Invasive plant species in Hawai‘i can be very problematic. Not only do they displace native species, but they can also cause damage to property and roads. Plants like albizia (Falcataria moluccana) grow really fast and are susceptible to falling during strong winds. One strategy that arborists use to kill albizia is a technique called girdling (Figure $5$), where the outer layer of the stem is removed all the way around and the tree is left standing. Eventually the tree dies, because as the outer layer is removed, the phloem and the cambium are removed from the tree. The tree is still able to photosynthesise, but the sugars coming from above the girdled region cannot reach the roots to feed the cells there, therefore the plant eventually starves to death. Since the cambium is also removed, the tree cannot produce new phloem. The only thing the tree is left with is the xylem, so it is still able to transport water up the stem. The tree is able to survive like this for several months, but it will eventually die. A standing dead tree can be dangerous since it will drop branches and can damage structures and harm people. Tree killing and removal should be done by professional arborists so that accidents don’t happen.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/03%3A_Stems/3.02%3A_Secondary_growth.txt
Stems come in different shapes and sizes and some plants have modified or specialized stems that serve other purposes. For example, some stems grow underground and are used by the plant to store food reserves. How can you tell if an underground plant structure is a stem or a root? Remember that stems have nodes and axillary buds, so if you look closely, you can see these structures in modified stems. Below are different types of modified stems. Rhizomes Rhizomes are underground stems that grow horizontally, with the function of storing nutrients and water. Examples of rhizomes include ginger (Zingiber officinale) and ‘olena or tumeric (Curcuma longa). From these rhizomes you can clearly see the nodes and internodes, with the roots emerging from the nodes (Figure $1$). Stolons Stolons are similar to rhizomes, but instead of growing horizontally underground, they grow mostly above ground (some will grow very shallow right below the surface). Stolons are used as asexual plant reproduction, since a new plants (clone) can grow out of the nodes present in the stolons (Figure $2$). Some grasses produce stolons and are able to spread from one area to another. At the base of each node, adventitious roots can grow and take hold. Tubers Some plants will form rounded or cylindrical structures called tubers on the tips of the stolons, which eventually detach from the main structure. The main function of tubers is the storage of carbohydrates. The plant may do this to store food underground to survive a drought or cold period. A good example of tubers is potato (Solanum tuberosum, Figure $2$). If you look closely at a potato you will see little “eyes”. These “eyes” are the nodes and axillary buds, which can be used for plant propagation, as planting of these potato “eyes” will result in the growth of new plants. Another example is pia (Tacca leontopetaloides) which is a Polynesian introduced plant that is used for its starches (e.g. haupia). Bulbs Bulbs are modified short stems with many fleshy leaves. One example is onions and shallots. Bulbs have a very short and flattened stem that is called the “basal plate”. The structures above it are modified leaves (Figure $2$). Corms Corms are underground stems that are vertical. It is normally an organ for the plant to store nutrients. In non cultivated plants, this is important to survive winter or drought times. In cultivated plants, these structures are selected for and eaten for their carbohydrates. For example, the corm of taro/kalo (Colocasia esculenta) is steamed and made into poi or eaten in a diversity of dishes (Figure $3$). Prior to European contact, kalo provided one of the main sources of carbohydrates for Hawai’i’s population. There are about 80 varieties remaining in the Hawaiian Islands (Lincoln and Vitousek, 2017) which are cultivated in lo‘i (wetland agricultural systems developed by Native Hawaiians) and dryland. Roots grow out of the nodes of the corm and they are normally removed prior to cooking. Axillary buds are also located on the nodes and will give rise to other shoots (‘oha). All these plant parts have names in the Hawaiian language (see Levin, 2008) and are used as morphological keys to identify varieties. Prior to European contact, kalo provided one of the main sources of carbohydrates for Hawai’i’s population. Cladodes Cladodes are flattened stems like the stems seen in cactus. They are green and may look like leaves because they are able to photosynthesize. The leaves (spines) are modified as a protection structure against herbivores (Figure $4$).	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/03%3A_Stems/3.03%3A_Modified_stems.txt
Learning Objectives After studying this chapter, you should be able to: • Identify where stomata are located. • Identify the internal structures of a leaf. • Identify the external forms and parts of leaves. • List the leaf tissues and their functions. • Describe the difference between pinnate, palmate, and parallel venation, and the differences between simple and compound leaves. • List some of the most important economical uses of leaves. 04: Leaves Leaves are commonly used in our day to day lives, from the fresh salad we may eat for dinner to perfumes, leaves are used to make a diversity of products. Some leaves even have great economical importance. The most important product derived from leaves is tea (Camellia sinensis), which is the most widely consumed beverage. The growing, harvesting, and processing of tea is very intricate and the end product is highly valued around the globe, an industry worth billions of dollars per year. Other products derived from leaves include essential oils extracted used in cleaning products, medications and bug repellent. The oil from citronella/lemongrass leaves (Cymbopogon citronella) are extracted and used to enhance flavor in foods, in cosmetics, perfumery, and in vitamins, among other products. The leaves of lemongrass, mint (Mentha spicata), and māmaki (Pipturus albidus) are used to make herbal teas (Figure $1$). Many people around the world use the leaves of hundreds of plant species for medicinal purposes. In Hawaiʻi, māmaki leaves are used for traditional medicinal uses. Leaves are variable in shape, size, and color. Some palm tree leaves can measure 4–6 m (13–20 ft) in length, while duckweed leaves are tiny as 1 millimeter (0.04 inch). In regards to shape, some leaves are like needles, as in pine trees, or they can be very broad like in kalo leaves. Plants are able to synthesize their own food using sunlight and carbon dioxide. In turn, humans and other animals rely on plants for food and oxygen that they also produce. Parts of the leaf and leaf attachment The flat part of the leaf is called the lamina or blade. Leaves normally attach to the stems by the petiole (add description of petiole here). The leaf lamina has a midrib where the vascular tissues are located. From the midrib, smaller veins, also containing vascular tissue, branch out. The edge of the blade is called the margin (Figure $2$). Leaf margins differ in plants and are used as an identification tool for species. They can also vary in different environments, for example, most plants in tropical rainforest have entire(smooth) margins, while plants in temperate regions usually have margins with teeth. Leaves attach to the stems at the nodes, and the space between nodes is called internodes. If we take a closer look at the nodes, we will find that in the angle between the leaf stalk (petiole) and the stem there is a little rounded bump called a bud, which is composed of dormant meristematic tissue that can develop into flowers, branches, or leaves (Figure $3$). The pattern of leaf attachment to the stem (phyllotaxy) varies in plants and it is commonly used for identification purposes. For example, in some plants two leaves attach on opposite sides of a node (opposite), in others there is only one leaf per node (alternate), in others 3 or more leaves attach around the stem at the same node, forming a whorl of leaves (whorled), or even forming a spiral around the stem by slightly rotating the attachment position in each subsequent node (spiral; Figure $4$). Simple vs. Compound leaves Leaves may be simple or compound, meaning they can have one or several lamina (blades). In a simple leaf, the lamina is undivided or it has lobes, but the lobes do not reach the midrib (Figure $5$). In a compound leaf, the leaf lamina is completely divided, forming smaller independent “leaves” called leaflets (Figure $5$). Each leaflet has its own petiole but is attached to the midrib, which in compound leaves is called rachis. There are different types of compound leaves, depending how the leaflets are arranged. In pinnately compound leaves the leaflets are arranged on both sides along the raquis (e.g. starfruit, Figure 5B). Double pinnately compound leaves or bipinnately compound leaves are similar to pinnately compound leaves, but each leaflet is further divided into even smaller leaflets (e.g. albizia; Figure $6$). In palmately compound leaves leaflets attach to a single point and radiate from there, resembling the palm of a hand (Figure $6$). An example of a plant with palmate compound leaves is Schefflera sp. (umbrella plant). Leaf venation Veins in leaves are arranged in different patterns and they are another characteristic that is very helpful in plant identification (Figure $7$). Pinnate leaf venation is the first to come to mind when we think about a typical leaf. In pinnate venation there is a midvein or midrib and there secondary, smaller, veins branching to either side of the midvein. An example of a plant with pinnate venation on their leaves is avocado (Figure $7$). In parallel venation there are several secondary veins that are parallel to the midrib and to each other. Parallel venation is characteristic of monocots, like grasses and kī/ tī (Figure $7$), although there are some exceptions (e.g. kalo). In palmate leaf venation there are several main veins of similar thickness that radiate from a single point at the base of the leaf (e.g. kukui leaf; Figure $7$). In eudicots the branching pattern seen as the veins further divide into smaller veins resembles a net, so it is called reticulate (netted) venation. Leaf Margins Leaves have a diversity of margin types or edges, which is a very useful characteristic in plant identification. Examples of the most common margin types are entire, dentate, and serrate (Figure $8$). If you are trying to identify a plant to the species level, you will likely encounter keys and descriptions that include leaf margins and there are many to choose from.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/04%3A_Leaves/4.01%3A_Leaf_structure.txt
Leaves have three main internal regions; the epidermis, the mesophyll, and the veins. The epidermis is the outermost layer, being present on the top and bottom of the leaf, the upper and lower epidermis, respectively (Figure $1$). The epidermis is usually one cell layer thick, but it can be several layers thick in plants growing in arid environments, to prevent excessive water loss. A waxy layer known as the cuticle is found outside of the epidermis. The cuticle is made of a waxy substance that helps to reduce water loss. Some leaves may have small hairs (trichomes) on the leaf surface, which help to decrease herbivory either mechanically (reducing insect movement) or chemically (producing chemicals). They can also reduce transpiration by reducing airflow on the leaf surface or by reflecting sunlight, protecting the plant against UV damage. The epidermis protects the inner leaf tissues and helps in the regulation of gas exchange. It possesses small openings called stomata, that facilitate gas exchange (Figure $2$). Carbon dioxide (CO2), needed for photosynthesis, enters the leaf through the stomata, while oxygen, a product of photosynthesis, and water vapor from transpiration exit. In most plants stomata are usually located in the lower epidermis. The opening and closing of stomata is controlled by guard cells, which surround each stoma. Climatic conditions, water availability in the soil, and the time of the day affect the opening and closing of stomata. For example, most plants close their stomata during the nighttime as the CO2 required is only needed when sunlight is available for photosynthesis. In between the upper and lower epidermis is the mesophyll, which has two differentiated regions. The palisade mesophyll is found just below the upper epidermis and it is composed of parenchyma cells closely arranged in a brick-like fashion. These cells are packed with chloroplasts and it is here where most of the photosynthesis takes place. The other region is called the spongy mesophyll and it is composed of loosely arranged parenchyma cells that have numerous air spaces in between (Figure $1$). The veins are the third tissue present inside leaves. Veins contain bundles of vascular tissue, xylem for transporting the water for photosynthesis and transpiration, and phloem for transporting the sugars produced in photosynthesis. 4.03: Photosynthesis One of the most amazing things about plants is that they can make their own food through photosynthesis. Photosynthesis is the chemical process in which plants transform sunlight into chemical energy. The process has evolved for millions of years and thanks to it, humans are able to survive by eating the bounty produced by plants and breathing the oxygen released as a by-product. How does that happen? To photosynthesize plants need the energy of the sun, water from the soil, and carbon dioxide from the atmosphere. The chemical reaction then gives rise to glucose (sugars/carbohydrates), water, and oxygen (Figure $1$). The sugars produced are either used by the plant for growth and development, or are stored in the plant. Sweet potato plants are known to store carbohydrates in their roots while aloe plants store it in their leaves. There are two main phases of photosynthesis. A light-dependent reaction and the Calvin Cycle (light-independent reaction). During the light-dependent reactions, sunlight and water are needed. Water molecules split releasing oxygen. The energy generated by it is used to fix the carbon dioxide into glucose (sugar) during the second phase of photosynthesis or the Calvin Cycle (Figure $2$). 4.04: Modified leaves Some plants have leaves that have been modified to do jobs besides photosynthesis. Here are some examples: Bracts Leaves in some species are modified to have different colors and look like petals. Their main function is to attract pollinators. In the case of Bougainvillea sp., flowers are small and creamy and are found in the middle of three pink petal-like modified leaves known as bracts (Figure $1$A). Spines Spines are modified leaves used for protection against herbivores. They have also evolved as a water-saving strategy in some plants. For example, most cacti, like dragon fruit, have spines instead of regular leaves (Figure $1$B). Reproductive leaves Some plants, like Bryophyllum daigremontianum, produce plantlets along the margins of its leaves. Eventually the new plants fall off and become separate from the main plant. This is an example of asexual reproduction. The new plants are identical to the mother plant (Figure $1$C). Tendrils Tendrils are modified leaves used for climbing or support. For example, cucumbers use tendrils to climb and serve as a support structure for the plant (Figure $1$D). Storage leaves These leaves are modified to store water and/or nutrients for the plant. One example is aloe. There are about 500 species in this genus, and most of them are drought resistant. Aloe vera is cultivated as a medicinal plant and the leaves are used to treat sunburn, among other things (Figure $1$E). Trap leaves Some leaves are modified to trap insects. These type of leaves have evolved due to low nutrient availability in the soil where it grows, so plants with these leaves are able to gather nitrogen and other nutrients from the bodies of the insects they trap. For example, the venus flytrap (Dionaea muscipula) and sundew (Drosera spp.) grow in bogs where nitrogen is not easily available. Drosera anglica or mikinalo is indigenous to the island of Kaua‘i. Its leaves are covered with glands that secrete mucilage used for trapping insects (Figure $1$F).	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/04%3A_Leaves/4.02%3A_Internal_leaf_characteristics.txt
Learning Objectives After studying this chapter, you should be able to: • Identify the parts of a flower. • Identify a monocot or an eudicot based on the flower characteristics. • Identify different types of fruits . • Identify the parts of a seed. • List some uses of flowers, fruits, and seeds. 05: Flowers fruits and seeds Angiosperms (flowering plants) are the only group of plants to produce flowers. Flowers are rather diverse, coming in different colors, sizes, and shapes (Figure $1$). Some have fragrances to attract pollinators and many offer pollen and nectar to reward the pollinator’s visit. Flowers are in great part responsible for the incredible success of this group, as they are able to enlist help from animals like bees, butterflies, and birds to transfer pollen from one flower to another, while other groups of plants, like conifers have to rely only on the wind for this same purpose. Flowers co-evolved with pollinators assuring that flowering plants could reproduce successfully and ensuring genetic diversity in the population. Nectar and pollen are not the only rewards offered by plants, flowering plants also offer fruits as reward to dispersers who, in turn, take the seeds away from the mother plant and are; therefore, able to colonize new areas. For thousands of years humans have been fascinated by flowering plant’s reproductive structures; flowers and fruits. Many fruits are sweet and can be eaten, while flowers have been used in cultural, medicinal, and religious practices. For example, in pre-European contact Mesoamerica, in what is now called Mexico, flowers were used in many aspects of day-to-day life. Today these traditions remain strong, with flowers being used to decorate altars and graves, as well as for medicinal purposes. In Hawai‘i cultural practices can be observed with the use of flowers, fruits, and seeds for hula, lei making and celebrations such as weddings and graduations. Flower Parts To understand how flowers are involved in the sexual reproduction of plants, we first need to identify the flower parts. Flowers contain the female and male reproductive structures of flowering plants. The female reproductive structures are organized into the pistil, which consists of the stigma, style and ovary. The stigma is the very top part of the pistil. It is usually flattened and sticky, as pollen grains that come from other flowers need to be collected here for sexual reproduction to happen. The style is a tube that connects the stigma to the ovary. And finally, the ovary is the rounded portion at the base of the flowers, and it contains the eggs (ovules). The male parts of the flower, on the other hand, are called stamen and they are composed of the anther and the filament. The anther is a double canoe-like structure where pollen grains are produced, and the filament is the stalk that supports the anther (Figure $2$). Besides containing the plant sexual organs, flowers also have other parts, which are collectively called the perianth. The perianth is composed of petals and sepals. The petals are the colorful flower parts that attract pollinators. At the base of the flower are the sepals, which are green leaf-like structures that protect the flower in bud. Flowers from different species are unique, with variations in the way these basic parts described above are distributed. When you think about a typical flower, as the one shown above (Figure $2$), the stamen and pistil are normally found independently. However, this is not always the case. Flowers in the Hibiscus genus, for example, have the style from the pistil and the filaments from the anthers fused together forming a single long tube, in which the anthers branch out close to the stigma (Figure $3$). Flowers can be perfect, having both male and female parts, or imperfect, having just one sex (male or female). Kokiʻo keʻokeʻo is an example of a perfect flower, with both stamen and pistil (Figure 3). Imperfect flowers also come in different arrangements. Male and female flowers (imperfect) may be found growing in the same plant, as it happens in the breadfruit tree (Artocarpus altilis, Hawaiian ‘ulu or Samoan and Tongan ma‘afala), pictured below (Figure $4$). Imperfect flowers can also be found in separate trees. For example, hala (Pandanus) has female flowers growing on one plant while male flowers grow on another, so the plant is either male (Figure $5$) or female (Figure $6$). A plant is called dioecious when it has male and female flowers on separate plants. This only happens in a minority of plants, as most plants are monoecious, having both male and female flowers on the same plant. How can you remember this? Breaking down the words into their roots is a good way. For example “di” means two, so you have two houses while “mono” means one (one house). Or just think about animals, we are dioecious because you can have either a male or a female. Flowers of Monocots and Eudicots Monocots and eudicots are the two largest groups of flowering plants, and they can be easily recognized based on their flower parts. Flower parts (e.g. petals, sepals, stamens) in monocots are arranged in 3 or multiples of 3, while eudicot flowers are arranged in 4 or 5 or multiples of 4 or 5. Therefore a monocot flower may have 6 stamens and 6 petals (Figure $7$). Eudicot flowers, on the other hand, may have 5 petals (Figure $8$). This comes in handy when you are trying to identify plants in the field. Finding out if a plant is a monocot or an eudicot is the first step in plant identification because you can rule out several plant families. If the plant is a monocot, then you will only look at monocot families from that point onward.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/05%3A_Flowers_fruits_and_seeds/5.01%3A_Flowers.txt
The process of sexual reproduction in plants consists of several chronological steps: 1. Production of flowers 2. Pollination 3. Fertilization (produces seeds) 4. Formation of fruits As with animals, for sexual reproduction to happen in plants the sperm needs to join the egg. The sperm of plants is contained in the pollen grains, therefore it is necessary for the pollen to be transferred to another plant for sexual reproduction to take place. Since plants cannot walk to find a mate, they have to use other means of bringing the pollen to the egg. Pollination is defined as the transfer of pollen from the male part of a flower to the female part of the flower, usually the flower on another plant. Some species of plants will self-pollinate (pollen is transferred to the stigma of the same flower); however, the majority of flowering plants out-cross (are pollinated by another plant). This interchange of genetic material, a characteristic of sexual reproduction, increases diversity in the population. Genetic diversity is important because that’s how plants are able to adapt to new challenges. If all plants in a population have the same genetic makeup (clones), as is the case with plants that reproduce mainly asexually (e.g. bananas), they may all get killed by a disease. However, if some plants in the population have a different gene that provides resistance to that disease, they will survive and be able to pass on their genetic material to their offspring. Flowers provide a clear advantage to flowering plants, allowing them to reproduce sexually. This is one of the reasons why flowering plants are so successful and are the dominant group of plants in most of the terrestrial ecosystems on our planet. In some plants, like pine trees, the pollen is transported by water or by wind. This strategy is very energy consuming for the plant, as it requires the plant to produce millions of pollen grains to ensure that at least some of them will reach a nearby female flower of another plant. Flowering plants have evolved an innovative strategy where they enlist the help of animals to transfer the pollen to the female parts. Through this strategy plants do not need to produce as much pollen, since pollinators will visit the same type of plant, ensuring the successful transfer of pollen to the right target. However, the plant will likely have to produce other substances, like nectar, to attract pollinators. Insects are the most famous pollinators, with bees and butterflies attracting the attention of many of us. However, some plant species are pollinated by birds, bats, or even lizards. In Hawai‘i, native plants have coevolved with certain animals for millions of years, forming some unique pollination strategies. For example, lobeliads can only be pollinated by native nectariferous birds like the ʻi‘iwi (Drepanis coccinea). If you look at the shape of the lobeliads flowers you will see how they fit to the shape of the bird’s beak (Figure $1$). Because of the specificity of this pollination strategy, these plants are in danger of extinction, as many of the native Hawaiian forest birds have gone extinct or are so rare that the plants are not getting pollinated. Once the pollen that is brought in by a pollinator gets in contact with the stigma of the flower, a pollen tube grows down into the style of the flower. The tube elongates to reach the ovary, where it releases two sperm cells. One of these sperm cells will find the ovule (egg) and it will fertilize it to form the zygote. Fertilization is the fusion of the male and female gametes (reproductive cells), forming a zygote and eventually an embryo (baby plant). Flowering plants have a unique process of fertilization, called double fertilization, where through the process of fertilization they produce an embryo as well as an energy pack to feed the embryo (endosperm). We will describe this process here in the simplest terms. As mentioned above, one of the two sperm cells that were released from the pollen grains and delivered to the ovary via the pollen tube will join the egg to give rise to an embryo, while the other sperm cell will fuse with a structure, found inside of the plant egg, called the polar nucleus giving rise to a nutritive tissue called the endosperm. Both embryo and endosperm are located inside the seed (Figure $2$). The endosperm is really important because it is the energy reserve that the embryo will use to grow during the germination process.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/05%3A_Flowers_fruits_and_seeds/5.02%3A_Plant_reproduction-_pollination_and_fertilization.txt
A fruit is the swollen ovary of the flower, the last step in the process of sexual reproduction of flowering plants. After seeds are formed through fertilization, the tissue around those seeds starts to grow, forming the fruit. Fruits help the plant to disperse the seeds, through different mechanisms that depend on the type of fruit. Fruits can be either dry or fleshy fruits. Animals who eat fruits will often disperse the seeds to other areas. Some dry fruits can attach themselves to the feathers and fur of animals and “catch a ride” to another area where they can grow without competition. Other fruits resemble wings and will fly with the wind. Here we will review only some of the types of fruits. Fleshy Fruits Berries In Botany, berries are defined as a fleshy fruit where the two innermost tissues are fleshy (endocarp and mesocarp) and they usually contain lots of seeds inside (Figure $1$). Endocarp is the tissue that is directly in contact with the seeds (endo = inside), while the mesocarp (meso = middle) is the tissue found in between the endocarp, and the external fruit tissue, the exocarp (exo = outside). This definition might be very confusing because in the English language we use the term “berry” to describe fruits that don’t necessarily comply with this botanical definition. For example, strawberry fruits are not considered berries in a botanical sense because their fruits and seeds are located on the outside of the edible red fleshy part (Figure $1$). If we follow the botanical definition, then lilikoʻi (passion fruit), tomato and bananas are berries (Figure $1$). The banana varieties you see in the supermarket have been heavily domesticated by humans and no longer produce seeds. The brown specks you see inside a banana are unfertilized ovules. Wild bananas still produce seeds because their flowers get pollinated. Orange lilikoʻi (Passiflora laurifolia), native to Brazil, is an invasive species in Hawaiʻi. It’s berries contain lots of pulp and seeds inside. This species is not as tart as yellow lilikoʻi or passionfruit (Passiflora edulis var. flavicarpa), and it is not cultivated commercially. Drupes Drupes are fleshy fruits where the endocarp forms a hard enclosure (pit) that surrounds the seed (Figure $2$). Drupes usually have a single seed. Examples of drupes include mangoes, peaches, nectarines, and apricots. Hesperidium The hesperidium is a modified berry where the endocarp is separated into segments, and the mesocarp is a thick and leathery whitish tissue, that we usually call a rind. This includes many citrus varieties, like the cara cara orange below (Figure $3$). Pepo Squashes, watermelons and cucumbers are all examples of pepos. Pepos are modified berries with a hard rim (exocarp). Just like berries, they have fleshy endo and mesocarp and contain lots of seeds inside (Figure $4$). Multiple fruits Multiple fruits are formed as the result of fused ovaries of nearby flowers. Each “eye” in a noni fruit (Morinda citrifolia; Figure $5$) is the scar where each flower used to be located. After pollination they fall off the fruit. Examples of multiple fruits include noni, pineapple, mulberry, and breadfruit. Dry Fruits Achenes Achene is a type of dry fruit that does not split open (indehiscent) and contains a single seed (Figure $6$). The small brown dots on top of strawberries are examples of achene fruits. Strawberries are a special type of fruit called an accessory fruit, which does not develop from the ovary of the flower but instead develops from the receptacle (the part that connects the flower to the stem). Capsules A capsule is a dry fruit that splits open (dehiscent) in 3 or more ways. Pua kala (Hawaiian poppy; Argemone glauca) is a native Hawaiian species that produces capsule fruits. The capsules pop open when dry, releasing dozens of black seeds (Figure $7$). Legumes Legumes are fruits commonly found in the members of the Fabaceae family (legume or bean family). These dry fruits normally split open along two seams when mature (Figure $8$). Caryopsis The caryopsis is a dry fruit that has the seed coat fused with the ovary wall or pericarp (Figure $9$). You can’t distinguish between the seed and the fruit because the two are fused together. Cereal grains in the family Poaceae such as rice, barley and corn have this type of fruit.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/05%3A_Flowers_fruits_and_seeds/5.03%3A_Fruits.txt
Seeds are contained inside fruits. This is a good characteristic that you can use to differentiate between a fruit and another plant part. If it has seeds then it is a fruit (e.g. tomato, watermelon, pepper). If it does not have seeds then it is another plant part (e.g. sweet potato, cassava, onion). These other plant parts are normally referred to as “vegetables”. Keep in mind that there are some varieties of fruits, like bananas, that for our convenience have been bred to be seedless. Seeds come in all shapes and sizes (Figure $1$). A seed is a flowering plant's unit of reproduction and has all the materials needed to develop into another plant. Seeds have three main parts: an embryo, a sead coat (testa) and the endosperm (cotyledon; Figure $2$). The function of each of these parts is very specific: Seed coat (testa): The outer layer that surrounds the seed. It protects the embryo against microbes and the environment. Embryo: Embryo is the end product of fertilization (the baby plant). The embryo will germinate and become a new plant. Endosperm (cotyledon): A second product of the double fertilization process previously discussed. The endosperm is the nutrient tissue that will feed the embryo during germination. Seeds of monocot plants have 1 cotyledon (e.g. corn) while seeds of dicot (eudicot) plants have 2 cotyledons (e.g. beans). Seed germination Seed germination is a process by which the embryo contained in a seed develops into a seedling. Usually seeds are dormant, meaning they are in a state of inactivity. When seeds find the right conditions, there is a metabolic activation (chemical reactions) in the seed, which leads to seed germination or growth of the embryo to become a new plant. There are three distinct phases of seed germination: 1. Water uptake by the seed (imbibition): The embryo soaks up water from the environment causing the seed to swell. The seed coat then splits. 2. Lag phase: In this phase, the metabolism of the seed kicks in, the endosperm starts to break down, and those sugars are used by the embryo to grow. 3. Radicle emergence (part of the embryo that will become the root): In this phase, the radicle grows out of the seed coat and starts to develop into a root (Figure $3$). Once these three phases are completed, the embryo will continue to grow and develop into a photosynthetic seedling that will be able to make its own food. Seed viability and dormancy There are three requirements that must be met before germination can happen: 1. The embryo must be alive. Seed viability is the ability of the embryo to germinate. If the embryo is dead, non-functional or non-existent (some seeds do not have embryos. a.k.a. empty seeds), the seed will not germinate. 2. Dormancy must be overcome. Seeds can lay dormant for many years. For wild species this is very important and a matter of survival. A seed will remain dormant until the right conditions are in place. For example, a seed lays dormant when there is a drought and will only germinate when there is enough water in the environment. 3. The right environmental conditions must be in place: water, oxygen, temperature and light. Some seeds will not germinate in high temperatures or in the presence of light. All seeds will not germinate in the absence of water. In agriculture and conservation there is a need for high quality seeds. When you purchase a seed packet in the store, you should feel confident that most of the seeds in the package will germinate. There are federal and state standards for this, but the quality of seeds vary widely depending where you are getting your seeds from. This is why some gardeners and farmers decide to save their own seeds. When looking into seed quality, people consider a few things. In the conservation field, for example, people are always trying to understand how long seeds will last in the ground before they germinate or when is the best time to harvest seeds for restoration projects. High viability of seeds is what people look for if they are trying to grow a crop. This can be measured by looking at germination percentage and the rate of germination. The germination percentage is the proportion of seeds that germinate from all seeds subject to the right conditions for growth. If you try to germinate 100 seeds and 20 of those do not germinate, you have an 80% germination percentage. This number should be included in the seed package when you purchase one in the store. It gives you a clue that the seeds you are purchasing are good. The germination rate is the length of time it takes for the seeds to germinate. Again, if we tried to germinate 100 seeds in 7 days and only 50% of the seeds germinated, this is your rate of germination. Why is the rate of germination important? Imagine you planted a field of beans. In the first 7 days, 50% of your seeds germinated and the other 50% germinated a month later. This can be very frustrating for a farmer who wants to harvest all the crops at the same time. In nature, this is not a bad strategy, since it may give the plants some advantages. For example, if the environmental conditions are not right when the first batch of seeds germinates, a second germination event a month later may have better success. Finally, seed vigor is a measure of the quality of seed, and involves the viability of the seed, the germination percentage, germination rate, and the strength of the seedlings produced. Seed Saving and Conservation Wild plants have evolved in their natural habitat for millions of years. In certain instances plants become endangered due to negative human impacts on the environment, such as the introduction of invasive species and habitat destruction. One strategy used in plant conservation is to collect seeds of threatened and endangered plants, store them in the right conditions, and eventually germinate them to reintroduce them to restored areas so that the future of the species can be ensured. Seeds of native species are collected all over the world by different organizations involved in conservation and are stored in seed banks. In Hawaiʻi several organizations, like Plant Extinction Prevention Program (PEPP), collect seeds of endangered Hawaiian plants, grow them in greenhouses, and then outplant them in the wild to restore native ecosystems. Seeds are obviously crucial in agriculture. Humans have been domesticating crop species for the past 15,000 years. Once wild species, crop species have been selected by humans for some characteristics that benefit us such as seed and fruit, taste, and uniformity in maturation. For example, corn (Zea mays) was domesticated in Mexico around 9,000 years ago (Figure $4$). The wild relative of corn, Teosinte (Figure $5$), looks like a large grass. Several changes needed to happen for teosinte to develop into modern corn. Humans played a direct role by selecting plants with larger and larger seeds, and growing only those. This process is called artificial selection. If you were relying on corn for subsistence, you would want plants that produce larger seeds for higher caloric intake. Saving seeds from the wild relatives of crop species (like Teosinte) is important because those genes can be used for future plant breeding. The Crop Trust Project has been doing just that. Sometimes plant breeders will look for wild relatives to cross with domesticated crops so that they can acquire genes that provide some resistance to diseases or drought. An example of this application is the use of the Hawaiian species of cotton, ma‘o (Gossypium tomentosum, 5.4.6) in breeding projects to increase disease resistance in domesticated cotton (Akhtar et al., 1996). Although the fibers of ma‘o (Figure $6$) are short and are not used commercially to make cotton, the plants have been crossed with varieties of commercial cotton to make stronger varieties.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/05%3A_Flowers_fruits_and_seeds/5.04%3A_Seeds.txt
Learning Objectives • List the features that distinguish the Plant Kingdom from other Eukarya Kingdoms. • Describe the general concept of alternation of generations in plants. • Recognize the gametophyte and sporophyte life stages of a moss. • List the main characteristics of non-vascular plants. • Within non-vascular plants identify mosses, liverworts and hornworts and list their main characteristics. • List five uses of non-vascular plants by humans. 06: Plant evolution and non-vascular plants All living organisms on Earth are divided into three domains (groups): Bacteria, Archaea, and Eukarya. Bacteria and Archaea are grouped in an informal category called prokaryotes, small unicellular organisms (smaller than the tip of a needle) that lack a nucleus and membrane-bound organelles. Eukaryotes, on the other hand, are composed of bigger cells that have a nucleus and membrane-bound organelles and they can be unicellular or multicellular. Domain Eukarya is further divided into four Kingdoms (groups; Figure $1$): plants (Plantae), animals (Animalia), fungi (Fungi), and protists (Protista). Both prokaryotes and eukaryotes have a cell membrane, ribosomes, and genetic material (DNA and RNA). Plants are multicellular photosynthetic organisms that have unique organelles and compounds, setting them apart from other eukaryotes. Specialized plant organelles, that are not found in animal cells, are chloroplasts for photosynthesis, a central vacuole to store water, and a cell wall to provide protection and structure to the plant cell. Other groups of organisms also have cell walls, like some bacteria, fungi, and some protists, but in plants, the cell wall is mainly composed of a substance called cellulose, while in other organisms it is composed of other substances, like chitin in fungi. There are also other organisms capable of performing photosynthesis, like some bacteria, and some protists (algae). Plants have green pigments called chlorophyll a and chlorophyll b, which are involved in photosynthesis. Origin of plants Plants are well known for their crucial role in producing oxygen. About 16% of the modern Earth’s atmosphere is constituted by oxygen, but a couple of billion years ago it did not have any oxygen, so it could not support life as we know it today. Around 2.8 billion years ago a group of bacteria started to perform an innovative process called photosynthesis in the Earth’s oceans, and over time oxygen accumulated in the atmosphere until it was high enough to support oxygen-breathing creatures, like animals. For millions of years algae and blue-green algae (bacteria) were the main photosynthetic organisms on Earth. The first true plants evolved from a green algae, probably from a Class (group) of green algae called Zygnematophyceae (Cheng et al., 2019; Figure $2$). Because the ancestors of terrestrial plants were aquatic, land plants had to adapt to new challenges brought by the dry conditions inherent to terrestrial environments. Some of the most notorious plant adaptations to life on land were the development of a physical barrier to prevent desiccation (drying out), specialized cells for water and nutrient transport, mechanical support to stay upright, anchoring mechanisms, specialized mechanisms to transfer the reproductive cells (gametes) from one plant to another, and the development of protective cell layers around the spore- and gamete-producing structures. The physical barrier plants developed to prevent desiccation is called a cuticle, a waxy layer that covers all the aerial surfaces of a plant to help prevent desiccation. All living land plants have a cuticle. The Zygnematophyceae algae are hypothesized to have acquired genes from soil bacteria that help prevent desiccation (Cheng et al., 2019). These genes are currently found in land plants and bacteria, but not any other algae, adding support to the hypothesis that these green algae are the ancestor of all land plants. When plants colonized land they also had to redesign the way sexual reproduction took place. In aquatic environments gametes just swim or float to another plant, which is not possible in most terrestrial environments. Land plants developed drought resistant spores that could survive on dry land as well as enclosed the gamete- and spore-producing structures with several layers of cells to protect them from drying out. Some land plants, like bryophytes, still have swimming sperm, which confine them to wet environments. In aquatic environments water and dissolved minerals are readily available and easily absorbed by plants. Land plants, in contrast, had to develop specialized cells to be able to transport water and dissolved nutrients from the soil. Most of these specialized cells look like narrow tubes, where water is transported from the roots to the leaves via the stem. These transporting cells are also related to the newly required mechanical support, as they have fortified cell walls to be able to withstand the physical forces involved in transporting fluids (Niklas, 1997). Mechanical support is required for vertical growth outside of a water environment and as plants seek to reach the most sunlight to be able to perform photosynthesis, growing vertically is beneficial for many of them. Most land plants developed a cylindrical stem that provided efficient means of mechanical support (Niklas, 1986), which could explain the general shape of most plant stems. Bryophytes do not have these conducting tissues, and therefore are short, while plants that have them, like flowering plants, can grow taller. The development of an upright position in plants was also accompanied by the development of an anchoring mechanism, or roots. The earliest evidence of roots dates back to the early Devonian 408 million years ago (Erick et al., 1998). The major extant (living) groups of plants are non-vascular plants, seedless vascular plants, Gymnosperms, and Angiosperms. The first evidence of terrestrial plants are fossil spores from the late Ordovician (~450 Ma; Gray, 1985; Appendix 1). From bryophytes (the oldest plant group) to flowering plants (the most recent plant group), plants have acquired unique characteristics that allow them to survive and thrive in different terrestrial environments (Figure $3$). Plants have been able to colonize all terrestrial ecosystems on Earth, including mountains, islands, sand dunes, rainforests, and deserts. In the following chapters, we will explore the main characteristics of each plant group and learn about important economic or cultural uses for each. Learning about the basic characteristics of each group is the first step in identifying plants. For example, if you go hiking and find an interesting plant you want to identify, you can start by identifying the plant’s group. By eliminating the other groups, you can get closer to an identification. 6.02: Alternation of generations Before embarking on the exploration of the different groups of plants, let’s introduce the concept of alternation of generations in plant life cycles, which is inherited from the green algal ancestors of land plants. Alternation of generations means that plants alternate between two different life stages, or generations, in their life cycle; a haploid stage called gametophyte and a diploid stage called sporophyte. The terms haploid and diploid refer to the number of chromosomes contained in the cells. For example, most of the cells in the human body contain two sets of chromosomes (n) meaning they are diploid (2n): one set that we inherit from our mother (n) and one set we inherit from our father (n). However, humans also have special reproductive cells (eggs and sperm) that only have one set of chromosomes, and we call this haploid (n). These reproductive cells are called gametes and they are produced via cell meiosis (reductive cell division). When a male gamete (n) joins a female gamete (n) through fertilization, they form a diploid organism (2n). Most of the plants we are familiar with, like trees, grasses, and tomatoes, have a dominant sporophyte stage, so the visible plant is diploid. Just like humans, plants also have specialized gametes that are haploid (n), which are found in their reproductive organs like flowers. However, instead of producing their gametes on a specialized structure on their diploid body (e.g. a flower on a tree), some plants have a prominent life stage where the whole entire plant is composed of haploid cells (n), and that haploid plant produces gametes. We call this haploid plant a gametophyte. The visible green body of some plants, like mosses, are actually the gametophyte. The alternation of generations in plants is an alternation between the gametophyte stage and the sporophyte stage. In general, this is how alternation of generations works: a male gametophyte (n) and a female gametophyte (n) produce gametes (sperm and eggs, respectively), which combine in fertilization to form a diploid plant called a sporophyte (2n). This sporophyte will grow and then produce spores, through meiosis, that will germinate into a new gametophyte (n), thus the alternating cycle is complete (Figure $1$). The specifics of this alternation is unique for each plant group, so we will revisit the alternation of generations for each one of the plant groups in subsequent chapters.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/06%3A_Plant_evolution_and_non-vascular_plants/6.01%3A_What_defines_a_plant.txt
Non-vascular plants are a diverse group of plants with approximately 20,000 living species presenting a wide geographical distribution, ranging from tropical forests to high latitude tundra, to high mountain ranges. They are the most ancient group of land plants, being the closest relatives to green algae and the earliest diverging lineages of land plants. Informally, they are called “bryophytes” which include mosses, liverworts, and hornworts. In this chapter, you will see the term used to refer to non-vascular plants. Bryophytes can grow in a variety of substrates, like rocks, tree stems, or fallen logs. They are an important part of the environment because of their ability to grow on bare surfaces, interact with non-living elements like rocks and boulders as part of the biogeochemical cycles (Lindo and Gonzalez, 2010) and even filter water. Bryophyte communities (also known as Bryospheres), are complex micro ecosystems that house a variety of species of bacteria, fungi, and other organisms. They are small so most people won’t notice them; however, they are very important for ecosystem functioning. For example, a bryophyte mat can retain water and serve as a nursery for native plants (Figure $1$). Bryophytes lack vascular tissue which translates in them being short, as they cannot perform any significant vertical transportation of water. Instead, they absorb water directly from their surroundings through osmosis, especially via the lower surface of the leaf. Consequently, they are mostly confined to places where water is readily available. They also require water for sexual reproduction, as bryophyte sperm is flagellated and needs to swim to the egg. With this in mind, in which type of ecosystems would you likely find bryophytes? Here in Hawai‘i, they can be found in areas with high precipitation and high humidity, like on the Windward side of the islands, or along streams banks. On higher elevations where precipitation is high, they can be found growing on rocks and logs on the forest floor. Bryophytes are an ancestral group of plants, because besides lacking vascular tissue they also lack true roots and true leaves, which are characteristic of more recent plants.There are three main bryophyte groups (liverworts, hornworts and mosses), each one possessing easy to recognize characteristics (Figure $2$). There are about 9,000 species of liverworts on Earth (Christenhusz and Byng, 2016). The name of this group originated at a time botanists thought the shape of a plant could be used to treat diseases of the part of the human body it resembled. In this case, liverworts look like human livers because they are lobed. This method of treating diseases took place in the 15th century and it is no longer an accepted practice, but the name stayed. Liverworts play a crucial role in their habitats. For example, in tropical forests they play a role in water absorption and retention. In arid regions they help form a soil crust that allows other species to survive while stabilizing the area. Some species of liverworts have the characteristic flattened leaflike body (thallus) from which the group name is derived and are small (less than 10 centimeters or 4 inches) with lobed “leaves” (Figures 6.3.3). Interestingly, most species of liverworts are similar to mosses and can be differentiated from them by the presence of single cell rhizoids in liverworts (primitive root structure), rather than the multicellular rhizoids present in mosses. This might not be very useful when trying to identify a mossy looking liverwort in the field because you would need a microscope to see these structures. Some characteristics that can help tell the difference in the field is that most mosses have spirally arranged leaves, a distinct midrib, and same size leaves. The dominant life stage of a liverwort is the gametophyte, which is the green leafy part of the body. From the gametophytes, they produce the male and female reproductive structures, archegonium and antheridium, respectively. These photosynthetic structures usually tower over the thallus and it is here where eggs and sperm are produced. Liverworts, just like mosses and hornworts, require water for reproduction because the sperm needs to swim to the female structure for sexual reproduction to take place. The sperm swims through a hollow tube in the archegonium (female) to reach the egg. Once fertilization is accomplished, the embryo becomes the diploid sporophyte (2n) and it remains attached to the gametophyte (Figure $4$). Liverworts also reproduce asexually, by producing gemmae in cuplike structures on their gametophytes (Figure $4$). Gemmae are small pieces of haploid tissue that can grow into new gametophytes. Rain usually splashes the gemmae out of the cups, dispersing them to other environments. A few liverworts are very popular in the aquarium hobby as submerged plants or as plants growing in terrariums. Floating crystalwort (Riccia fluitans), Asian liverwort (Monosolenium tenerum) and mini pellia (Riccardia chamedryfolia) are all species used by hobbyists. There are about 12,700 species of mosses in the world (Christenhusz and Byng, 2016). In Hawai‘i, there are approximately 255 species of mosses, consisting of 75 endemic, 166 indigenous and 14 introduced species (Staples et al., 2004). If you are walking around a wet rural or urban area you will likely find mosses. By looking closely, you may see mosses growing in cracks of a sidewalk or on the bark of trees on the windward side of O‘ahu (Figure $5$). If the environment is moist enough, mosses will be there. Some moss species can live in drier environments, going dormant during times when water is not available only to spring back to life when it rains. The visible green fluffy plant that we call moss is the gametophyte, which is their dominant stage. Since mosses are part of the bryophyte group, they don’t have true roots to absorb water; instead, they are able to do it directly from the surface of the gametophyte. Once mosses are ready to reproduce, the egg and sperm combine to form a sporophyte that grows from the top of the gametophyte (Figure $6$) or on lateral areas of the stem in prostrate species, and produces spores, which germinate into male and female gametophytes (Figure $7$). These in turn, will produce eggs and sperm that when combined, will give rise to a new sporophyte (the cycle continues!). Sporophytes are not photosynthetic, and they depend on the gametophyte. Some mosses may live a long time without undergoing sexual reproduction. Instead, they form colonies composed of gametophytes. Sometimes small clumps will break off due to a flood or animal disturbance and one of those clumps may start a new colony elsewhere in the process of asexual reproduction via fragmentation. Mosses are important ecologically for several reasons. They act like sponges that are able to absorb and retain rainwater. For this reason, they are important in the establishment of epiphytic fern gametophytes because they can retain moisture for prolonged periods so that spores can germinate and develop (McCarthy 2007, Miles Thomas Pers. Com.). They can also serve as a nursery for native seedlings (Rehm et al., 2019; Kimmerer, 2003); when a seed is dispersed, if it finds a moss colony it can be protected from predators and will have a moist environment to develop and grow (Figure $8$). Mosses have been used for quite a long time by humans. Because of their immense absorptive capacity, native people in different regions have used mosses as diapers and for menstrual supplies. Given their antimicrobial properties, they were used as bandages by several native communities and even during WWI (Kimmerer, 2003). They have also been extensively used as packaging material, and even today they are used for live shellfish shipping. Today, mosses are used in the horticultural industry as potting media for plants (peat moss) and for decorations. The harvest of moss from natural communities can have a significant impact on these populations because they may take a very long time to recover. There are about 225 species of hornworts worldwide, the smallest group of bryophytes (Christenhusz and Byng, 2016). In Hawai‘i there are a total of 8 species (one endemic, three indigenous, 2 introduced, and two of dubious origin). The sporophyte of this group looks like a little horn, which gave the group its name (Figure $9$). On the evolutionary scale, hornworts seem to have diverged from the green algae common ancestor much earlier than mosses and liverworts. They have a unique gene not found in mosses or liverworts called LCIB. This gene is also found in algae and is responsible for concentrating carbon dioxide in the chloroplasts of the cells, making the production of sugars more efficient. The gametophyte, which is the dominant stage in hornworts, grows in a loose circular arrangement from where the green photosynthetic horn-like sporophytes grow. Hornworts have stomata in their sporophytes, a feature that is absent in liverworts and most mosses (Figure $10$). On O‘ahu, hornworts can be found on stream banks (Figure $9$), which may be one of the only places they can grow without competition from weeds or leaf cover (Vitt et al., 2018). There, colonization is facilitated by the presence of exposed mineral substrates and microhabitats full of moisture (Figure $9$). The dominant life stage of a hornwort is the gametophyte (Figure $10$). From the gametophytes, they produce the male and female reproductive structures, archegonium and antheridium, respectively. These structures are located on the surface of the gametophyte and are where eggs and sperm are produced. Hornworts, just like mosses and liverworts, require water for reproduction because the sperm needs to swim to the female structure for sexual reproduction to take place. Once the sperm reaches the egg and fertilization takes place, a zygote (diploid, 2n) forms which then develops into the sporophyte which remains attached to the gametophyte (Figure $10$). 6.04: References Cheng, S., Xian, W., Fu, Y., Marin, B., Keller, J., Wu, T., ... & Melkonian, M. (2019). Genomes of subaerial Zygnematophyceae provide insights into land plant evolution. Cell, 179(5), 1057-1067. Christenhusz, M. J., & Byng, J. W. (2016). The number of known plant species in the world and its annual increase. Phytotaxa, 261(3), 201-217. Gray, J. (1985). The microfossil record of early land plants: advances in understanding of early terrestrialization. Philosophical Transactions of the Royal Society of London, Series B 309, 167-195. Lindo, Z., & Gonzalez, A. (2010). The bryosphere: an integral and influential component of the Earth’s biosphere. Ecosystems, 13(4), 612-627. Kimmerer, R. W. (2003). Gathering moss: A natural and cultural history of mosses. Corvallis, OR: Oregon State University Press. McCarthy, M. R. (2007). Bryophyte Influence on Terrestrial and Epiphytic Fern Gametophytes (Doctoral dissertation, Miami University). Niklas, K. J. (1986). Evolution of plant shape: design constraints. Tree, 1, 67-72. Niklas, K. J. (1997). The evolutionary biology of plants. Chicago, Chicago University Press. Rehm, E. M., Thomas, M. K., Yelenik, S. G., Bouck, D. L., & D'Antonio, C. M. (2019). Bryophyte abundance, composition and importance to woody plant recruitment in natural and restoration forests. Forest Ecology and Management, 444, 405-413. Staples, G. W., & Imada, C. T. (2006). Checklist of Hawaiian anthocerotes and hepatics. Tropical Bryology, 28, 15. Staples, G. W., Imada, C. T., Hoe, W. J., & Smith, C. W. (2004). A revised checklist of Hawaiian mosses. Tropical bryology, 35-68. Vitt, D. H., House, M., & Kang, R. (2018). The stability of moss populations on stream banks along two first-order, temperate-forest, headwater streams. The Bryologist, 121(2), 205-213.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/06%3A_Plant_evolution_and_non-vascular_plants/6.03%3A_Non-vascular_plants.txt
Learning Objectives • List and describe the distinguishing characteristics of lycophytes and ferns. • Identify the gametophyte and sporophyte generations in the life cycle of a fern. • List five important uses of seedless vascular plants. 07: Ferns and lycophytes Seedless vascular plants reproduce via spores but, unlike non-vascular plants (hornworts, mosses, and liverworts) have a vascular system with xylem and phloem, which transport water and nutrients (Figure $1$). They do not produce flowers, fruits, or seeds. There are two major distinct evolutionary lineages: lycophytes (Lycopodiopsida) and ferns (Polypodiopsida) with approximately 12,000 species worldwide (PPG I, 2016). On an evolutionary scale, ferns are more closely related to seed plants than to lycophytes, but these two classes of plants are usually grouped together as seedless vascular plants because they share several characteristics. These relationships are still being studied by evolutionary biologists and they will likely be clarified in the near future. Lycophytes and ferns share a similar life cycle with independent photosynthetic gametophytes and sporophytes, with the sporophyte being the dominant phase. This is different from bryophytes, where the sporophyte grows from and remains attached to the gametophyte, and the gametophyte is dominant. The sporophytes of vascular plants are usually large and visible, having differentiated plant organs, as leaves, roots, and stems, while the gametophytes are small. Lycophytes have microphylls (leaves with single unbranched veins), while other vascular plants (ferns, gymnosperms and angiosperms) have megaphylls (leaves with multiple branched veins). Lycophytes have microphylls, while ferns and other vascular plants (gymnosperms and angiosperms) have megaphylls. 7.02: Lycophytes There are approximately 1,300 species of lycophytes worldwide (Christenhusz and Byng, 2016) and they can be found in arctic, temperate and tropical regions. In Hawai‘i there are 17 native species and varieties and at least 4 introduced species that have become naturalized (Ranker et al., 2019). Lycophytes first appeared in the Silurian period approximately 425 million years ago (Appendix 1). By the Carboniferous period (350 million years ago), they had become the dominant plant group and formed extensive dense forests. The species living at that time that are now extinct, ranged from short plants to massive trees up to 30 meters (98 feet) in height (Figure $1$). These plants were very common in swamp forests and their biomass was responsible for the formation of coal deposits, from which we extract coal today. In the late Carboniferous the climate on Earth changed, drying the swamps and pushing most lycophytes to extinction. Today the living species of lycophytes are all relatively few and small compared to their once lush diversity. Lycophytes are divided into three groups (orders): Lycopodiales, Seleginellales and Isoetales: Lycopodiales (club mosses, fir mosses) There are four groups of Lycopodiales in Hawai‘i (Huperzia, Lycopodium, Palhinhaea, Phlegmariurus, per PPG I, 2016). Some species may resemble small pine trees with “cones” growing on the tip of their branches. These cones are spore-bearing structures called strobili (singular, strobilus). They are made up of tiny, closely spaced leaves with sporangia (spore cases) hiding at their bases. Species in this group are usually smaller than 30 centimeters (1 foot), but are able to reach more than a meter (5 feet) tall in some tropical ecosystems. Hawai‘i has fifteen species and a few hybrids (Ranker et al., 2019), which are commonly found in wet forests (Figure $2$). Selaginellales (spike mosses) Spike mosses have stems with many branches and scale-like leaves that grow in a spiral-like pattern, each having a little tongue-like extension called a ligule (Figure $3$). Spikemosses can be found in wet environments, growing alongside mosses and liverworts. In Hawai‘i there are 2 native species (one endemic and one indigenous) and four introduced species that became naturalized (Ranker et al., 2016). Isoetales (quillworts) Quillworts are aquatic plants with long narrow leaves that are wider at the base and are arranged in a spiral (Figure $4$B). Hawai‘i only has one species of quillwort, Isoëtes hawaiiensis, which is endemic (Taylor et al., 1993). This species is quite rare and has only been found on Maui and Hawai‘i Island. On Maui, it occurs in the West Maui Mountains (Mauna Kahālāwai) on top of Pu‘u ‘Eke elevation 1372 meters (4,500 ft; Figure $4$A).	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/07%3A_Ferns_and_lycophytes/7.01%3A_Seedless_vascular_plants.txt
There are about 10,560 species of living ferns worldwide (PPG I, 2016). Hawai‘i has approximately 188 species with 111 of them being endemic and 35 indigenous to the Hawaiian Islands. Additionally, 40 species of introduced ferns have become naturalized (Ranker et al., 2019). As with lycophytes, the sporophyte is the dominant stage in the fern's life cycle, and the gametophyte is a separate, free-living plant (Figure $1$). Ferns are a common sight in most rural and urban areas and are widely used as indoor plants and in landscaping. In Hawaiian forests, remaining fern understories play critical roles. Fern leaves (megaphylls) are commonly referred to as fronds, which grow from an erect of creeping rhizome (stem). They start as fiddleheads that uncurl. Fern sporophytes range in size from small, herbaceous plants of a few centimeters to tree-like plants more than 7 meters (25 feet) tall. The spore-bearing structures in ferns are called sporangia (singular sporangium), which are clustered together in structures called sori (singular, sorus; Figure $1$). Sori are usually found on the underside of fertile fronds, and they can be rounded or linear, depending on the species. Sori shape and arrangement are used as key characteristics for the identification of different fern species. Spores germinate into gametophytes (Figure $2$), which then produce gametes (sperm and egg) that, when combined, grow into sporophytes (what we typically see and think of as ʻferns’), completing the fern life cycle (Figure $3$). The gametophyte is smaller than a fingernail, and independent from the sporophyte (Figure $2$). Ferns can grow in a variety of environments, but they are more common in wet ecosystems, since they need water for sexual reproduction so that the sperm can swim to the egg on the gametophyte (Figure $3$). Ferns can also reproduce asexually (vegetative reproduction) from the rhizome with new plants emerging from it. In the horticulture field, ferns are propagated by division (a plant can be split up into many). Ferns are divided into four main groups (subclasses; PPG I, 2016): Equisetidae, Marattidae, Ophioglossidae, and Polypodiidae. Equisetidae (horsetails) Equisetales were once a diverse group of seedless vascular plants that were very common in the Carboniferous (300 million years ago) and have a rich fossil record. Today there is only one living genus, Equisetum, which is herbaceous, commonly reaching up to 1 meter in height (3 feet), but with some species able to reach 10 meters (32 feet). The name of this group is derived from the horsetail appearance that some branched species have. They are easy to recognize because of their green photosynthetic stems with vertical ridges (Figure $4$). Leaves are usually brown or black, triangular, small and arranged as a whorl around the stem at the nodes (dark rings on Figure $4$). Stems have silica on their cells, making these plants useful as polishing material. Some species have been used medicinally in Europe, the Americas and Asia (especially in India) including as a diuretic and an anti-inflammatory medication (Carneiro et al., 2013). They are also used as food, eaten boiled or raw in different cultures, especially the tender young stems. There are no native species of this group in Hawai‘i. Several horsetail species were recently introduced to the islands to be used in gardening and landscaping, especially around ponds. Marattiidae (mule’s foot) This group has only one living family and 110 species worldwide (PPG I, 2016). It is the most ancient group of ferns. These species are known to have very large, vertical rhizomes. The leaf bases are swollen, with large fleshy stipules on either side (stipules of some species can be eaten). Muleʻs foot leaves can be very large, reaching up to 9 meters (30 feet) in length. Hawai‘i has one native species, pala (Marattia douglasii). Another species, Angiopteris evecta, known as Madagascar’s tree fern or mule’s foot, is introduced and is listed as an invasive species in Hawai‘i (Figure $5$). Ophioglossidae (whisk ferns, adder’s-tongues) Subclass Ophioglossidae has two orders: Psilotales (whisk ferns) and Ophioglossales (adder’s tongues). Whisk ferns are very easy to recognize since they look like a green whisk broom with triangular stems that branch dichotomously (in twos). They do not have roots. Their leaves are tiny, therefore the green stems perform most of the photosynthesis. Their sporangia (spore-bearing structures) are rounded, yellow, and can be seen suspended on the upper portions of the branches. Whisk ferns are found in all tropical environments around the world. In Hawai‘i there are two indigenous species of whisk fern (Figure $6$). Moa nahele (Psilotum complanatum) has flat stems and moa (moa or Psilotum nudum) grows upright. These species are found in a wide variety of environments on all the main Hawaiian islands. Traditionally moa has been used for lei making as well as medicine; for example, as a laxative tea and the spores were used as powder to prevent chafing (Krauss 1974). Species of the Ophioglossales (adder's-tongue ferns) are often characterized by producing only one fleshy leaf at a time. Also, their gametophytes occur underground and they rely on mycorrhizal fungi for nutrition. Hawai‘i has four indigenous and one endemic species in the Ophioglossales. An example is puapua moa or old-world adder's-tongue (Ophioderma pendulum). Its sporangia are held within a spike that dangles from the middle of a leaf (Figure $7$). Polypodiidae This is the largest group of ferns with most species of ferns in Hawai‘i belonging to it. Species in this group are very important for the ecology of native ecosystems in Hawai‘i. They flourish in wet and mesic forests, in which they may become the dominant group covering the soil, as well as being present in the mid-canopy as epiphytic species (growing on trees without harming them). Some ferns are pioneers on recent lava flows, where they start to break down the rock into soil and prepare the way for subsequent plant colonization, an important step in the formation of plant communities. Ferns also colonize areas where landslides have occurred. For example, uluhe (Dicranopteris spp.) can be seen growing in steep areas where the soil has been exposed by landslides (Figure $8$). Uluhe species grow in thick mats, preventing invasive seeds from germinating and establishing, which helps the native species in the area by reducing competition. In native forests, Polypodiidae species cover the soil surface (Figure $9$). Ferns break the force of the rain passing through the forest canopy so more water can get absorbed by the soil, and go into the aquifer, and erosion is reduced. Water runoff can be seen in areas where ferns and native forests are either disturbed or not present. After heavy rains, the ocean will turn brown due to all the sediment carried by the rain runoff from these mid-elevation disturbed areas. The presence of introduced ungulates (pigs, deer, and mouflon sheep) has negatively impacted fern communities in Hawai‘i. Pigs dig around the soil to uncover worms and insects, disturbing the root system of ferns. Once the fern ground cover is removed, invasive species have a better chance to colonize the area. Fencing to keep pigs out has been a successful strategy in Hawai‘i that tremendously helps the conservation of native ecosystems. It gives fern communities a chance to recover, improving the chances that other native species can thrive. In Hawai‘i there are several traditional uses for ferns in this group: lei making, fiber, and food. Some species of ferns were used medicinally (see Gutmanis, 1976). There are at least two species of ferns used for food. One species, hō‘i‘o or pohole (Diplazium sandwichianum), is endemic to the Hawaiian Islands and grows in mid-elevation mesic to wet forests. The most common fern used for food is Diplazium esculentum, an introduced fern often called hō‘i‘o or warabi in Hawaiʻi. Throughout the Pacific and Southeast Asia it is known as paca (Palmer, 2003). It grows very well in lowland wet areas. The newly emerged fiddleheads of both species are harvested before they uncurl (Figure $10$) and are eaten raw or steamed. Another native Hawaiian fern, the hāpu‘u pulu (Cibotium glaucum) is a species of tree fern that produces hairs on its unfolding fronds, at the base of the stem (Figure $11$). These soft hairs were used as filling material, including for the stuffing of pillows. These ferns are also ornamentals, being transplanted into gardens for their beauty, and their stems are often used as a substrate for other plants such as orchids (Buck, 1982). Wild harvest of tree ferns has been of conservation concern in some parts of the globe including Hawai‘i. In Hawai‘i ferns are also commonly used in lei making (Figure $12$), with two native species often used: pala‘ā (Sphenomeris chinensis) and palapalai (Microlepia strigosa). Both of these ferns have special connections to Hawaiian culture and are seen as the physical representations (kinolau) of Laka, goddess of hula (palapalai), and Hi‘iaka (pala‘ā). The fronds of palapalai are also used to decorate hula altars (Ticktin et al., 2006). Both species are harvested from the wild and in some areas there are protocols in place to maintain populations that have been negatively impacted by invasive species (Ticktin et al., 2006). The cultivation of pala‘ā in gardens can be challenging, however, palapalai is easy to grow and is used in landscapes in urban areas. If grown in the right conditions, this fern can produce many fronds that can then be harvested. 7.04: References Buck, M. G. (1982). Hawaiian tree fern harvesting affects forest regeneration and plant succession (Vol. 355). US Department of Agriculture, Forest Service, Pacific Southwest Forest and Range Experiment Station. Carneiro, D. M., Tresvenzol, L. M. F., Jardim, P. C. B. V., & Cunha, L. C. D. (2013). Equisetum arvense: scientific evidence for clinical use. IJBPAS, August 2(8). Christenhusz, M. J., & Byng, J. W. (2016). The number of known plant species in the world and its annual increase. Phytotaxa, 261(3), 201-217. Gutmanis, J. (1976). Kahuna la'au lapa'au: The practice of Hawaiian herbal medicine (Vol. 13). Island Heritage. Krauss, B. H. (1974). Ethnobotany of Hawaii. Honolulu. University of Hawaii Press. Palmer, D. D. (2003). Hawai‘i’s ferns and fern allies. University of Hawaii Press. PPG I. (2016). A community‐derived classification for extant lycophytes and ferns. Journal of Systematics and Evolution, 54(6), 563-603. Ranker, T. A., Imada, C. T., Lynch, K., Palmer, D. D., Vernon, A. L., & Thomas, M. K. (2019). Taxonomic and nomenclatural updates to the fern and lycophyte flora of the Hawaiian Islands. American Fern Journal, 109(1), 54-72. Taylor, W. C., Wagner Jr, W. H., Hobdy, R. W., & Warshauer, F. R. (1993). Isoëtes hawaiiensis: a previously undescribed quillwort from Hawaii. American fern journal, 67-70. Ticktin, T., Whitehead, A. N., & Fraiola, H. A. (2006). Traditional gathering of native hula plants in alien-invaded Hawaiian forests: adaptive practices, impacts on alien invasive species and conservation implications. Environmental Conservation, 185-194.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/07%3A_Ferns_and_lycophytes/7.03%3A_Ferns.txt
Learning Objectives • List the four major groups of gymnosperms and provide distinguishing features and examples of each. • Explain the characteristics that made gymnosperms and other seeds plants dominate in terrestrial ecosystems compared to bryophytes and earlier vascular plants. • List at least five uses of gymnosperms. 08: Gymnosperms Gymnosperms produce seeds (Figure $1$) and, together with flowering plants, constitute the seed plants. Although gymnosperms do not produce flowers and fruits, they still have embryos enclosed in a protective barrier or seed coat. This neat little package called a seed is an innovative step in plant evolution that helped some plants thrive in terrestrial ecosystems. Seeds allowed plant embryos to withstand freezing, desiccation, and ultraviolet light damage in terrestrial environments while providing energy storage (endosperm). The name gymnosperm is derived from gymno meaning nake and sperm meaning seeds (i.e., their seeds are uncovered) while angiosperm (flowering plants) seeds are usually covered by a fruit. Most gymnosperms produce seeds in structures called cones or strobili (singular strobilus; Figure $2$). Cones evolved from modified leaves, and they can either be male cones that produce pollen, or female cones that produce ovules. There are approximately 1,100 gymnosperm species in the world today (Christenhusz and Byng, 2016) representing only 1% of plant diversity on the planet. However, they are an important part of the ecology of boreal regions (located in the Northern Hemisphere between 50° to 70°N latitude) and high elevation environments including in the tropics (Crepet and Niklas, 2009). For example, in North America, entire forests are composed of large gymnosperm trees: redwoods, cedar, and pines. Besides having a protected embryo, seed plants also protect and nourish the gametophytic stage of their lifecycle, an advantageous characteristic for terrestrial life. In non-vascular plants (bryophytes), the gametophyte is the dominant stage, while in seedless vascular plants (ferns and lycophytes) the gametophyte is independent and reduced in size, leaving the sporophyte as the dominant stage. This pattern of gametophyte reduction continues in seed plants, in which the gametophyte becomes so reduced that it is only a microscopic entity found inside the ovules and pollen grains that grow on the sporophyte. Because the gametophyte develops inside the sporophyte, they are protected from environmental pressures and get nourishment from the sporophyte. Another advantageous characteristic is the type of spores seed plants produce. While ferns produce one type of spore, making them homosporous, gymnosperms and other seed plants produce two types of spores (heterosporous), megaspores, which give rise to female gametophytes inside the ovule, and microspores, male gametophytes inside the pollen grain. The development of pollen and ovules has contributed to the success of seed plants on land. The pollen containing the male gametophyte gets transported via wind and sometimes by pollinators, so that seed plants no longer rely on water for fertilization to take place. Most gymnosperms are wind pollinated, therefore they produce millions of pollen grains to increase the chances of them reaching the eggs on the female cones. Today, Gymnosperms are the group of plants most threatened by extinction with 40% of species being categorized as high risk (Forest et al., 2018). For example, ginkgo is cultivated outside its natural range, but in China only a few natural populations remain, making it vulnerable to extinction. Another example is Araucaria (Araucaria angustifolia) which is native to Brazil and Argentina. This species has received critically endangered status because its natural habitat has decreased 97% in the past century (Forest et al., 2018). Gymnosperms are divided into four groups: Conifers, Cycads, Ginkgo, and Gnetophytes.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/08%3A_Gymnosperms/8.01%3A_Gymnosperms.txt
8.2 Conifers (Phylum Pinophyta) Conifers are the most diverse group of gymnosperms, with 629 species worldwide (Christenhusz and Byng, 2016). A large number of conifer species are native to the Northern Hemisphere where they are an important part of native ecosystems, providing forest structure with many organisms depending on them for survival. The majority of conifer species are trees with secondary growth (wood formation) and are evergreen, not shedding their leaves seasonally. Leaves on most species are adapted to cold climates and snowy conditions by growing in a needle-like shape, which prevents snow from accumulating on the tree and eventually breaking it. Instead, the snow falls through the needles and releases the pressure caused by its weight. Another advantage of the needle-like leaf shape is resistance to desiccation in the cold dry winter. All species of conifers are wind pollinated, with some species having male and female plants (dioecious) while others having male and female cones on the same tree (monoecious). There are several economically important species of conifers such as pines, cedars, and junipers, which are used for lumber and paper making. Conifers are the main source of raw material for paper products in North America, with numerous species grown in timber lots and constituting a big part of the world’s economy. Culturally, many species of conifers are important and are used during the holidays for decorations or part of celebrations. For example, several species of Christmas trees are grown in tree farms and pine cones and juniper foliage are used for wreaths and other seasonal decorations (Figure $1$). Another example of how conifer species are used by people is the harvesting of juniper berries to make gin. The berries are actually female cones, not real fruits, that are used to flavor the alcoholic beverage. The seeds of two Araucaria species are also eaten in Chile and Australia by indigenous peoples. Pine trees are the most iconic group of conifers (Figure $2$). They are considered by many as the most important genus of trees, as they have been used extensively by humans and their range of distribution occupies a vast area that extends from subtropical areas to subarctic zones. Pine trees grow in the coastal plains of Florida, mid-elevation forests in Mexico, and all the way to the boreal forests of Canada (Richardson et al., 2007). Pine “nuts,” which are pine seeds, are very nutritious and are harvested from 29 species of pine trees in different parts of the world, including most of the Mediterranean, Asia, and Middle East (Awan and Pettenella, 2017), as well as in the Southwestern United States. Redwood trees, Sequoia sempervirens and Sequoiadendron giganteum, are important species in the conifer group in California (Figure $3$). These trees are the tallest trees on Earth and can reach up to 110 meters (330 feet) in height and 11 meters (33 feet) in diameter. They can also live up to 2,200 years (Watson, 1993). These trees depend on humidity carried by fog for survival, and are able to absorb water directly through their leaves (Burgess and. Dawson, 2004). When fog or light rain occurs, the xylem reverses its direction, absorbing water directly from the leaves and transporting it to other places in the plant such as stems and sometimes all the way to the roots (Burgess and Dawson, 2004). This impressive mechanism is important for the survival of the California redwoods because during the summer months when droughts are common, fog coming from the ocean is still commonly present (Limm et al., 2009). Douglas fir (Pseudotsuga menziesii) is a conifer native to the Pacific Northwest (Oregon, Washington, and British Columbia). It has been used extensively by native peoples, who eat the seeds, harvest and consume crystallised sugar from the branches at certain times of the year, and use the sap for medicine. This species has been logged for over 160 years (late 1800’s to today) in the Pacific Northwest, being one of the most important US timber exports (Cubbage et al., 2020; Walter and Maguire, 2004). Its wood is used to make poles, plywood, and railroad ties, among many other things. This tree can live up to 1,300 years and it is an integral part of the ecosystem where it is native (Figure $4$). Several mammal and bird species depend on its seeds as a source of food and the structure of the forest created by these tall trees allows a high diversity of plant and animal species in these areas. There are no native gymnosperms in Hawai`i, but conifers can be found in different parts of the islands as introduced species. Several conifer species were introduced in experiment plots. In the 1920s and 1930s approximately 15 million trees were planted by different organizations as an experiment to reforest degraded areas (Woodcock, 2003). If you go hiking in a forest reserve, you will likely see stands of these species in their original plots as well as naturalised species that escaped cultivation. The following are some of the species that were planted in O‘ahu: Sugi (Cryptomeria japonica; 499,000 trees), Monterey cypress (Cupressus macrocarpa; 216,000 trees), maritime pine (Pinus pinaster; 173,000 trees), redwood (Sequoia sempervirens; 130,000 trees), Monterey pine (Pinus radiata; 121,000 trees) and several Araucaria species, including Cook’s pine (Woodcock, 2003). Araucarias are native to the Southern hemisphere and they eventually became naturalized in Hawai‘i after being introduced as part of these experimental plots. Now these areas have trees growing and producing seedlings which compete with native species (Figure $5$).	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/08%3A_Gymnosperms/8.02%3A_Conifers.txt
Cycads (Phylum Cycadophyta) Cycads are easy to recognize because they look like a palm tree. However, they bear large cones rather than fruits. Their leaves are quite large compared to the stem and grow out in a rosette around the stem (Figure 8). They can be either male or female, and their cones vary in shape and size, depending on the species. There are approximately 340 species worldwide (Christenhusz and Byng, 2016) and are native to tropical and subtropical areas. They can grow in deserts as well as wet forests. Even though we don’t have any native cycad species in Hawai‘i, you have probably seen them around homes, botanical gardens, and parks. There are two main families of cycads: Cycadaceae and Zamiaceae (another family, Stangeriaceae, has only two living species). Many cycad species are endangered in their natural habitat, although some species are very common in cultivation. The seeds in some cycad species are considered toxic and can negatively affect humans by entering the food cycle through bats, which eat the seeds. Humans then eat the bats, acquiring the poison through second-hand exposure. Another interesting characteristic of cycads is that their roots form a special relationship with bacteria that are able to fix nitrogen. 8.04: Ginkgo Ginkgo (Phylum Ginkgophyta) There is only one living species of ginkgo, Ginkgo billoba, which is a native to China, but is cultivated across the world in temperate regions. The fossil record shows that this group was once diverse and had a widespread distribution in the Northern Hemisphere during the middle Jurassic (170 million years ago). Fossils of these Jurassic plants look very similar to modern gingko, indicating their characteristics have changed little over time, granting the status of “living fossil” to the only surviving species. Gingko is easy to recognize because of its fan-shaped leaves (Figure $1$). It is also known as the maidenhair tree, as the leaves resemble maidenhair fern fronds. Gingko can be either male or female. They are widely cultivated in urban areas because of their beautiful leaves, which change color in the fall. However, female plants produce a “fruit like” structure that is actually a seed surrounded by a fleshy seed coat (they do not produce cones; Figure $2$). Seeds emit a foul odor, therefore male trees are preferred for cultivation in most urban areas. In Asia, however, ginkgo seeds are consumed boiled or roasted, therefore female trees are predominantly grown. Ginkgo is also used for medicine, such as a dietary supplement that is used to improve blood circulation. 8.05: Gnetophytes Gnetophytes (Phylum Gnetophyta) Gnetales are the least familiar group of gymnosperms. There are 112 species in the world (Christenhusz and Byng, 2016), being divided in three main subgroups: Welwitschia (1 species), Gnetales (43 species) and Ephedrales (68 species). Welwitschia is an odd looking plant adapted to extremely arid environments, being native to the Namib Desert in Africa (Angola and Namibia). It has a short stem and only develops two leaves over their long lifetime. Some of the oldest plants can be 3,000 years old. The leaves can reach up to 2 meters (6 feet) in length and will continue to grow the entire life of the plant. The leaves usually coil and get split by the wind (Figure $1$). An example of a plant in the Ephedrales group is Mormon tea (Ephedra spp.), which are common in arid regions of Southwestern United States (Figure $2$). Mormon tea, and a similar species in China from which ephedrine is extracted, have been used for millennia for treating asthma. Currently ephedrine is used to prevent low pressure during anesthesia and most of it is synthetically manufactured, although some Ephedra species are still cultivated for extraction of natural ephedrine. 8.06: References Awan, H. U. M., & Pettenella, D. (2017). Pine nuts: a review of recent sanitary conditions and market development. Forests, 8(10), 367. Burgess, S. S. O., & Dawson, T. E. (2004). The contribution of fog to the water relations of Sequoia sempervirens (D. Don): foliar uptake and prevention of dehydration. Plant, cell & environment, 27(8), 1023-1034. Christenhusz, M. J., & Byng, J. W. (2016). The number of known plant species in the world and its annual increase. Phytotaxa, 261(3), 201-217. Crepet, W. L., & Niklas, K. J. (2009). Darwin's second “abominable mystery”: Why are there so many angiosperm species?. American Journal of Botany, 96(1), 366-381. Cubbage, F., Kanieski, B., Rubilar, R., Bussoni, A., Olmos, V. M., Balmelli, G., ... & Abt, R. (2020). Global timber investments, 2005 to 2017. Forest Policy and Economics, 112, 102082. Forest, F., Moat, J., Baloch, E., Brummitt, N. A., Bachman, S. P., Ickert-Bond, S., ... & Buerki, S. (2018). Gymnosperms on the EDGE. Scientific reports, 8(1), 1-11. Limm, E. B., Simonin, K. A., Bothman, A. G., & Dawson, T. E. (2009). Foliar water uptake: a common water acquisition strategy for plants of the redwood forest. Oecologia, 161(3), 449-459. Walter, S. T., & Maguire, C. C. (2004). Conifer response to three silvicultural treatments in the Oregon Coast Range foothills. Canadian Journal of Forest Research, 34(9), 1967-1978. Watson, Frank D. (1993). Sequoia sempervirens and Sequoiadendron giganteum. In Flora of North America Editorial Committee (ed.). Flora of North America North of Mexico (FNA). 2. New York and Oxford. Retrieved 25 June 2021 – via eFloras.org, Missouri Botanical Garden, St. Louis, MO & Harvard University Herbaria, Cambridge, MA. Woodcock, D. (2003). To restore the watersheds: Early twentieth-century tree planting in Hawai ‘i. Annals of the Association of American Geographers, 93(3), 624-635.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/08%3A_Gymnosperms/8.03%3A_Cycads.txt
Learning Objectives • State the basic differences between angiosperms and gymnosperms. • Within angiosperms, identify and describe monocots and eudicots. • Identify some economically important families. 09: Angiosperms Angiosperms are the group of plants that we are most familiar with, as most of the fruits and vegetables we eat belong to this group. They are currently the dominant group of plants in most terrestrial ecosystems and are easy to recognize since they produce flowers (Figure $1$). Angiosperms are the most diverse group of plants, with 416 families and approximately 352,000 species (APG, 2016). The first fossils of angiosperms date back to the Lower Cretaceous (~130 million years ago; Magallón et al., 2013; Appendix 1). Overtime, they diversified and became more prominent in terrestrial ecosystems, slowly displacing and replacing gymnosperms and other plants. Today, angiosperms represent 90% of terrestrial plants on the planet. The remaining terrestrial plant species comprise gymnosperms (approximately 1% of species; Crepet and Niklas, 2009) and bryophytes, lycophytes and ferns (9% of species). The diversity and success of angiosperms can be attributed to the evolution of flowers and fruits within this group. The development of flowers was an innovative characteristic, as it allowed the ovules to be enclosed and protected inside an ovary, which after fertilization turns into a fruit that aids seed dispersal. Flowers also allowed for male and female parts of the plant to be clustered into a single structure (Figure $2$). Flowering plants developed relationships with pollinators (Hu et al., 2008). Instead of dispersing their pollen via wind, like gymnosperms, early angiosperms started to offer rewards in their flowers to attract animals, who in turn started to visit the flowers of a given species for the food rewards they offered. Through this relationship, flowering plants got the guarantee that their pollen would likely reach another individual of the same species: therefore, increasing the probability of successful fertilization (Figure $3$). This transfer of pollen from one plant to another, otherwise known as outcrossing, ensured higher genetic diversity in the population. Since the origin of flowers, pollinators have driven floral diversity in angiosperms by increasing the richness of species (Van der Niet and Johnson, 2012). Pollinators have preferences for flower shape, size, color and even type of reward. They also come in all shapes and sizes and they include birds, reptiles, beetles, and bats. Over time, some plants and pollinators have developed a specific relationship, where a plant species is pollinated by a specific animal. However, many plants (and animals) are generalists and are pollinated by different species of pollinators. The Hawaiian honeycreepers are a great example of the relationship between pollinators and flowering plants. At least five genera of a group of plants called Hawaiian lobeliads (Delissea, Clermontia, Cyanea, Lobelia and Trematolobelia) are pollinated by native forest birds (Pender et al., 2014). The shape of the flowers, the nectar content, and other characteristics match this kind of pollination syndrome. The native Hawaiian honeycreeper ‘i'iwi (Vestiaria coccinea) feeds on the nectar produced by these flowers thanks to its long, curved beak which has a similar shape to the curved flowers of many of the Hawaiian lobeliads (Figure $4$). When feeding on nectar, pollen from the flower is deposited on the head of the ‘i'iwi, and the bird inadvertently moves pollen between flowers. Unfortunately, it is believed that many Hawaiian lobeliad species produce reduced amounts of seed because some native bird species are so rare or have become extinct; therefore, the flowers are not adequately pollinated by these native birds. A long, tubular Hawaiian lobeliad flower could not be pollinated by insects like bees because of its curved shape. On the other hand, some plant species like ʻōhiʻa (Metrosideros polymorpha) are known as generalists, as they can be pollinated by either birds or insects (Figure $5$). The flower shape and other characteristics, like color, allow for this type of pollination strategy. Fruits are another evolutionary adaptation present in angiosperms. Once the plants are pollinated and the ovules fertilized, the ovary grows into a fruit. One of the main functions of the fruit is to assist in the dispersal of the seeds, which is achieved through different mechanisms. For example, fruits can be attractive to animals because they offer a food reward. After being eaten, the seeds contained in the fruit are usually dispersed a distance from the parent plant, allowing the species to spread. Other fruits have spurs to attach themselves to animal fur and bird feathers to aid the dispersal of seeds. An example of the importance of animals in the dispersal of angiosperm seeds is exemplified by the long distance dispersal of seeds to Hawai‘i from distant land masses; bird dispersal is the principal mode in which native plant genera arrived in the islands.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/09%3A_Angiosperms/9.01%3A_Angiosperms.txt
Angiosperms can be divided into several groups: Basal clades, Magnoliids, Monocots and Eudicots. Most angiosperm families fall into the monocots and eudicots groups. These two groups have very specific morphological (external) characteristics. We will look at them closely here, but they were also explored briefly in previous chapters of this book. Seeds Monocots have one cotyledon (mono = one; cotyledon = seed leaf) and eudicots have two (eu = true; di = two; cotyledon = seed leaf). For example, beans are eudicots and when their seeds germinate it is easy to see the two cotyledons (Chapter 5, Figure $1$). The same thing happens when you cook beans, some of the seeds may split into two parts. Monocot seeds don’t do that, they stay intact. Corn is an example of a monocot. Flowers Dicot flower parts are organized in multiples of four or five, while in monocots flowers are organized in multiples of three. Some plants have petals and sepals while others have tepals. Tepals are the ancestral condition in flowering plants and are undifferentiated (they look the same). You may see a flower that has flower parts that look identical and you can’t tell if they are sepals or petals like in daylilies (Hemerocallis spp.; Figure $1$) and in spider lily (Crinum asiaticum; Chapter 5). An example of a monocot is a spider lily, which has six petals, while an example of a dicot is a Hibiscus, which has five petals (Figure $1$; Chapter 5). Roots Overall, eudicots generally have tap roots while monocots have fibrous roots (Figure $1$; Chapter 2). There are exceptions to this rule, for example eudicot species may have adventitious roots. Tap roots have a prominent primary root that develops when the seed germinates and the radicle emerges. From there, secondary or lateral roots grow. Fibrous roots, as the name suggests, look like fibers, with all the roots being of similar length and diameter. Fibrous roots usually form a dense shallow root system. Fibrous roots are also known as adventitious roots because the primary root that forms when a seedling germinates is eventually replaced by lateral roots from the stem of the plant. Leaves Eudicots have reticulate (net-like) venation on their leaves, while monocots usually have parallel venation (Chapter 4). However, there are exceptions to this rule. For example, kalo/taro is a monocot that does not have parallel veins on the leaves (Figure $2$). In reticulate venation the branching pattern further divides into smaller veins resembling a net. In parallel venation there are several secondary veins that are parallel to the midrib and to each other. Other characteristics Several anatomical characteristics can also be used to distinguish monocots and eudicots. focus on the internal structure of plants (anatomy). You won’t be able to see them with the naked eye, but you could use them to differentiate between plant groups if you had a microscope. For example, monocots have their vascular bundles scattered in the stem, while eudicots have them organized in a ring around the stem (Chapter 3). In monocots, like corn, these vascular bundles are scattered throughout the stem tissue. Eudicots, like beans, are a little more complex. Eudicot stems can be herbaceous or woody. In herbaceous or young woody eudicots the vascular bundles are arranged in a ring around the stem. In older stems, these bundles tend to fuse to each other to form concentric rings. Also, pollen grains in eudicots have three apertures, while monocots have only one.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/09%3A_Angiosperms/9.02%3A_Monocots_and_eudicots.txt
Families are large groups within the Kingdom Plantae (plants) that share certain characteristics and have a common ancestor. Originally, these families were defined based on their morphological characteristics (shape). Today, we are able to use additional sources of data, like deoxyribonucleic acid (DNA) to group plants into families and to more accurately reconstruct the evolutionary relationships of plants. The visible characteristics of plants (morphology) are still very useful for plant identification and can have practical uses. For example, some diseases may affect members of a specific family, some families are known to produce poisonous compounds, or some families may have specific germination requirements, like the case of Orchidaceae. The more you learn about plant families and their characteristics, the easier it is to identify plants. You start to notice that a plant you know may have similar characteristics with other plants. Here we will cover just a few examples of plant families in the monocot and eudicot groups (Figure $1$). These families have been selected due to their diversity of species, cultural, ecological, and economic importance. Of course we encourage you to learn about other plant families; the ones listed here are just to get you started. Examples of Monocot families Orchidaceae The Orchidaceae is the largest plant family with approximately 28,000 species (Christenhusz and Byng, 2016). All species are herbs, but they can either be terrestrial or epiphytic. Terrestrial orchid species in temperate zones spend part of their lifecycle under the ground and at a certain time of the year the leaves may grow above ground and they may bloom and form fruits. The cycle may continue with the plant dropping its leaves and going dormant for a period of the year. In the tropics, terrestrial species may grow year round. Epiphytic orchid species are found in tropical and subtropical environments. They use trees for support without damaging them. This is an important strategy when growing in a forest since little sunlight gets to the forest floor. These plants can grow high up in the canopy of trees where they benefit from more sunlight and access to pollinators. Orchid species are highly diverse, presenting different flower shapes and colors. Researchers attribute the diversity of species in the Orchidaceae to co-evolution with pollinators and fungi. Some orchid species offer nectar as a reward, while others mimic insect shape or pheromones that trick insects into believing the flowers are their mating partner. Many species in this family rely on specific animals for pollination. For example, vanilla (Vanilla planifolia), which is native to Mexico, is pollinated by a native species of bee. When the plant is grown outside of its natural range, like in Hawai‘i, hand pollination is required for plants to produce fruit capsules (Figure $2$). The fruit of vanilla is the part of the plant used to make vanilla extract. Hawai‘i has three native orchid species, all found in high elevations. All of them are terrestrial and likely arrived here by air currents. Non-native orchids are very popular in Hawai‘i and many growers focus on propagating hybrids for the horticultural market. Common Characteristics Habit: Either epiphytic or terrestrial herbs . Flower: Instead of having petals and sepals, orchids have six tepals including a modified lip. The anthers are grouped into a structure called the pollinia. Fruits and Seeds: The fruit is a capsule. Seeds are very small and do not have food reserves. Instead, they rely on fungi to germinate (mycorrhizal association). When the seed gets dispersed from the capsule, it needs to land on a location with a specific fungus present. This fungus then inserts its mycelium into the seed and provides it with nutrients. The seed is completely dependent on the fungus until it is able to photosynthesize. Figure 9 shows orchid seeds that are germinating in association with mycorrhizae. Leaves: Leaves are often simple with parallel veins (i.e. typical monocot leaf characteristics). Stems: All species have herbaceous stems. Stems can either be monopodial (grow from a single shoot like in vanilla; Figure $2$) or sympodial (grow from new shoots emerging from a rhizome base). Many species have a specialised stem called a pseudobulb which can store water and nutrients. Other: Epiphytic orchids have velamen (specialized epidermis) on their roots which protects the exposed roots from ultraviolet light damage, while allowing the root to absorb nutrients and water directly from the surrounding environment. Poaceae The Poaceae is the fifth largest plant family with 12,000 species (Christenhusz and Byng, 2016), and includes some very important species for human consumption: corn, rice, wheat, barley and millet, as well as for animal feed (corn), construction materials (bamboo and grasses for tatch), and biofuels (ethanol made from corn and sugarcane). Several species of grasses were domesticated thousands of years ago and today they are known as cereal crops. For example, corn was domesticated in central Mexico around 10,000 years ago (Tian et al., 2020). The ancestor of corn (wild relative) is teosinte, a large grass. Since its domestication, corn has been taken all over the globe and it is now one of the most important crops worldwide. Grasses are very important for the ecology of natural habitats. Grasslands can be found all over the globe, sustaining diverse food webs, as in the African savannas. Grasses are also important components of forests, tundras, wetlands and even in marine habitats. For example, marine grasses provide food and habitat to organisms like the Florida manatee, while also providing nursery grounds for the young of many fish species. Polynesians introduced bamboo (ohe; Schizostachyum glaucifolium) to Hawai‘i. It has been used to make musical instruments (e.g. nose flutes). They also introduced sugarcane (, Saccharum spp. ). Pili grass (Heteropogon contortus), which is a native grass species and an important component of drylands, was used to thatch roofs. Hawaii’s environment did not evolve with large herbivores such as cattle, goats, or deer, so native grasses have been severely impacted by the introduction of these large herbivores, as well as with the introduction of non-native grasses that have become invasive. Native grasses are still important in the native environments, being part of the understory and crucial for coastal erosion control. For example, ʻakiʻaki grass (Sporobolus virginicus) is a native grass species that plays an important role in reducing the erosion of coastal environments in Hawai‘i. Common Characteristics Habit: Herbs. Flowers: Small and normally wind pollinated. Flowers are formed into a spikelet which is composed of many different parts (glume and lemma). Fruits and Seeds: The fruit is a caryopsis (Figure $4$) and the seed has one cotyledon as in other monocots. Leaves: The leaves are normally alternate and have parallel veins. The base of the leaf encloses the stem of the plant creating a “leaf-sheath” while the top of the leaf (the blade) is detached to the stem (Figure $3$). Stems: The stems are hollow except at the nodes. Arecaceae The Arecaceae or palm family has 2,600 species (Christenhusz and Byng, 2016). This family is known for its tree-like species (palm trees) which inhabit tropical and subtropical areas. Even though palms are monocots, which do not develop wood, the stems of these species are extremely strong. They are used to make furniture and musical instruments. The species are also used for food (e.g. coconut, palm sugar, and heart of palm), thatching, as well as handcrafts such as baskets and hats. Many palm species have edible fruits that are consumed in different locations. For example, dates (Phoenix dactylifera) are grown in dry areas and are part of the cuisine in the Middle East, North Africa and certain parts of Asia. Açaí palm (Euterpe oleracea) is cultivated in the Amazon and its fruit is used to make very nutritious and savory meals. It has been a staple part of the diet of local habitants for centuries. Recently, açaí became a healthfood trend around the world and it is now eaten as a sweet treat. Hawai‘i has an incredible diversity of native palms, with 22 endemic species of loulu (Pritchardia spp.; Figure $5$). Most species are native to specific islands or even specific mountain ranges on an island. The large leaves of these species were used to thatch roofs and make baskets and other items. The trunks were used for construction. The immature fruit (a drupe) was used as food (Hodel, 2012). Many loulu species are currently threatened or listed as endangered due to damage from invasive animals, such as pigs and rats. Rats eat the fruits, impacting the ability for the population to regenerate. In some areas you can find old trees, but no young plants or seedlings. This happens when rats remove all the viable seeds making it impossible for new seedlings to establish. Eventually the old trees die and the population disappears from the wild. Pigs damage the bark and root systems as well, negatively impacting older plants in the populations. The coconut palm (Cocos nucifera) is very important in many cultures. The fruit can be used as food and for coconut milk, the fiber can be used for cordage, and the leaves for handcrafts. The oil is important for many African (including the diaspora in the Americas) and Pacific Island cultures. Coconut oil has recently begun being used world wide due to its nutritional benefits. Polynesians introduced coconut (niu) to Hawai‘i and this plant has been used for the purposes described above. This plant is considered one of the most versatile plants, since every part of the plant has a use (Figure $6$). Common Characteristics Habit: Lianas (climbers) and tree-like (palms). Flowers: Small and symmetrical with three petals and three sepals. The flowers are arranged in an inflorescence (a cluster of flowers originating from a main branch). Fruits and Seeds: Drupe with a single seed inside (sometimes two). Leaves: Leaves are large and either palmately compound or pinnately compound. Stems: Most common species have a single dominant stem that does not branch. Although some species grow in clusters. Like in other monocots, the stems do not produce wood (secondary growth). Examples of Eudicot families Fabaceae The Fabaceae, also known as the bean or legume family, is a very important plant family with approximately 19,500 species. Many members of this family are able to grow in soils with low nutrient levels because they are able to form root nodules and house nitrogen fixing bacteria, making them an important crop in areas with poor soil. Fabaceae are also known for being very rich in protein, which makes it a staple food in many diets. Plants in this family are important for human food (beans, lentils, peas, beans, soy beans), cattle forage (e.g. Leucaena), and as cover crops (species that are planted to enhance soil health on a farm). Several species in this family are known for their hard woods, making them important as a source of lumber. There are several native species in this family in Hawai‘i (Figure $7$). These include koa (Acacia koa; Figure $8$), wiliwili (Erythrina sandwicensis) and māmane (Sophora chrysophylla; Figure $7$). The wood of koa is highly valued and it is used to make furniture, jewelry and art. The wood of māmane was used for house posts, fences, and digging sticks (o‘o), and the seed is used for lei making (Figure $9$). On Mauna Kea, the palila bird (Loxioides balleui) depends on the seeds of this plant as a food source, and the plants as nesting and roosting habitat. In ancient times, Native Hawaiians used wiliwili to make surf boards because the wood is buoyant. The beautifully colored seeds are used in lei making (Figure $10$). Common Characteristics Habit: Herbs, shrubs, trees, vines and lianas. Flower: Flowers are very diverse, varying among the six subfamilies in this family. Three of the most common flower types can be seen on Figure 14. Pea-shaped flowers are in the subfamily Faboideae. Flowers with multiple stamens and very small petals (as in monkey pod; Figure 14) can be found in the Caesalpinioideae subfamily. From afar they may look like puff balls. Flowers of the orchid tree (Bauhinia variegata) are large and colorful with five petals and are in the Cercicoideae subfamily. Fruits and Seeds: Most fruits are legumes or loments. The seed is bean-like. Leaves: Alternate and entire. Compound. Stems: Stems can be herbaceous or woody. Other: Nodules on roots contain nitrogen fixing bacteria. Solanaceae The Solanaceae is also known as the nightshade family and it has about 2,600 species (Christenhusz and Byng, 2016). Many species are poisonous, while others have medicinal and ornamental uses. For example, belladonna/deadly nightshade (Atropa belladonna) is very toxic and causes hallucinations if ingested, as it contains several alkaloids. An ornamental plant that is commonly seen in Hawai‘i and that is extremely poisonous is the angel’s trumpets (Brugmansia sp.). This plant is used as a psychoactive drink in rituals in some cultures in South America and causes hallucinations. It was introduced to Hawai‘i in the 1800s from South America and can be seen growing in gardens. Tobacco (Nicotiana sp.) is also in this family. It can be highly addictive because it contains the alkaloid nicotine, which is a stimulant. There are many plants in this family that are not toxic. For example, many crop species such as potato tubers, tomatoes, peppers, and eggplants are used in cuisines all over the globe. Potatoes, tomatoes, and peppers are originally from the Americas, where they were first domesticated, and were introduced to the rest of the globe after European contact (Figure $11$). Tomatoes, for example, were first domesticated in Mexico and were introduced to Europe after the Spanish colonized the Americas in the 16th century. It’s now an iconic component of several European cuisines. It is hard to imagine Italian food without the tomato, or even peppers, but it was only after Europeans brought those crops back from the Americas that they were introduced to Italy. The same thing is true about peppers anywhere in Asia. Thai food did not have hot chilies until they were introduced from the Americas. Common Characteristics Habit: Herbs, shrubs, trees and vines. Flowers: Flowers have five petals and five sepals. The stamens also occur in multiples of five and can fuse together around the pistil, forming a column (Figure $11$A). Fruits and Seeds: Fruits are either berries or capsules. Leaves: Frequently have prickles. Stems: Stems are very diverse in this family due to the different growth habits. Other: Many species are poisonous and many are edible domesticated crops (e.g. tomato, pepper, eggplant, and potato). Asteraceae The Asteraceae, also known as the sunflower family, has 24,700 species (Christenhusz and Byng, 2016). Species in this family can grow in a wide range of environments, but they most commonly occur in dry areas and deserts, including high elevation zones. In Hawai‘i, for example, āhinahina or silversword (Argyroxiphium sandwicense subsp. macrocephalum) grows near the summit of Haleakalā at approximately 3,000 meters (10,000 feet) in elevation. The plant has leaves with furry hairs (trichomes) to protect the plant against sun and wind (Figure $12$). This family has many economically important species that are used to make oil (e.g. sunflower), teas, and medicine (e.g. camomille, echinacea). Several species are used for food: lettuce (Lactuca sativa), artichoke (Cynara cardunculus var. scolymus), and sunflower (Helianthus annuus). There are many ornamental species and cultivars in this family including marigolds (Tagetes spp.), chrysanthemum (Chrysanthemum spp.), zinnia (Zinnia spp.), and dahlia (Dahlia spp.), which are very important to the horticultural industry. Asteraceae have very characteristic flowers. They are grouped into clusters called heads or capitulum, which are made up of dozens and sometimes hundreds of individual small flowers (Figure $13$). There are two main types of flowers composing the head. Ray flowers are on the outside of the heads with the petals on the very outside. Disk flowers, on the other hand, are in the inner part of the head. This arrangement likely evolved to attract pollinators. Common Characteristics Habit: Mostly herbs, but also shrubs and trees. Flower: The inflorescences (cluster of flowers) are showy and the flowers are many and packed in heads. A single flower can fall into one of three different types: disk florets, ray florets and ligulate florets (Figure $13$). Fruit and Seeds: Achene. Leaves: Leaves can be arranged differently on the stems depending on the species (opposite, alternate or whorled). Stems: The stems are most often herbaceous. Myrtaceae This family has many important edible species in Hawai‘i such as guava, strawberry guava, and mountain apple/‘ohi‘a ‘ai (Figure $14$). Today, 5,950 species exist worldwide in this family. The petals on the flowers can be reduced and the stamens numerous, giving the flower a fluffy appearance (Figure $14$). Some species in the family are important sources of timber (e.g. Eucalyptus spp.). Some species in this family produce essential oils (e.g. allspice; Pimenta dioica). One of the most important native forest species in Hawai‘i is ōhiʻa, Metrosideros polymorpha, which belongs to this family (Figure $14$D). Native birds depend on their flowers for nectar, they play an important role as watershed forests, and are also highly important culturally. Common Characteristics Habit: Woody trees and shrubs. Flowers: Flowers have five petals but they are often reduced, with numerous colorful stamens present (Figure $14$D). Fruits and Seeds: Fruits are capsules or berries. Leaves: Essential oils are present in the leaves of some species. Stems: Stems are woody. 9.04: References APG - Angiosperm Phylogeny Group IV. (2016). An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Botanical Journal of the Linnean Society 181: 1-20. Christenhusz, M. J., & Byng, J. W. (2016). The number of known plant species in the world and its annual increase. Phytotaxa, 261(3), 201-217. Crepet, W. L., & Niklas, K. J. (2009). Darwin's second “abominable mystery”: Why are there so many angiosperm species?. American Journal of Botany, 96(1), 366-381. Hodel, D. R. (2012). Loulu: The Hawaiian Palm. University of Hawaii Press. Hu, S., Dilcher, D. L., Jarzen, D. M., & Taylor, D. W. (2008). Early steps of angiosperm–pollinator coevolution. Proceedings of the National Academy of Sciences, 105(1), 240-245. Lerner, H. R., Meyer, M., James, H. F., Hofreiter, M., & Fleischer, R. C. (2011). Multilocus resolution of phylogeny and timescale in the extant adaptive radiation of Hawaiian honeycreepers. Current Biology, 21(21), 1838-1844. Magallón, S., Hilu, K. W., & Quandt, D. (2013). Land plant evolutionary timeline: gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates. American Journal of Botany, 100(3), 556-573. Pender, R. J., Morden, C. W., & Paull, R. E. (2014). Investigating the pollination syndrome of the Hawaiian lobeliad genus Clermontia (Campanulaceae) using floral nectar traits. American journal of botany, 101(1), 201-205. Tian, F., Stevens, N. M., & Buckler, E. S. (2009). Tracking footprints of maize domestication and evidence for a massive selective sweep on chromosome 10. Proceedings of the National Academy of Sciences, 106(Supplement 1), 9979-9986. Van der Niet, T., & Johnson, S. D. (2012). Phylogenetic evidence for pollinator-driven diversification of angiosperms. Trends in Ecology & Evolution, 27(6), 353-361.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/09%3A_Angiosperms/9.03%3A_Angiosperms_families.txt
Learning Objectives • Learn the terminology associated with plants in Hawai‘i. • Describe how native Hawaiian plants originated. • Summarize how the original colonizers of native Hawaiian plants arrived in Hawai‘i. • Describe Polynesian introduced and recently introduced plants. 10: Plants in Hawaii Hawai‘i is a special place with amazing ecosystems such as alpine deserts, ocean coast lines, dry shrublands, and rainforests. Learning more about the plants and the different environments present in the Islands can enhance our relationship with nature and our role in island sustainability. Humans have strong connections to plants and animals. We depend on them for food and medicine, and they are utilized in cultural practices, stories, and belief systems. A great way to get to know the place we live is by knowing local plant names and their stories. How did they get here? Who or what brought them in? What is their significance? While strolling anywhere in the Hawaiian Islands, we may find ourselves surrounded with an abundant diversity of plants. However, not all the plants that currently inhabit Hawai‘i are native to Hawai‘i. Every single plant you find has a different history: some evolved here; some are found elsewhere on the planet, but arrived in Hawai‘i without any human assistance, and others were brought by humans. A species is considered native when it naturally inhabits a region and got there without any human assistance. Native plants are divided into two categories: endemic and indigenous. Endemic plants are plants that are only found naturally in a specific area and nowhere else in the world. These terms are used anywhere on the globe. For example, a plant that is endemic to China grows naturally only in China. An example of a Hawaiian endemic plant is koki‘o ‘ula (Hibiscus clayi) which does not naturally occur anywhere other than Hawai‘i. Indigenous plants are native plants that can be found in a specific area as well as in other locations. For example, naupaka kahakai (Scaevola taccada) is a plant that naturally grows in Hawai‘i, but also grows on other Pacific islands (Figure $1$). Hawai‘i has 1,606 species of native plants, divided as follows: • 421 non-vascular plants (Staples and Imada, 2006; Staples et al., 2004) • 146 ferns and 15 lycophytes (Ranker et al., 2019) • 1,039 angiosperms (Price et al., 2018). The flora of Hawai‘i is very unique compared to other parts of the world, with 88% of those species being endemic to the Hawaiian Islands. How did plants originally get to Hawai‘i? The Hawaiian archipelago is one of the most isolated places on Earth. It is located 3,700 km (2,300 miles) from the coast of the United States and 5,863 km (3,643 miles) from Asia. Plants in Hawai‘i evolved in isolation from people and other influences for 47 million years (Gustafson et al., 2014). This long history of isolation coupled with the many diverse environments on the islands gave rise to a great diversity of endemic species evolving from the original plants that arrived to the archipelago. The Hawaiian archipelago was created by volcanic activity. A stable hot spot beneath the ocean floor releases magma while the Pacific plate moves northwest over it. This creates seamounts underwater that eventually break the surface and become islands. As the plate moves away from the hot spot, the hot spot starts creating another island under the ocean. This is why islands away from the hot spot such as Kaua‘i, O‘ahu and Maui no longer have active volcanoes while Hawai‘i’s volcanoes are still active, and those farther away from the hot spot are smaller, due to erosion of the once massive shield volcano islands. The hot spot has already started creating a new island called Lōʻihi, east of the island of Hawai‘i that is still submerged (Figure $2$). Some cultural practitioners call this island Kamaʻehu (“reddish child”). When the first plants arrived in the Hawaiian Islands millions of years ago, they encountered a land devoid of vegetation. These plant arrivals were rare; for flowering plants (angiosperms), it is estimated that there were only 259 colonizing events. These original 259 events gave rise to the 1,039 species we have today (Price et al., 2018). These species originally arrived in Hawai‘i carried by wind, water, and wings (birds). Wind (1.4%) Transportation by trade winds and storms is responsible for the arrival of the smallest percentage of ancestral species. This is probably because seeds or spores have to be light enough to be carried by the air, and need to be able to survive the very cold temperatures in the upper atmosphere. Ōhiʻa lehua, Metrosideros polymorpha, seeds likely arrived in Hawai‘i carried by the wind, as they are small and light. Water (17%) Plants also arrived in Hawai‘i attached to clumps of soil and wood (rafting) or by floating in the ocean (oceanic drift). In order to do this, their seeds had to float and be able to survive long term salt water exposure. One example is naupaka kahakai (Scaevola taccada), which is naturally found in coastal environments and has fruits that float in saltwater. Wings (83%) The most successful way for plants to reach the Hawaiian archipelago was by catching a ride with a bird. Sticky fruits and seeds could attach themselves to a bird’s feathers or even to the bird’s feet with the help of some mud. Seeds and fruits could also be eaten by birds elsewhere and end up in Hawai‘i after passing through the bird’s digestive system. Where did early plants come from? There are people who are very interested in figuring out where the plants that gave rise to the Hawaiian flora came from. Plant ʻcolonists’ arrived from different parts of the globe (Figure $3$). Some plants arrived directly from their home regions while others “island hopped'' arriving on other Pacific islands and then eventually getting another ride to Hawai‘i. Some of these plants (30%) are native to more than one region and are therefore classified as “widespread”. Below are the descriptions for each region along with the percentages for the plant colonists that arrived in Hawai‘i from each source: Australasian (10.8%) This region includes Australia and New Zealand which is 6,832 km (4,245 miles) from Hawai‘i. Indo-Malayan (12%) This region includes tropical areas of South and Southeast Asia. It encompasses the Malay Archipelago, New Guinea, and nearby islands. This region is 5,841 km (3,629 miles) from Hawai‘i. East Asia (3.9%) This region includes non-tropical areas of Asia. This region is 5,863 km (3,643 miles) from Hawai‘i. Neotropical (13.1%) This region includes tropical regions of Mexico, and Central and South America. This region is 4,648 km (2,888 miles) from Hawai‘i. North American (11.6%) This region includes the non-tropical areas of North America. This region is 3,631 km (2,256 miles) from Hawai‘i. Widespread (30.1%) If the colonist species comes from more than one of the regions above, then it falls into this category. Unknown (18.5%) A large percentage of plants have unknown origins and fall into this category. Pacific This area includes the islands of Fiji 4,715 km (2,930 miles), the Society Islands 3,937 km (2,446 miles), and the Marquesas 3,398 km (2,111 miles). This area serves as stepping stones for island hopping species. Plants may arrive in one of these islands from one of the regions included above, and eventually arrive in Hawai‘i by one of the dispersal methods (likely by birds or oceanic currents). How did early plants colonize Hawai‘i? Besides having some of characteristics discussed above that helped plants get to Hawai‘i, they also needed traits that once here allowed them to settle, compete, reproduce, and flourish in their new environment. These plants are often referred to as “early colonists” because they were the first ones to arrive. Some of the characteristics early colonists had were self pollination, fast growth, and adaptations to coastal environments. Plants that were able to self pollinate had a clear advantage, because the chance of finding another plant of the same species in the same place at the same time for cross pollination to occur was quite small. Plants that were able to produce seeds without the need to pollinate with another plant of the same species were one step ahead in the game. Fast growing plants are often considered “weedy” because they can grow fast and in environments that are not very specific or ideal. For example, they will grow on sandy soils without a lot of nutrients. For the plants arriving in Hawai‘i, being annual (only living for one year), or being able to complete their life cycles relatively quickly, was a good way to establish new populations faster. Finally, plants that were adapted to coastal environments (Figure $4$) often had an advantage. Since the largest percentage of plants arrived in Hawai‘i with birds, many of them seabirds, they had to be able to grow near the coast where seabirds spend much of their time and, therefore, are most likely to deposit the seeds they inadvertently carried. Initially, each of the Hawaiian Islands were barren with very little or no vegetation. Eventually some of these plants were able to move inland, but originally they had to survive in these coastal environments. An example of a plant that originally arrived in a coastal environment and made it to higher elevations is naupaka kahakai /beach naupaka (Scaevola taccada) which is an indigenous species. This species is also native to several Pacific islands. There is another naukaka species, naupaka kuahiwi/mountain naupaka (Scaevola gaudichaudiana) which grows in wet forest of higher elevations. This species is endemic to Hawaii. It likely originated from naupaka kahakai through speciation (a process in which populations of a species split and become new species). Some plants did not arrive on coastal areas, but likely got deposited by birds directly at high elevation areas. For example, the Hawaiian raspberry, ‘ākala (Rubus hawaiensis; Figure $5$), likely arrived in Hawai‘i from North America in the digestive tract of birds (Carlquist 1974; Morden et al., 2003). Once in Hawai‘i, these early plant colonists diversified because they encountered new and different environments. They eventually dispersed from coastal areas and moved inland towards the mountains, became isolated from their original populations, and often evolved into new species. Approximately 88% of native Hawaiian plants are endemic, all derived from those early colonizers that were able to arrive, survive, and establish populations here. For example, one colonist species in the Lobeliad group (Campanulaceae family, Figure $6$) gave rise to 126 new species, and the Silversword alliance (Asteraceae family, Figure $7$) likely originated from one colonist species that came from California and diversified into 30 new species (Price, 2004). When you compare the native flora of the Hawaiian Islands to the flora of the mainland source regions, you will notice that several families of plants are missing (a concept called disharmony; Christian et al., 2019). This is because not all seeds and spores were able to make the long trip to get here. Also, as discussed above, seeds had to be salt tolerant to survive floating in oceanic currents, or small enough to travel in air currents, or have the right shape and size to be carried by birds. A mango seed, for example, could never reach Hawai‘i, because they are not salt tolerant and are too heavy to be carried by a bird or by air currents. Therefore there are many plant families that are not naturally present in the Hawaiian Islands.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/10%3A_Plants_in_Hawaii/10.01%3A_Native_plants.txt
Polynesian Introductions are plants introduced by early Polynesians who migrated to the Hawaiian islands from other islands in the Pacific. The history of Polynesian migration is well documented though archaeological, linguistic, and DNA studies as well as through oral histories passed on through generations. Humans started to migrate eastward from Southeast Asia and Melanesia around 3,500 years ago (Kirch, 2010). They initially migrated to islands that were relatively easier to get to, as ocean levels were lower at this time. As they moved east, the distance between islands became greater and the biodiversity decreased. This meant the technology for successful voyaging had to become more advanced, such as the development of double hulled canoes that could withstand longer journeys in open water. The dependency on domesticated plants and animals also increased because more distant islands did not have wild plants and animals that could be used for food and other survival means, compared to islands closer to Asia. Polynesians arrived in Hawai‘i around 800 years ago (Kirch, 2010) and brought with them approximately 23 species of plants (Table 1). These plants were incredibly important, as they ensured the survival of the newly established human populations. While the first arrivals could survive for a time on native bird populations and seafood, successful human settlements depended on the successful introduction and production of domesticated agricultural crops (Kirch, 2010; Figure $1$). The plants introduced by Polynesians did not all arrive at the same time, as there were multiple trans-oceanic voyages to and from the Hawaiian Islands. For example, ‘ulu (Artocarpus altilis, Figure $2$) arrived much later, and voyages to acquire it are well documented through oral histories. ‘Uala or sweet potato (Ipomea batatas, Figure $3$) was very likely acquired by Polynesians who traveled by canoe from islands in the Pacific Ocean to South America where this plant was first domesticated by indigenous people there. These plants were part of highly sophisticated agricultural systems developed over time and passed on from generation to generation. For more information regarding traditional agricultural systems in Hawai‘i, see Lincoln and Vitousek (2017). Based on Whistler (2009). 10.03: Recent introduced plants Plants introduced to Hawai‘i after 1778 (post European contact) are known as recent introductions. Starting in the 1800s, different crops were brought in and tested to determine the viability of growing them in the Islands (Table 10.4.1). For example, pineapple and coffee were introduced to the Islands in 1813. Coffee became one of the most important crops, along with pineapple and sugarcane. Although sugarcane was introduced to Hawai‘i by Polynesians before European contact, the first variety for commercial production ('Lāhainā') was introduced in 1854 to Maui (Lincoln, 2017). Pineapples were tested in 1885 in Mānoa, O‘ahu; the starting point for commercial production. Rice was first introduced in 1858. Later trials were conducted to see if it could be grown commercially, and it soon became one of the most commonly grown crops in the 19th century (HDOA, 1998). Today, rice is no longer grown commercially in Hawai‘i, but it is still part of the diet. Table $1$: Some commercially important crops introduced to the Hawaiian Islands. Sources: HDOA, 1998 and Lincoln, 2017. Crop name Species Year Introduced Orange Citrus × sinensis 1792 Coffee Coffea spp. 1813 Pineapple Ananas comosus 1813 Mango Mangifera indica 1824 'Lāhainā' sugarcane Saccharum spp. 1854* Eucalyptus Eucalyptus spp. 1870 Macadamia Macadamia spp. 1881 Rice Oryza sativa 1858 ‘Solo’ Papaya Carica papaya 1911 Seed corn (commercial) Zea mays 1966 Pineapple and sugarcane production drove the plantation era (1850-1980s) in Hawai‘i with many immigrant groups coming to the Islands for work. People from different cultures who arrived brought with them their own staples, and these crops were frequently incorporated into the plants that are grown and consumed in Hawai‘i today (Figure $1$). Plantation agriculture changed the way land and water were managed, used, and controlled, and had negative impacts on traditional agriculture (Figure $2$). Starting with plantations, water was taken from the windward side of islands to the leeward sides to irrigate sugar and pineapple fields, negatively impacting kalo production. Today, plantations have mostly disappeared from Hawai‘i, and seed crops such as corn, as well as diversified agriculture have taken hold (Perroy et al., 2016). The horticultural trade also brought many ornamental plants to Hawai‘i over the past century. For example, plumeria (Plumeria spp.) and monkeypod (Samanea saman) are introductions from Latin America (Figure $3$). These plants have become part of life in Hawai‘i since they are abundant in gardens and lowland areas where people live. Many of these introduced species remain in cultivation and do not naturalize (grow and reproduce in wild spaces without human assistance). For example, plumerias do not produce seedlings that can grow without human help. They need to be propagated by cuttings. However, many other horticultural species have become naturalized and have become invasive. Although some Polynesian introduced plants escaped cultivation and have become naturalized (e.g. kukui), most naturalized species are plants introduced after 1778. The invasive species we have in the Islands are mostly recent introductions. These have escaped cultivation and naturalized in wild habitats. Some of the names used for this group of recent introductions are exotics, aliens, and weeds. There are hundreds of naturalized species in Hawai‘i, and many have negative impacts on native ecosystems. For example, strawberry guava (Psidium cattleianum), from South America, grows in such thick stands that they overcrowd native species, eventually killing them (Figure $4$). Another example of an invasive species in Hawai‘i is fountain grass (Pennisetum setaceum) which is native to Africa and southeast Asia. Fountain grass dominates the understory of native dryland forests and competes with native trees. It also creates a fire risk in an environment that did not evolve with the frequent wildfires we see today (Cordell and Sandquist, 2008). On O‘ahu, for example, the introduction of fire-prone grasses has created problems not only to native ecosystems, but also to communities on the west (leeward) side of the Islands. Fires have become far more common in the past decades, and increasingly cause damage to houses and businesses. The fires open dry lowlands to the invasive koa haole (Leucaena leucocephala), from Central America, which, along with fire prone grasses, dominates these areas (Figure $5$). The introduction of numerous invasive plant and animal species, along with other factors, has resulted in the decrease of native species, to the point where a significant number of them have become endangered. Hawai‘i has more endangered species (species that have a higher risk of extinction) per square meter than any other place on Earth, and this is linked to habitat loss and invasive species (Czech et al., 2000). Invasive species displace natives species, and a plant community dominated by non-native species does not function the same way as a native-dominated community (Kagawa et al., 2009). For example, water gets absorbed into the soil way less in non-native forests compared to native forests, and during big rain events the water runs towards the ocean instead of recharging the aquifer. This has a direct impact not only on the environment, but on the quality of life for humans as well since we all need freshwater. Learning about the plants in Hawai‘i can not only be interesting, but it connects us to our environment, to cultural practices, and to food security. We depend on plants for survival in many ways, and plants bring beauty to our lives. Plants bring us together around the table for a good meal, while helping us celebrate cultural traditions through food recipes and as part of life rituals. 10.04: References Carlquist, S. 1974. Island biology. Columbia University Press, New York. Christian, K., Weigelt, P., Taylor, A., Stein, A., Dawson, W., Essl, F., ... & Kreft, H. (2019). Disharmony of the world’s island floras. Biorxiv, 523464. Cordell, S., & Sandquist, D. R. (2008). The impact of an invasive African bunchgrass (Pennisetum setaceum) on water availability and productivity of canopy trees within a tropical dry forest in Hawai‘i. Functional Ecology, 22(6), 1008-1017. Czech, B., Krausman, P. R., & Devers, P. K. (2000). Economic associations among causes of species endangerment in the United States: associations among causes of species endangerment in the United States reflect the integration of economic sectors, supporting the theory and evidence that economic growth proceeds at the competitive exclusion of nonhuman species in the aggregate. BioScience, 50(7), 593-601. Gustafson, R. J., Herbst, D. R., & Rundel, P. W. (2014). Hawaiian plant life: vegetation and flora. University of Hawai‘i, O‘ahu Press. Hawai‘i Department of Agriculture (HDOA). (2009). Available at: https://hdoa.Hawai‘i.gov/wp-content/uploads/2013/01/HISTORY-OF-AGRICULTURE-IN-Hawai‘i.pdf Lincoln, N. (2017) Description of Hawaiian Sugarcane Varieties. Retrieved from: http://cms.ctahr.Hawai‘i.edu/cane Morden, C. W., Gardner, D. E., & Weniger, D. A. (2003). Phylogeny and biogeography of Pacific Rubus subgenus Idaeobatus (Rosaceae) species: Investigating the origin of the endemic Hawaiian raspberry R. macraei. Pacific Science, 57(2), 181-197. Perroy, R. L., Melrose, J., & Cares, S. (2016). The evolving agricultural landscape of post-plantation Hawai ‘i. Applied Geography, 76, 154-162. Price, J. P., & Wagner, W. L. (2004). Speciation in Hawaiian angiosperm lineages: cause, consequence, and mode. Evolution, 58(10), 2185-2200. Price, J. P., & Wagner, W. L. (2018). Origins of the Hawaiian flora: Phylogenies and biogeography reveal patterns of long‐distance dispersal. Journal of systematics and evolution, 56(6), 600-620. Kagawa, A., Sack, L., Duarte, K. E., & James, S. (2009). Hawaiian native forest conserves water relative to timber plantation: species and stand traits influence water use. Ecological Applications, 19(6), 1429-1443. Kirch, V. P. (2010). Peopling of the Pacific: A holistic anthropological perspective. Annual Review of Anthropology, 39, 131-148. Whistler, W. A. (2009). Plants of the canoe people. National Tropical Botanical Garden.	textbooks/bio/Botany/Botany_in_Hawaii_(Daniela_Dutra_Elliott_and_Paula_Mejia_Velasquez)/10%3A_Plants_in_Hawaii/10.02%3A_Polynesian_introduced_plants.txt
Here in the Pacific Northwest, we are fortunate to work in a landscape of varied landforms – from volcanic peaks to wide valleys; from steep, forested hillsides to gently rolling savannas; from rapidly cascading mountain streams to meandering river floodplains. Our varied topography is an integral part of our forest ecosystems, influencing our climate, soils, water, plant life and fish habitat (Figure 1.1). As natural resource technicians, we are often called upon to assess the topography, and one of the common elements we measure is the slope of the land. How steep is the hillside? Does the slope drain to a stream? Are there cliffs or bluffs present? Field data collected by technicians lead to informed decisions about land management activities such as providing shade for streams, building roads or trails, and prescribing timber management operations. Figure 1.1. The Muddy Fork of the Sandy River originates from snowfields on the west flank of Mt. Hood, carrying coarse gravels and sand downstream. Fine soils from the surrounding steep, forested slopes also make their way down the slope to the river. Defining Slope Slope of the land is essentially the gradient or incline of the land. A steep slope refers to a sharp incline; a gentle slope refers to a slight incline. The steep, forested slopes in Figure 1.1 contrast with the gentler slope of the river’s path as it flows between them. Driving down a highway you may see a road sign that reads “6% Grade” or “steep grade.” The grade of the road is essentially the slope of the road. The sign in Figure 1.2 indicates that the road descends at a 6% grade or a 6% slope. Figure 1.2. A road sign indicating an 8% grade, or 8% slope. (www.dot.state.co.us) A 6% slope means that the road elevation changes 6 feet for every 100 feet of horizontal distance (Figure 1.3). Figure 1.3. A road climbs at a gradient of 6%. The road gains 6 feet in elevation for every 100 feet of horizontal distance. Note that the length of the road itself is longer than 100 feet. Mathematically, slope is defined as “the rise over the run” (or the rise divided by the run), where rise equals change in elevation and run equals horizontal distance: or or in this case: To express slope as a percent slope, we simply multiply the slope fraction by 100. So, .06 = 6% %slope 6% In our road example, the six foot change in elevation is the rise and the 100 foot horizontal distance of the road is the run. Driving uphill, we climb a +6% slope (Figure A below). Driving downhill, the “rise” is actually a “drop,” so we have a negative slope, or a downhill slope (Figure B below). When dealing with slope, a positive slope simply means uphill and a negative slope means downhill. A negative number does not mean “minus” as in algebraic expressions. Note that the actual road distance is the hypotenuse of the illustrated slope triangle. Its length is called slope distance. Slope distance is always longer than the horizontal distance, or run. Applying the Pythagorean Theorem (a2 + b2 = c2) to this triangle, we can calculate the slope distance, or hypotenuse (c). a2 + b2 = c2 where: 1002 + 62 = c2 10,036 = c2 ft. a = horizontal distance or run (in this example 100 ft.) b= change in elevation or rise (in this example 6 ft.) c = road distance or slope distance (in this example 100.2 ft.) We calculated a slope distance of 100.2 ft. for a run of 100 ft. As you can see from this example, in a forest, a 6% slope would be considered a gentle slope. Note that %slope is unitless and proportional. Therefore, it can be applied to any unit of measure (inches, yards, centimeters, etc.) and to any length. For example, a 25% slope is simply a 25:100 ratio. The 25% slope below shows that for every inch of horizontal distance, the slope rises .25 inches. For every 10 centimeters of horizontal distance, the slope rises 2.5 cm, and for every 5 inches of horizontal distance, it rises 1.25 inches. Using Slope When writing field notes about a site, we include information about the slope of the land. Sometimes a rough estimate of the average slope is sufficient; sometimes detailed measurements of slope are required. For example, a site description might read: “A timber cruise was conducted on 20 acres of mixed conifer forest …………Approximately half of the acreage was flat, on slopes ranging from 3-7%. The other half of the acreage was steeper; with southwest slopes 40-60%.” This tells us much more about the site than simply stating that there were 20 acres of mixed forest. We would expect different soil conditions and different vegetation to be present on the different slopes, and therefore, perhaps different management. Let’s say, for example, that these 20 acres are to be logged in the near future. If this is so, the forester will have to plan where to place any new access roads, where to locate landings for yarding the logs and what type of harvesting equipment to use. He knows that the slope of any new spur roads should not exceed 10%, and a cable system should be used to haul logs up to landings on slopes greater than 30% (Figure 1.4). Figure 1.4. A cable logging system can be used on steep slopes to suspend logs above the ground as they “yard” the logs up the slope to a landing. Profiles may be run to get a detailed picture of the slope. When profiling a hillside, slope distances and %slope readings are taken where each major change in slope occurs (Figure 1.5). With this precise information, a logging system can be designed that will lift logs off the ground while yarding to reduce erosion. Figure 1.5. A hillside is divided into segments where major changes in slope occur. For each segment, a %slope reading is taken. These %readings are combined with measurements of the slope distance for each segment to create a profile or sketch of the hill like the one illustrated. Note that slopes can exceed 100%. When a slope equals 100%, it simply means that the rise is equal to the run. And although it certainly feels like you are climbing straight up on a 100% slope (pulling yourself up using roots and anything else you can grab), you are really walking up at a 45° angle, not a 90° angle. %slope If rise = run as illustrated above: 100% 100% slope = 45º angle slope Other examples of where %slope is measured in natural resource settings include hiking trails and streams. Switchbacks on steep slopes reduce trail erosion and make hiking easier. Some trails are kept to 8% to comply with American with Disabilities Act (ADA) guidelines for wheelchair access. Stream gradients vary, reflecting the terrain over which they flow at each stage of their journey to large rivers. Small tributaries often are the steepest, cascading down steep forested slopes at gradients of 60-100% slope or more. As streams merge downriver, the terrain often flattens out, and milder gradients of 3-10% slope may be measured (Figure 1.6). Figure 1.6. Streams rush down steep slopes at their headwaters. As they reach valley bottoms and merge with other streams, their gradients are reduced and a more meandering route may result.	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/01%3A_Slope/01.1%3A_Assessing_Slope_of_the_Land.txt
Slope is generally measured with an instrument called a clinometer. When sighting through a clinometer, the measuring line is placed on the target, and %slope is read from the scale. Both eyes are open, as one eye reads the scale, and the other eye sights on the target (Figure 1.7). Figure 1.7. A clinometer generally has two scales. In this figure, the scale on the left is the %slope scale. The scale on the right is a topographic slope scale (see Chapter 2). Also note the “plus” signs below zero on each scale, and the “minus” signs above zero on each scale. In this illustration, the %slope reading is just under 3%. Since the reading is on the “minus” side of zero, the person using the clinometer is looking slightly downhill. 1. Measuring %slope for profiles is easiest to do with a partner. First determine where 0% slope (eye level) is on your partner. Then use this point as the target when taking readings with the clinometer (Figure 1.8). This way, you will be measuring parallel to the slope, mirroring the land. Figure 1.8. Standing on level ground close to each other, partners first determine where 0% slope is on the other person. In this example, the technician on the left will sight on her partner’s nose when taking %slope readings with the clinometer. 2. To determine %slope, one partner walks up or down the slope to a point where a reading should be taken, such as a major change in slope. A reading is taken and recorded to the nearest % (Figure 1.9). Figure 1.9. Sighting on a partner at eye level (as determined beforehand in Figure 1.8) allows a person to obtain an average %slope reading, paralleling the slope of the land. 3. When working where there is a lot of brush, it may be difficult to see your partner. A brightly colored target held at the sighting point, such as a painted piece of cardboard, can substitute for your partner. Your partner’s hard hat will work in a pinch as well. 4. When working individually on forested slopes, you will have to substitute a tree for your partner. Estimate eye level on a tree that you can see clearly, and take a reading on that point. When determining average slope on a long hillside, try to pick a point as far down or up the hill as possible, to even out the slight dips and bumps on the ground. 01.3: Tips for Measuring Slope on Contour Maps To calculate %slope of the land from contour maps, we still need to determine the rise and run. On a map, the rise is the difference in elevation between two points. The run is the horizontal distance between two points. Map distance is always horizontal distance. The Rise is the difference in elevation between two points. Using the elevations printed on the map and the contour line interval, an elevation can be determined for the top and bottom of the slope in question. It generally works better to simply determine the elevation at each point and subtract rather than to “count the contour lines” between the two points. Doing the latter often results in rounding errors or double counting a contour line that can throw slope readings off by 10% or more. To determine the run, the map distance is measured between the two points, and converted to the same units as the elevation. If difference in elevation is measured in feet, distance should also be calculated in feet. If difference in elevation is measured in meters, distance should also be calculated in meters. Example $1$: An excerpt from a contour map is shown below. To determine the %slope from Point A to Point B, we must first determine the rise and run. Rise: If the map has 40’ contour intervals, then Point A is located at 3000 feet. Point B is located at 2840 feet. Therefore: Rise = change in elevation = top (Point A elevation) minus bottom (Point B elevation): 3000’ – 2840’ = 160 feet Run: If the map scale is 1inch = 500 feet, then the run is calculated as follows: The map distanced measured 1.8 inches with an engineer’s scale. 900 feet %slope: %slope 18% From Point A to Point B, the slope is –18% (downhill); from B to A the slope is +18% (uphill). 01.4: Summary Problems 1.4 Summary Problems 1. Using the measurements provided, determine the %slope of the following slopes between Points A and B. 2. On a 60%slope, Todd wants to walk up a slope a distance equivalent to 100 feet horizontal distance. How far should he walk from Point A? 3. On the contour maps below, determine the average slopes between Points A and B. The scale is 1”=2000’. The contour interval is 80’. Answers to Summary Questions 1. %slope 1a. 111% 1b. 35% 2. On a 60% slope, we know that the rise is 60% of the run. Therefore, the rise here should be 60% of 100 feet or 60 feet. Using the Pythagorean Theorem, we can solve for the hypotenuse. a2 + b2 = c2 where: 1002 + 602 = c2 13,600 = c2 ft. 3. The answers to these questions will depend upon how you measured the horizontal, or map distance – hard to do on a screen. My measurements are shown on the maps below: At left. Point A is ≈ 3440’. Point B is ≈ 3720’. The rise is 280’. The run is ≈ 2200’. Therefore, the average slope is (280)(100)/2200 = 13%. At right. Point A is ≈ 4040’. Point B is ≈ 3280’. The rise is 760’. The run is 1300’. Therefore, the average slope is (760)(100)/2200 = 58%	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/01%3A_Slope/01.2%3A_Field_Technique_Tips_for_Measuring_Slope.txt
Forests of the Pacific Northwest can produce very tall trees. Fertile soils, a mild climate, and a long growing season west of the Cascade Mts. yield old-growth Douglas-fir (Pseudotsuga menziesii) forests that rise 250 feet in the air (Franklin 1988). East of the Cascades, ponderosa pine (Pinus ponderosa), reaching over 150, feet is no less impressive (Burns and Honkala 1990). Tree height is an important ecological trait, as the competition for sunlight determines which trees flourish, and which trees become suppressed and eventually die out. It also influences shade in streams, changes in understory vegetation over time and cover for wildlife. As such, it is an important part of many natural resource data collections. Here are some examples of where height measurements are used: • Stand exams. Stand exams are conducted to characterize the forest vegetation. They provide basic, baseline data on the species composition, forest structure, and condition for a variety of stand management uses, ranging from wildlife habitat to timber production. • Riparian/stream surveys. Height of the vegetation and physical landforms (such as bluffs) along streams can be used to predict the amount of shade a stream will receive throughout the day and year. This in turn, can determine the width of streamside vegetation buffers reserved during any logging activity. • Nesting sites. Some birds and cavity nesters prefer to nest and/or feed at particular heights in the forest canopy. Assessing tree and snag heights can help determine nesting suitability of forest stands. • Site quality. Tree height is the most widely used indicator of a site’s ability to grow trees. Timber cruises. Forest inventories that determine the volume and value of wood require a height measurement – the most important factor for estimating wood volume. 02.2: Determining Tree Height Most forest applications use one of two types of tree height measurements: 1. Total height. Total height is the height of the tree from its stump to its tiptop (Figure 2.1). A one-foot stump is standard, although there are times when another base is used. Figure 2.1. Total tree height, measured from a one-foot stump. 2. Merchantable height. Merchantable height is the height of the tree from its stump to a diameter at which the trunk is too small to be marketable (Figure 2.2). This “merchantable top” diameter is commonly 6” or some percentage of a diameter low in the tree, such as dbh (see Chapter 3). “Taper height” is very similar, without the emphasis on the top diameter being the end of merchantability. Figure 2.2. Merchantable height is the height from the stump to a trunk diameter where the tree can no longer be cut into logs for sale. The principles and techniques for measuring any of these heights are essentially the same. We will focus on total height in this text. So how in the world do we figure out how tall a tree is? Surely we don’t climb each tree with a tape or cut every tree down to measure it. We need a simple, straightforward, and quick way to measure tree height to make it a feasible part of our inventory data. Here is the easiest way for good precision: In determining tree height, we presume that the tree is perpendicular to the ground. Therefore, the tree makes a right angle with the ground, and a right triangle can be drawn from it. The triangle’s three sides are: 1) the tree, 2) the horizontal distance along the ground, and 3) an imaginary diagonal line running from the top of the tree to the ground. Likewise, the tree’s height can be considered the rise and the horizontal ground distance the run. (Sound familiar?) If we can measure a horizontal distance from the tree to a place where we can see the tree’s top, we can determine the tree’s height using %slope (Figure 2.3). Figure 2.3. A tree makes a right angle with the ground, so a triangle or slope can be drawn using it and the ground.	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/02%3A_Tree_Height/02.1%3A_Why_Tree_Height.txt
2.3 Using Percent Slope to Determine Tree Height When using percent slope to determine tree height, the tree is the rise, and the horizontal distance from the tree along the ground is the run (Figure 2.3). We can easily measure our horizontal distance from the tree, and we have instruments for measuring the percent slope to the top of a tree. So, with those two measures (run and %slope) we can solve for rise. Figure 2.3. A tree makes a right angle with the ground, so a triangle or slope can be drawn using it and the ground. %slope To solve the %slope equation for “rise” we do the following: 1. Multiply both sides of the equation by “run” to cancel out run on the left side of the equation (run)(%slope) 2. Divide both sides by “100” to cancel out 100 on the left side of the equation (%slope) That leaves us with the following equation: (%slope) where rise =height Notice that the %slope multiplier (100) becomes the denominator. This remains a constant. The run and %slope values are measurements, so they will change with each tree. Here are some examples using %slope for tree height: Example 1: Georgia walks out a horizontal distance of 50 feet from a tree (Figure 2.4). She looks through her clinometer to determine the %slope from her eye to the top of the tree. Looking up, she reads “+124%.” Using our formula to determine the “rise:” (%slope) (+124) = +62 or 62 feet Figure 2.4. Using a clinometer and %slope to determine total tree height. Therefore, the height of the tree from her eye to the top is 62 feet. Next, we use the same procedure to determine the height from Georgia’s eye level down to the stump. Georgia takes a reading down to the stump. She reads -16%. (%slope) (-16) = -8 or 8 feet Georgia measured 62 feet from her eye to the top of the tree, and 8 feet from her eye to the stump of the tree. We add those two measures together to get the total height of the tree. 62 ft (top) + 8 ft (base) = 70 ft. Remember that a negative slope measurement simply means you are looking downhill. It is important to recognize that the -8 feet is a drop in elevation, not a negative value. We can do the two calculations in one step as follows: (%slope) (124+16) = 70 or 70 feet Notice Georgia put “+16” in the formula, even though the reading to the stump was a negative number. She wants to add in the bottom height, not subtract it. Again, a negative slope simply means we looked downhill. You have to think about your eye position in relation to the tree, and what the readings actually mean. Using %slope symbols algebraically can be misleading. Example 2: Tobias walks out a horizontal distance of 100 feet from the same tree (Figure 2.5). He looks to the top of the tree and reads “+62%” on his clinometer. He looks down to the stump and reads “-8.” (%slope) (62+8) = 70 or 70 feet Notice that by walking farther from the tree (having a longer run), Tobias’ slope readings were smaller than Georgia’s , even though they both ended up with the same height. The angles at which Tobias was looking at the tree were smaller (less acute). Figure 2.5. A tree can be measured from any distance, but the farther back one is from the tree, the less foreshortened the view, and generally, the more accurate the slope readings. Also notice that when Tobias walked out 100 feet from the tree, his run equaled the denominator, 100, cancelling it out and leaving the tree equal to the readings from the clinometers. This “shortcut” makes it much easier and faster to determine tree height by reducing the number of conversions that have to be made. (62+8) = 70 or 70 feet What happens at a horizontal distance of 150 feet? The slope readings are even smaller. (%slope) (42+5) = 70 or 70 feet Thus, the farther one walks from the tree, the better the perspective for seeing the tree top. Being too close to the tree can result in an obscured top, as side branches will be in the way (Figure 2.6). In the photo on the left, the tree’s top can clearly be seen. The right photo however, illustrates a foreshortened view of the top where side branches could be mistaken for the top. Figure 2.6. Examples of height measurement error from sighting on a side branch thought to be the top, on both a hardwood and a conifer. Height is overestimated. 02.4: Using Topographic Slope to Determine Tree Height For most natural resources management purposes, land areas and distances are measured in English units. (Research data are collected in metric units.) Therefore, we measure area in acres, tree height in feet, and commonly, horizontal distance in chains (1 chain = 66 ft.). For this reason, many instruments for measuring slope have two scales: %slope and topographic slope. Topographic slope (or Tslope) is essentially the same as %slope, except that instead of expressing the ratio of rise over run as a proportion of 1:100, Tslope is expressed in a proportion of 1:66 as follows: $\left(\frac{rise}{run}\right)(66)=\text { Tslope }$ The different multiplier (66) is the only difference between Tslope and %slope. To solve the Tslope equation for “rise” we do the following: 1. Multiply both sides of the equation by “run” to cancel out run on the left side of the equation $\frac{(r u n)(r i s e)(66)}{r u n}=(run)(\text { Tslope })$ 2. Divide both sides by “66” to cancel out 66 on the left side of the equation $\frac{(\text {rise})(66)}{66}=\frac{(r u n)}{66}(\text { Tslope })$ That leaves us with the following equation: $rise=\frac{(run)}{66}(\text { Tslope })$ where $rise =height$ So, just as with %slope, the Tslope multiplier (66) becomes the denominator. Topographic slope is most commonly used when measuring merchantable height, but is also fine for measuring total height on shorter trees. Here is an example (Figure 2.7): Example $1$ If Jake walks out a horizontal distance of 66 feet (one chain) from the tree, his run will equal the $Tslope$ multiplier. The “66” will cancel out, and he can simply add his top and stump slope readings together. Solution $rise=\frac{(run)}{66}\left(T_{\text {slape }}\right)$ $rise=\frac{(66)}{66}(41+9)$ $\text { rise (height) }=50 \text { feet. }$	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/02%3A_Tree_Height/02.3%3A_Using_Percent_Slope_to_Determine_Tree_Height.txt
Species considerations: It is quite easy to measure tree height on conifers because conifers have a very distinct top. Each year’s whorl of growth produces a clear tip with short lateral branches, even on hemlocks (Tsuga spp.)(Figure 2.8). Figure 2.8. Conifers have clear, distinctive tops that make finding the top easy. Figure 2.9. Hardwoods such as this oak (Quercus kelloggii) have rounded or uneven crowns that can make finding the top a little more difficult. Hardwoods on the other hand, have rounded crowns that are often a function of the amount of sun they are able to capture (Figure 2.9). Under shaded conditions, they may be very one-sided. On hardwoods, it is extremely important to get a clear view of the whole crown, so that side branches are not mistaken as the top. Broken tops Trees in which the top has blown out can be tricky. The short or nonexistent tip is often hidden by long lateral branches near the top of the tree. If the top cannot be seen clearly, it is easy to mistake the tips of the lateral branches for the top. A rounded or flat top in a conifer suggests a missing top, and this type of tree should always be examined closely (Figure 2.10). As we saw in Figure 2.6, measuring a lateral branch instead of the tip can overestimate the tree’s height. The closer one is to the tree, the greater the error. This is another reason why it is important to walk a distance far enough from the tree to get a clear view of the top. Figure 2.10. A flat-topped fir tree. When conifers have such “eagle nest” tops, it indicates that the main stem has broken out of the tree. Note how large the diameter is at this point. When measuring total height on trees with broken tops, the tree top must be “reconstructed,” in order to maintain the tree’s correct taper, or “original” shape. Incorrect taper will affect wood volume estimates. A normal tree that is 124’ tall (A below) has a very different shape than a tree whose top has broken out at 124’ (B below). The standard method for reconstructing a tree’s top is to look at the surrounding trees and estimate the broken tree’s missing height from their growth. Let’s say a tree similar in diameter and taper to the broken-top tree below (C below), runs 20 feet from a diameter of five inches to its tip (Figure 2.11). Using this as a guide, one could add 20 feet to the broken-top tree for a reconstructed total height of 144 feet. Figure 2.11. To estimate how much height to add on to a broken-top tree, a neighboring tree that is similar in size and taper is measured and used as a guide. In this example, the top broke out at a diameter of 5 inches. A similar tree was measured from a diameter of 5 inches to its top. This length was 20 feet. Therefore, 20 feet was added to “reconstruct” the top of the broken tree for a total height of 144 feet . (Adapted from [FS] 1990.) Leaning trees For a leaning tree, we have to adjust our image of the tree-to-ground triangle. In this case, the leaning tree is the hypotenuse of the triangle instead of the rise (Figure 2.12). The height of the tree can be estimated using the Pythagorean Theorem and the following steps: 1. Measure out a horizontal distance from the tip of the tree until it is clearly in view. 2. Calculate the perpendicular distance from the tip of the tree to the ground (rise), using %slope readings as before. 3. Measure the horizontal distance from the perpendicular drop to the base of the tree (the run). 4. Once these two sides of the triangle have been determined, estimate the total tree height using the Pythagorean Theorem to solve for the hypotenuse. See the example in Figure 2.12 below: Figure 2.12. Total height of a leaner tree is determined. (Drawing adapted from [FS] 1990.) 1. The technician walks out a horizontal distance from fall line AB (in this case 100 ft.). 2. A %slope reading is taken to the tip of the tree (A, +102%), and then to the point on the ground where the AB fall line intersects the ground (B, (-14%). Using the two %slope readings, the rise of the triangle is determined; in this case, 116 feet. 3. The horizontal distance between Point B and the stump of the tree (C) is measured with a tape to determine the run; in this case 42 feet. 4. Finally, using the Pythagorean Theorem, the hypotenuse or height of the tree can be determined. or so and c = 123 feet. Figure 2.13. On forked trees, total height is measured from the tree stump to the tip of the tallest fork. (From [FS] 1990.) Forked Trees On forked trees, the tallest, or dominant fork is measured (Figure 2.13). In some cases, the second fork occurs low enough in the tree to be counted as a second tree, but for most trees, the tallest fork is the only merchantable fork.	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/02%3A_Tree_Height/02.5%3A_Measuring_Height_on_Irregular_Trees.txt
A number of different instruments can be used to determine height. With the exception of the Biltmore stick, all work on the same principle of taking two slope readings. The scales in each instrument are just housed in a different setting. • Clinometer – as shown in Chapter 1 • Relaskop—see section 3.3 • Laser range finder/electronic hypsometer (these do the math for you!) • Biltmore stick hypsometer Though not commonly used, a Biltmore stick is an inexpensive tool for obtaining a rough estimate of tree height. It is based on the principle of similar triangles (Figure 2.14). Figure 2.14. A Biltmore stick is held 25” from the eye to measure tree height. Closing one eye, the bottom of the stick is placed at stump level. Without moving one’s head, tree height is read off the stick where the tree top crosses the stick. In most cases, purchased Biltmore sticks are marked with “logs” instead of feet, but it is easy to construct a stick with a variety of units. 02.7: Field Technique Tips for Measuring Tree Height Estimating total tree height is very easy to do correctly, but does require that we think about how we are taking our measurements. Here are some tips. 1. Always walk to where one can clearly see the tree top. This can be tough to do, especially in dense stands, on extremely foggy days, or in stands with heavy brush. Dragging a tape around in brush trying to get to that special spot where the tree tip comes into view can be frustrating, but it needs to be done. It is actually pretty rare to have a tree whose crown is impossible to see somewhere within 150 feet. This is why it is important to remain flexible in selecting horizontal distances. Commonly, errors in measuring tree heights come from measuring a branch instead of the tip, measuring the wrong tree top, or guessing where the tree top is in a dense canopy. 2. Do not always rely on that magical distance of 100 feet (Figure 2.15). Once you get comfortable with the instruments in the field, find a method that allows you to be flexible in choosing your horizontal distance from the tree. Discover a fast way to adjust your heights with varying horizontal distances. Some people have to follow a formula. I don’t want to mess with the formula, so I just think of 100 (for %slope) and 66 (for topographic slope) as “calibration” figures. For example: • At 33 feet, I am 1/2 of one chain (66 feet) from the tree, so tree height is half of my topog slope readings. • Likewise, at 50 feet, I am 50% of the way to 100; so the tree height is 50% of my slope readings. At 90 feet, the tree height is 90% of my slope readings, etc. • Let’s say I get +74% to the top, and –22% to the stump. 74+22 = 98. If I am 60 feet from the tree (60% of 100), then tree height is 60% of 90 = 54 feet. If I am 80 feet from the tree (80% of 100), then tree height is 80% of 90 = 72 feet. If I am 120 feet from the tree (120% of 100), then tree height is 120% of 90 = 108 feet. Figure 2.15. A tree is measured from a horizontal distance of 80 feet. Note that the tree height is less than the sum of the two slope readings (98). If one is closer to the tree than 100 feet, the slope readings will be more acute (steeper) than at 100 feet. Therefore, the tree must be shorter than the sum of the readings. Another way to think of it is that 80 feet is 80% of 100 feet, so the tree has to be 80% of the sum of the slope readings. Likewise, if one were 150 feet from the tree, the total tree height would be 150% or 1.5 times the sum of the slope readings. 02.8: Summary Questions 1. Determine the total heights of the trees illustrated below. Pay attention to the horizontal distances and slope scale used for each. 2. How should the total height of the flat-topped tree below be determined? 3. Calculate the height of the leaner tree below. Answers to Summary Questions 1. A. (%slope) (137+11) rise (height)= 74 feet I.B. (97+16) = 113 feet I.C. (107+12) = 143 feet I.D. (Tslope) (101+8) rise (height) = 109 feet I.E. (90+10) = 50 feet 2. The top of the tree will have to be reconstructed because of the broken top. This can be done by using a neighboring tree that is similar in size and taper as a reference. 3. a. The rise of the fall line from the top of the tree to the ground = (Tslope) (48+8) = 56 feet b. The horizontal distance from the base of the tree to the fall line is 54 feet. Thus we have two sides of the right triangle. Using the Pythagorean Theorem to determine the tree length (hypotenuse): a2 + b2 = c2 where: 562 + 542 = c2 6052 = c2 78 feet	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/02%3A_Tree_Height/02.6%3A_Instruments_Used_for_Measuring_Tree_Height.txt
3.1 Why Tree Diameter? In addition to satisfying our innate curiosity about how big trees are, measuring the diameter of trees can tell us quite a bit about a forest stand. As we will discuss in a later chapter on “Stand Characteristics,” there is a direct relationship between tree diameter and tree crown. The bigger the tree’s diameter, the greater the amount of foliage it has. Tree diameter data can provide essential information about crown competition, stocking levels, and forest health. Stand management decisions, such as when and how much to thin a stand, rely heavily on data derived from measuring tree diameters. In addition, tree diameter is needed in order to determine a tree’s wood volume. Look at the “diameter distribution curve” in Figure 3.1 below. Without having ever been to this stand, what can you infer about it by looking at the graph? The curve indicates that there are many small diameter trees around 14”, a group of large trees around 32”, and a smattering of trees with diameters over 50”. Do the groupings indicate different age cohorts? Is the stand approaching an old-growth condition? If we look more closely at the data, we see that the small trees are shade tolerant species, and the less tolerant Douglas-fir tends to be in the larger size classes. What might that tell you? Figure 3.1. Trees by diameter class. Data collected by MHCC Silviculture class January, 2001. 03.2: Determining Tree Diameter 3.2 Determining Tree Diameter Figure 3.2. A tree showing how diameters are not constant as one moves up a tree. Trees do not grow like cylinders, but rather taper upward, the tree’s diameter getting smaller as one gets closer to the top of the tree. Trees also have butt swell, a thickening of the wood and bark at the base of the tree to support the tree’s mass (Figure 3.2). Butt swell can create a very large diameter on trees exposed to heavy wind, on steep slopes and in sparsely populated stands. Thus, when you really think about trying to obtain useful diameter data, the question becomes, “where on the tree should I measure it?” To make tree diameter measurements meaningful and easy to perform, a standard location and protocol have been developed. Diameters are measured outside the bark at Diameter at Breast Height (DBH), or 4½ feet above the ground on the uphill side of the tree (Figure 3.3). This location is above most butt swell, above most of the brush, and is at a comfortable arm position for most people. Figure 3.3. The standard location for measuring tree diameter is at DBH, 4.5 feet above the ground on the uphill side of the tree. (From [FS] 1990.) For most trees in the forest, measuring dbh is quite straightforward. However, there are plenty of irregular trees that require adaptations (Figures 3.4 – 3.10). (All illustrations from or adapted from [FS] 1990.) Figure 3.4. On forked trees, measure as one tree if fork occurs at or above 4.5’ (left). Measure as two trees if fork occurs below 4.5’ (right). Figure 3.5. Measure directly above a bulge or branch whorl (left). On trees with extensive butt swell, measure at least 1½’ above the butt swell (right). Figure 3.6. For a large burl or canker, measure above the deformity and adjust the diameter down slightly (left), or take two measures equidistant from dbh above and below the deformity, and use the average (right). Figure 3.7. On leaning trees, the tape is held perpendicular to the tree bole, and is measured on the uphill side of the tree if on a slope (left); on the short side of the lean if on flat ground (right). Figure 3.8. On trees with roots above ground, measure at 4.5’ above the root crown (below). Figure 3.9. On trees that have grown together, count as two trees. Measure halfway around each, and double the measurement. Figure 3.10. On trees with scars, treat as a double tree if severe (left), or reconstruct the diameter if slight (right).	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/03%3A_Tree_Diameter/03.1%3A_Why_Tree_Diameter.txt
3.3 Instruments for Measuring Tree Diameter A number of different instruments can be used to determine dbh. Each has its merits and should be used according to the situation present. 1. A diameter tape, or d-tape, is the most common tool. The tape is wrapped around the tree, measuring its circumference. The tape is graduated to reflect a conversion from tree circumference to tree diameter. Thus, we measure circumference, but can record diameter to the nearest 0.1 inch (Figure 3.11). Granted, most trees are not perfect circles, so there is some error in this method. However, except on extremely irregular trees, this method seems to “average out” the tree’s shape to an acceptable estimate. Figure 3.11. A diameter tape is graduated so that diameter can be read from measuring the tree’s circumference. (Illustrations from [FS] 1990.) 2. A Biltmore stick can give quick estimates of dbh to the nearest 2 inches (Figure 3.12). The slanted edge of the stick is held against the tree 25” from a person’s eye. One end of the stick is lined up at dbh with the left edge of the tree. Without moving one’s head, the diameter is read off the stick where the line of sight crosses the stick on the right edge of the tree. In general, two measurements should be made on the tree, at right angles to each other, to account for the fact that trees are rarely perfectly symmetrical. The average of the two measures is recorded. Figure 3.12. Proper alignment of a Biltmore stick to determine dbh. 3. A relaskop can be used to determine diameter at any point in the tree. This makes it very useful for measuring merchantable tops, merchantable heights and taper heights in timber cruising. The diameter scales adjust for slope as one looks higher and higher in the tree (Figure 3.13). However, because it is slower and estimates dbh less precisely than a d-tape, this instrument is generally reserved for dbh measurements where you have to measure dbh from a distance—either because you physically cannot get to the tree, or because the correct measurement point for dbh on the tree is out of reach. Figure 3.13. A view of the scales inside a relaskop. The black and white vertical “bars” are used for measuring diameter. A %slope scale is found on the far left, and a topographic slope scale, or “Tscale,” is found to the right of the diameter bars. Notice at the “0” mark, the scales are indicated by “0%” and “0 ft” respectively.(illustration from Lemoine n.d.) 4. An electronic dendrometer gives a digital readout of diameter at any point in the tree. It is essentially an electronic relaskop. 5. In areas where vines are prevalent, getting a d-tape around the tree or finding a flat side on which to lay a Biltmore stick can be nearly impossible. In these circumstances, a tree caliper is handy (Figure 3.14). A graduated scale corresponds to the width of the caliper teeth. Again, two measurements should be made, at right angles to each other, in order to alleviate error that would crop up in trees that are rather elliptical. The average of the two measures is recorded. Tree calipers are somewhat heavy, and can be cumbersome to carry around all day, especially in heavy brush. Therefore, these are not as popular in the Pacific Northwest as they are in other regions. Figure 3.13. A tree caliper is held at right angles to the tree trunk. Diameter is read off the left side of the sliding scale at front.	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/03%3A_Tree_Diameter/03.3%3A_Instruments_for_Measuring_Tree_Diameter.txt
3.4 Field Technique Tips for Measuring Tree Diameter Measuring dbh is relatively easy, but it is important to keep the following in mind while measuring and recording. 1. To speed up your work, determine where dbh is on your body and then use that point as a reference for locating dbh on each tree. This is much faster and easier than measuring up 4½ feet on every tree. You may want to check this the first several days you measure to make sure you are consistent. Over time we tend to “slip” a little and measure where it is most comfortable for us rather than at dbh. 2. Make sure the d-tape is level, at right angles to the tree stem. Slack in the tape on the back side of the tree will inflate the true diameter of the tree. 3. When using a d-tape, “hug the tree” to wrap the tape around it. This is much faster and less tiring than hooking the tape and walking around the tree, and you will soon find the diameter limit of your arms. This can come in handy. On large trees, try swinging the tape behind the tree and catching it in your other hand to avoid having to walk around the tree. This takes practice, but is worth mastering. Walking around large trees in heavy brush on steep slopes, while trying to hold a d-tape at the correct height can get really old really fast. 4. When determining dbh, always record measurements to the precision of the instrument being used. In other words, if we can measure to the nearest 0.1 inch, we record to the nearest 0.1 inch. In this way, we maintain the highest flexibility in using the data later for whatever analyses are needed. So, DON’T ROUND OFF IN THE FIELD. 5. Try to guess the dbh before measuring it. You will be amazed at how quickly your eyes will calibrate. This not only makes a game out of the work, but can come in handy in situations where you need to check for errors – and you can impress your friends. 6. Work safely with the d-tape. The hook on the end can injure your hand or eyes, and the edges can give you “paper cuts.” 7. Once the data are brought back to the office, the diameters may be placed into their appropriate diameter classes. This is a way of grouping diameters for easier data analysis. Regardless of whether one is using one-inch or two- inch diameter classes, the diameter class “numeral” is always the midpoint of the diameter class. This is the easy way to remember how to assign the correct class. They are grouped as follows: One-inch classes: Two-inch classes: 8” class = 7.6” – 8.5” 8” class = 7.0” – 8.9” 9” class = 8.6” – 9.5” 10” class = 9.0”- 10.9” 10” class = 9.6” – 10.5” 12” class = 11.0” – 12.9” 11” class = 10.6” – 11.5” and so on…….. 12” class = 11.6” – 12.5” and so on……….. Note that if you record “11” in the field, it is not clear if the tree should be placed in the 10” two-inch class or the 12” class. Was the actual measurement 11.2” (12-inch class), or was the measurement actually 10.7” and rounded up to 11, placing the tree in the 12” two-inch class instead of the correct 10” class. So leave the rounding until the data are actually being analyzed. If the field measurement is 11.0”, record “11.0.” 8. As with all field data collection, when working with a partner, echo back your measurements to make sure the correct number is written down or entered into the data collector. 03.5: Summary Questions 3.5 Summary Questions 1. For each of the following, indicate where dbh should be measured. Answers to Summary Questions A. Measure dbh at 4.5’ on the uphill side of the tree. B. Measure dbh at 4.5’ above the ground. C. Measure as two trees (forks below dbh). Measure perpendicular to the bole of the tree. D. Measure above the bulge. E. Measure at least 1.5’ above the butt swell. This is a situation in which dbh may be out of reach and difficult to measure with a d-tape. In this case, a relaskop may be the instrument of choice.	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/03%3A_Tree_Diameter/03.4%3A_Field_Technique_Tips_for_Measuring_Tree_Diameter.txt
• 4.1: Determining Tree Age • 4.2: Young trees • 4.3: Field Technique Tips for Counting Whorls: • 4.4: Forest Setting Larger trees growing in a forest present the greatest challenge. As noted above, it is very difficult to estimate tree age simply from size. So much depends on the tree’s microenvironment (access to light, water, space and nutrients), its unique species-dependent growth habits, and the events that alter the tree’s environment or health over the course of its life. The frequency and intensity of disturbances such as fire, insect attacks, or windstorms profoundly influence tree growth over time. • 4.5: Increment Boring Counting a tree’s annual rings is a reliable way to estimate its age when records are unavailable; this method has been adapted for living trees. An instrument called an increment borer extracts a small, pencil-sized piece of wood, or core sample, from the trunk of the tree. A mini-auger is drilled by hand from the bark to the center (pith) of the tree, and the resulting core sample extracted from the hole displays the annual rings (or increments of growth) of the tree at that point in the tree. • 4.6:. Field Techniques for Increment Boring • 4.7: Summary Questions 04: Tree Age 4.1 Determining Tree Age How old is that tree? Trees, particularly big trees, fascinate us, and we often want to know how long a tree has been alive. Was it here when Lewis and Clark reached the Pacific Ocean in 1805, or when Oregon became a state in 1859? Did it survive the Columbus Day storm of 1962? Did it germinate and begin its life as a result of the Tillamook Burns or the 1996 floods in the Willamette Valley? Although we love to ask the question, it is usually nearly impossible to guess the right answer. Tree size, particularly for big trees, is as much a reflection of tree species and growing conditions as it is tree age. Consider a California redwood (Sequoiadendron sempervirens). This fast-growing species could easily reach 40 feet in ten years. On the other hand, it may take a lodgepole pine (Pinus contorta) twice as many years to reach the same height even if the two species were growing side by side (Burns and Honkala 1990). Nearly any species growing in the sun will grow significantly faster than in heavy shade (Figure 4.1). Grand fir (Abies grandis) or Douglas-fir growing in the moist, moderate climate of western Oregon will grow taller faster than the same species in the drier and colder climate east of the Cascade Mts. Knowledge of species, habitat, and available tools and techniques all help in estimating tree age. Figure 4.1. Douglas-fir seedlings growing in the sun (left) and shade (right). Note the bushier appearance and greater number of needles on the tree in the sun. 04.2: Young trees An approximate age for many young conifers can be determined by “counting the whorls.” Some trees, including most conifers growing in the Pacific Northwest, have determinate height growth. This means that they put on one “flush of growth” each year, and that this year’s growth is determined by last year’s bud. The terminal and lateral buds at the tips of the tree break bud, or “flush” in the spring (Figure 4.2). The stems or “leaders” produced by these buds elongate until some time in July, and then set new buds for the following spring. Figure 4.2. Terminal buds at the tip of the stem (left) flush and grow new branches and leaves each year (right). The center becomes the new leader, or main stem. The lateral or side buds become new lateral branches. A tree increases in height by the length of the new leader growth produced by the terminal bud (from old bud to new bud). In addition, the lateral buds flush and produce a new whorl of branches at the base of the leader (old bud location) (Figure 4.3). This process is repeated every year. Therefore, each whorl of branches and the stem growth immediately above it (up to the next whorl) represent one year of growth. Figure 4.3. An annual flush of growth represents one year, or one whorl of growth. 04.3: Field Technique Tips for Counting Whorls: 4.3 Field Technique Tips for Counting Whorls: Because each whorl represents one year of growth, one can estimate age on young trees with determinate height growth by counting the whorls. 1. On most trees, the lowest tree branches are systematically dropped as the tree grows and the sun no longer hits the base of the tree. Therefore, when estimating age using this method, it is important to include the bottom-most stubs and/or knots where it is evident branches once existed. 2. Two to four years should be added to most species to allow for the time between seedling germination and evidence of branch whorls on the trunk (Figure 4.4). 3. Small single branches between major branch whorls do not constitute a true whorl or year of growth. Do not count these false whorls. 4. A very short increase in length between whorls that seems unlike the other years’ growth may indicate a “lammas” year, in which the tree flushed twice, often in response to extraordinary growing conditions. Ignore those years unless it is evident that some injury is responsible for the very short internode (Figure 4.4). Figure 4.4. Counting the whorls to determine age of a young conifer. Lammas growth and false whorls are ignored. Lower stem is examined for knots, and time to first visible knot is estimated and added in — generally 2-4 years. This method of “counting the whorls” usually works very well up to fifteen years of age or so for conifers such as Douglas-fir, spruces (Picea spp.), pines (Pinus spp.) and true firs (Abies spp.). It is more challenging for cedars (Thuja spp., Chamaecyparis spp.), hemlocks (Tsuga spp.), and some hardwoods. One really has to get close to the tree, look carefully for evidence of bud scars, and know the growth habits of the species. 04.4: Forest Setting Larger trees growing in a forest present the greatest challenge. As noted above, it is very difficult to estimate tree age simply from size. So much depends on the tree’s microenvironment (access to light, water, space and nutrients), its unique species-dependent growth habits, and the events that alter the tree’s environment or health over the course of its life. The frequency and intensity of disturbances such as fire, insect attacks, or windstorms profoundly influence tree growth over time. Trees growing in managed forests, particularly evenaged “second growth” or “third growth” forests, were likely planted. Foresters record the year of planting and seedling age at time of planting. Most companies will have year of establishment printed on company forest maps or indicated on company aerial photos for ease of use. In these cases, simply researching office records before one goes out to the field will provide stand age. Trees growing in naturally regenerated stands, unmanaged stands, or stands managed for an unevenaged structure are harder to evaluate. In these cases, individual tree age can vary greatly from tree to tree. Knowledge of tree silvics can help with ballpark estimates. For example, a young (< 30 yrs.) true fir will have smooth bark with resin blisters. This gradually develops into plates or fissures as the tree ages. A tree over 100 years will have regular, geometric shapes in the bark patterns. The crown of a very old tree will also have a rounded top, different than the tiered leader of a young tree. On Douglas-fir, the smooth bark gives way to thick fissures in the bark. But these type of physical characteristics, without some site history clues, may only get a person to within about 30 years of the actual age. Annual Ring Counts The most direct way of determining tree age is to count the annual rings on a tree’s stump or a round “cookie” cut from the tree. In the Pacific Northwest, trees produce one “ring” of diameter growth each year, so the number of rings present on a cross-section of the tree’s trunk represents the tree’s age at that height. Counting rings on a stump will result in a pretty accurate estimate of the former tree’s age. Counting rings from a cookie cut at a height of ten feet or twenty feet will tell you how many years the tree grew after it reached that particular height (Figure 4.5). In fact, researchers examine cookies cut from regular intervals along fallen trees to derive information about species’ growth rates, and sometimes to investigate evidence of historical events such as fires, droughts, insect outbreaks, etc. in a science called dendrochronology.	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/04%3A_Tree_Age/04.1%3A_Determining_Tree_Age.txt
Since counting a tree’s annual rings is a reliable way to estimate its age when records are unavailable, this method has been adapted for living trees. An instrument called an increment borer extracts a small, pencil-sized piece of wood, or core sample, from the trunk of the tree. A mini-auger is drilled by hand from the bark to the center (pith) of the tree, and the resulting core sample extracted from the hole displays the annual rings (or increments of growth) of the tree at that point in the tree (Figure 4.6). The tree then “pitches” the hole over, filling the small cavity with resin. Figure 4.6. A cross-section of a tree that has been bored, showing the displaced core sample. The standard location for taking increment core samples from a tree is diameter at breast height (DBH). There are a number of reasons for doing so. • It is a comfortable height for most people to turn the handle of the increment borer, and to extract the core sample. (Imagine lying on your stomach to try to obtain a core sample from a one-foot stump!) • There is ample room for the borer handle to turn. (At the base of the tree, one would constantly hit the ground or roots of the tree.) • Brush and other vegetation do not have to be cut away in order to operate the borer. • There is generally room to avoid oddities in the tree’s trunk – branch whorls, cankers, etc. • Age/diameter relationships can be developed. Because increment core samples are obtained at dbh, it is important to note on a data sheet that the age estimate is “DBH Age.” If one is using tree age to track growth on a chart or determine site index, it is also important to note whether or not the chart uses dbh age or total tree age. If total tree age is required, then the technician must estimate how many years it took the tree to grow to dbh (4.5 feet). This number (usually 5-10 years depending upon the species) is added to the core sample age to estimate total tree age. Instruments for Increment Boring Increment borers are tidy instruments that consist of a handle (that serves double duty as a case), a bit and an extractor. (Figure 4.7). The bit is locked onto the handle, making a “T”-shaped instrument, then twisted into the tree. Once the bit has reached a little more than half-way through the trunk’s diameter, the extractor, a thin metal sleeve, is pushed in, then pulled out as described under Field Techniques for Increment Boring. Figure 4.7. Borer extractor (left), bit (center) and handle (right). The square end of the bit is inserted into the center of the handle where the clasp is located. Caution Ring counts are not foolproof! For example, many tropical trees and diffuse-porous hardwoods have growth rings that are nearly indistinguishable. Trees may also produce “false rings” during years of unusual weather conditions (e.g. drought followed by high rain, lammas years), or indistinct (missing) rings in years of extreme drought or defoliation. The older the tree, the more opportunities there are for abnormalities. Therefore, it is important to remember that we can only obtain estimates of tree age.	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/04%3A_Tree_Age/04.5%3A_Increment_Boring.txt
4.6. Field Techniques for Increment Boring Here are some tips and instructions for getting clean, usable core samples. In the office: 1. Inspect your borer bit! Make sure your bit is sharp and free of nicks. A jagged bit edge will result in a “torn up” core sample. It is extremely important to keep the bit edge clean and protected to get a smooth core sample that you can read easily (Figure 4.8). Figure 4.8. The far left image shows a jagged bit surface. This will chew the wood as it bores and result in an unreadable core sample. In the field: 1. Determine dbh. Note – the core sample does not have to be taken from the uphill side of the tree, but does have to be taken at dbh. If you are standing on a slope, it is best to bore the tree on the side slope to diminish the effects of its off-center pith. 2. Choose a spot on the trunk free of knots or bulges. 3. Put the extractor in a safe place while you are boring. Never put it in the ground! Abrasion of the extractor teeth by minerals and rock particles in the soil will dull them, making them unable to “grab” the core sample when it is time to extract the core. It is also too easy to lose or step on the extractor when it is under your feet. Some people stick the extractor into the bark of thick-barked trees, but most manufacturers discourage this as well. A nice place for it is in the pencil slot of your cruiser’s vest. It is also a good idea to wrap brightly colored flagging on the end of the extractor to make it more visible. This is particularly important when working in heavy brush. 4. Getting the bit started is often the most difficult part. You will be able to tell when the bit gets through the bark, “catches” the wood and begins to wind its way to the center. Lubricating the bit with beeswax or WD40 can make that initial catch easier to accomplish. 5. Estimate where you think the center of the tree is and bore two or three inches past that point. This accomplishes a couple of things. a) We often misjudge how far to bore. Adding a few inches reduces the chance that one will come up short in trying to reach the pith. Figure 4.9. (A) Off-center core sample showing curving rings near center. (B) Centered core sample on tree with off-center pith. b) Most trees are not perfectly round, nor is the pith always in the geometric center of a tree. A tree growing on a slope or where there are strong winds, will likely have an off-center pith. Boring past the pith will result in a better chance of hitting the center (Figure 4.9). c) It is generally easier to tell where the center of the tree is when you can see several rings past the pith. The rings on the core sample will start curving a little when you get close to the center; they then curve the opposite direction once you have passed the pith. Seeing the curves in both directions can help pinpoint the center. 6. After inserting the extractor into the borer, turn the handle in a reverse direction crisply to break the wood and allow the core to be extracted. (If the extractor is inserted on top of the core sample, make 1 ½ reverse turns; if the extractor is inserted below the core sample, make two full reverse turns.) 7. It may be difficult to pull the extractor out. Use your foot on the tree for leverage or use two hands, but never twist the extractor! This will not help get it out, and will result in a broken extractor. Wear gloves to protect your hands from “paper” cuts as the extractor comes out of the tree. 8. Remember that a growth ring representing one year’s growth consists of both the light colored earlywood (laid down in the spring) and the dark colored latewood (laid down in the summer). It is this contrast of last year’s latewood to this year’s earlywood that allows us to count the rings. Many people train their eye to simply count the dark latewood bands in each ring. 9. A hand lens or magnifying glass will help with distinguishing the rings, particularly on old or slow-growing trees where the rings are narrow. Also, wetting the core sample will make the rings stand out more. 10. If the pith is missed, try to “reconstruct” the center of the tree by placing your core sample on a piece of paper and drawing circles to extend the centermost rings visible on the core (Figure 4.10). Using the width of the growth rings closest to the center as a guide, estimate how many rings are missing from the center, and draw them in. Add these missing rings, if few in number, to the annual ring count. If you are adding more than three or four years, it is best to get a new sample. Figure 4.10. Use inner ring width and curvature to reconstruct “missing” center rings. For this core sample, one more year would be added to the ring count. 04.7: Summary Questions 4.7 Summary Questions 1. A 50 yr-old tree has a 20” dbh. A 50 yr-old tree of the same species has a 36” dbh. What are some possible reasons for the difference in the diameter of these trees even though they are the same age? 2. A Douglas-fir is cored at dbh, resulting in a ring count of 36. What is the tree’s estimated total age? 3. Estimate the age of the core sample illustrated below. 4. A young tree is illustrated below. Count the whorls to estimate its total age. 5. Would core samples from all sides of the tree result in the same ring count? Why or why not? (Consider trees on slopes, wind patterns, coring angles and false whorls.) Answers to Summary Questions 1. The key to remember here is that tree diameter is a function of crown volume. So any growing condition that would result in a greater crown for one tree, would also result in a larger diameter for it. These conditions might include: a) more physical growing space for the larger tree; b) greater access to light, nutrients, water and other necessary plant resources; c) a genotype (genetic makeup) more suited to the growing conditions present or less palatable to animals, insects or pathogens; or d) activities of neighboring trees over time that resulted in more favorable growing conditions. 2. For Douglas-fir, we generally add 7 years to a core sample to obtain total age in a stand that appears to have naturally regenerated. This number would increase if it appeared the tree was stagnated under shade for much of its early life (10-12 yrs) or decrease if it was planted from nursery stock and grew in full sunlight (4-5 yrs). 3. Assuming the lines on the drawing represent the dark summer wood or late wood on the tree, they indicate the end of the growing year, Therefore, there are 14 rings present; the shaded one being the bark. If the core sample had not hit the pith, we would have had to reconstruct the pith area, drawing circles as described in Field Techniques number 10. 4.The whorls and knots indicate 10 years. Add 3-4 years to that for the time it took the tree to grow to the first knot, and the total estimated age would be about 13 years. 5.Core samples do not vary widely from one side of the tree to the other, but it is possible for differences to be present. These may result from off-center piths or inconsistent coring directions (due to a tree’s position on a slope, subjectivity to strong winds, or tendency to grow toward a light source). Rot or fire scars may destroy evidence of rings. In addition, false rings do not always extend all the way around the tree.	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/04%3A_Tree_Age/04.6%3A._Field_Techniques_for_Increment_Boring.txt
5.1 Stand Structure One of the questions we often ask about forests is simply, “What’s out there?” What species are growing there? What does the forest look like visually? Are the trees young, old, or mixed? What is the proportion of small to large trees? Is there a tree canopy with a shrub layer underneath? Is the understory mainly herbaceous plants? Are there several layers of trees? Are snags or large fallen logs present? How dense is the forest? Do the trees have ample room to grow or are they crowded together? Forests display a vast array of species and structural arrangements (Figure 5.1.) Figure 5.1. Examples of various forest stand structures. A common task of the forest technician is to provide data to answer these questions. A survey called a “stand exam” is just that – an examination of the composition and structure of the forest. Once an assessment of the current conditions is completed, then questions about “What’s happening out there?” or “What will the stand look like in the future?” can be addressed more readily. Stand Structure refers to the overall “look” of the forest stand (Figure 5.1). It is the “horizontal and vertical distribution of components of a stand, including the height, diameter, crown layers and stems of trees, shrubs, herbaceous understory, snags and down woody debris” (Helms 1998). As one might imagine, the structure of a forest changes over time, as trees grow, as fungi rot the wood, as insects or fire move through, as light conditions change, and so on. Therefore, a stand exam is always a measure of the forest at a point in time; a snapshot, not a hard and fast truism. To successfully manage for wildlife habitat, wood quality, desired growth rates and a myriad of other forest management objectives, foresters often a) assess what is present, b) describe what is desired in the future, then c) develop guidelines for managing toward that future forest structure. We can’t wave a magic wand and proclaim, “Increase photosynthesis,” or “Speed up nutrient cycling,” so our current tools for influencing forest function center on influencing a forest’s species composition and structural elements. Figure 5.2. Tree density illustrates the horizontal distribution of trees. The top photo shows a dense forest with many trees (or stems) per acre. The lower photo is less dense, with fewer trees per acre. Let’s look at that stand structure definition again. “…horizontal and vertical distribution of components of a stand…..crown layers…” What terms can we use to adequately but briefly describe “distribution?” Horizontal distribution can be expressed in measures of density – trees per acre or basal area per acre (Figure 5.2). The crown is the foliar portion of the plant, and “crown layers” refers to distinct classes or stratification of the canopy. Since trees dominate the canopy of most forests, several forestry terms describe the vertical distribution, or layering of the tree crowns. An evenaged forest is has one or two distinct age or size classes of trees; thus one or two layers of tree crowns(Figure 5.3A). Figure 5.3A. Evenaged forests: a single layered canopy (left) and a two-aged stand (right). An unevenaged forest has three or more distinct age or size classes, thus three or more layers of trees (Figure 5.3B). Figure 5.3B. A multilayered unevenaged stand, with three or more cohorts. Although it is common to have a canopy of trees overhead, shrubs at midstory, and herbs on the forest floor, we would not refer to this as unevenaged unless there are several layers of trees. A multistoried stand is one with multiple layers of trees. As we learned before, tree size does not always indicate tree age; therefore, some foresters try to avoid the terms “evenaged,” “unevenaged” and “age classes,” and instead refer to forest “size classes” or “cohorts” to describe the distinct tree layers of a forest. So when you read “evenaged” think “one dominant layer in the overstory.” When you read “unevenaged” think “three or more tree layers.”	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/05%3A_Stand_Characteristics/05.1%3A_Stand_Structure.txt
5.2 Crown Classes Crown class is a term used to describe the position of an individual tree in the forest canopy. It can be used in both evenaged and unevenaged stands. Kraft’s Crown Classes are defined as follows (Smith et al. 1997 and Helms 1998 modified for clarity): • Dominant Trees These crowns extend above the general level of the canopy. They receive full light from above and some light from the sides. Generally, they have the largest, fullest crowns in the stand (Figure 5.4). • Codominant Trees These crowns make up the general level of the canopy. They receive direct light from above, but little or no light from the sides. Generally they are shorter than the dominant trees. • Intermediate Trees These crowns occupy a subordinate position in the canopy. They receive some direct light from above, but no direct light from the sides. Crowns are generally narrow and/or one-sided, and shorter than the dominant and codominant trees. • Suppressed Trees (Overtopped Trees) These crowns are below the general level of the canopy. They receive no direct light. Crowns are generally short, sparse, and narrow. Figure 5.4. An illustration of crown classes. “D” = Dominant; “C” = Codominant; “I” = Intermediate and “S” = Suppressed. “General layer of the canopy” refers to the size class or cohort being examined. Crown classes are most easily determined in evenaged stands, as depicted in Figure 5.4. In an unevenaged stand, a tree would be compared to other trees in the same layer. Crown classes are a function of tree vigor, tree growing space, access to sunlight (functions of stand density), and species shade tolerance. A “suppressed” Douglas-fir tree is likely of low vigor and will probably die out. It typically would not be able to respond to an increase in sunlight if a neighboring tree fell over. A shade tolerant “suppressed” western hemlock on the other hand, may survive very nicely and be able to take advantage of increased sunlight if a neighboring tree were to fall over. Crown class can also tell us something of the overall vigor of an evenaged stand. If most trees are in the intermediate crown class, then the stand is likely too crowded and the trees are stagnated. A stand with nearly every tree in the dominant category is either very young, and all of the trees are receiving plenty of sun, or very sparse and may be considered “understocked.” A typical evenaged stand has the majority of trees in the codominant class, and the fewest trees in the suppressed class. The relative ratios of dominant and intermediate classes are generally a function of species composition. Examine the data in Figure 5.5 and Table 5.1 below. Figure 5.5. Diameter and crown class data for an evenaged stand near Larch Mountain. Data collected by MHCC Forest Measurements I class on January 26, 2005. This 60-yr old stand of primarily Douglas-fir and western hemlock, displays a bell-shaped diameter distribution, typical of an evenaged stand. Most of the trees are clustered around the average DBH, with some smaller and some larger than the center range. Table 5.1. Percent of each Species by Crown Class. Data collected in evenaged stand near Larch Mt. by MHCC Forest Measurements I class on January 26, 2005. Species Dominant 29% of all trees measured Codominant 35% of all trees measured Intermediate 24% of all trees measured Suppressed 13% of all trees measured Douglas-fir 67 64 40 12 Western hemlock 33 36 60 88 Note that the majority of trees are in the codominant crown class (35%), which most likely makes up the bulk of the 16’’-22” trees. It is interesting to examine the species composition data. The majority of dominant and codominant trees are Douglas-fir, while the intermediate and suppressed trees are primarily shade tolerant western hemlock. Therefore, many of the trees in the small diameter classes (6’-10”) may survive over time, even though they are surrounded by large trees. So there is another element to examine besides position in the crown.	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/05%3A_Stand_Characteristics/05.2%3A_Crown_Classes.txt
5.3 Live Crown Ratio Another useful measurement to indicate tree vigor is live crown ratio (LCR). It is the ratio of crown length to total tree height, or the percentage of a tree’s total height that has foliage (Figure 5.6). Figure 5.6. Live Crown Ratio: the ratio of live crown to total tree height; expressed as a percentage. Crown length is partly a function of species’ shade tolerance. For example, Douglas-fir and most pines will self-prune (drop their lower branches as they become shaded). However, a shade tolerant species such as western hemlock will keep its lower branches in medium shade. Therefore, a western hemlock will have a longer crown (and higher LCR) under low light conditions than a Douglas-fir. Consider the data in Table 5.2. This young, evenaged forest stand (≈ 40 yrs), had a substantial riparian component supporting the hardwoods, and was growing on a southern slope. Note that the red alder, cherry and Douglas-fir had shorter LCR’s than the more shade tolerant hemlock and cedar. The hardwoods were shorter, but all the conifers were approximately the same height. Table 5.2. Mean live crown ratio (LCR) and height by species for an evenaged stand in the Latourell Creek watershed. Data collected by Mt. Hood Community College Forest Measurements I class March, 2003. Species LCR(%) HT (ft.) Red alder 40 62 Bitter cherry 28 52 Douglas-fir 43 74 Western redcedar 74 80 Western hemlock 64 78 Douglas-fir trees with large crown ratios (>50%) tend to be dominant trees, and/or trees growing with adequate light. Douglas-fir trees with ratios less than 30% generally have low vigor, and typically either a) occupy intermediate or suppressed crown classes, or b) are growing in very dense, uniform young stands. In the latter case, their root systems do not develop well, and the trees become subject to windthrow over time. These “dog hair stands” are often a result of planting seedlings at a high density, and failing to thin them later at the appropriate time. In general, LCR will reflect crown class, regardless of species. Trees growing in the dominant crown classes tend to have the longest crowns overall, followed by trees in the codominant, intermediate, and suppressed crown classes respectively (Table 5.3). The exception to this may be unevenaged or two-aged stands in which distinct second and third layers are composed primarily of shade tolerant trees. In these cases, each layer must be evaluated independently. Table 5.3. Mean live crown ratio (LCR) for species in an evenaged BLM stand near Larch Mountain. Data collected by MHCC Forest Measurements I class January 2003. Mean LCR by Crown Class Species D (%) C (%) I (%) S (%) Douglas-fir 48 47 38 Western hemlock 50 37 39 35 Overall 49 42 38 35 05.4: Field Technique Tips for Determining Crown Class and LCR Determining Crown Class 1. Crown class identification is somewhat subjective, so it is important to try to stick to the definitions and be consistent. Certainly, there will be many trees that do not fit neatly into the classification scheme, so expect some challenges and assign the crown class that most clearly illustrates the condition of the tree or its place in the stand. 2. This is particularly true when it comes to “suppressed” trees. They are still part of the canopy; they do not make up a second layer. Therefore, they do not have to have their entire crowns below the lowest branches of the tree canopy. Figure 5.7 illustrates a realistic interpretation of the definition. Figure 5.7. A simplified view of trees in different crown classes in an evenaged pure stand. The letters D, C, I and O denote dominant, codominant, intermediate and overtopped respectively. Note the suppressed trees extend into the canopy (after all they are in the same cohort or are the same age as the others); they just do not receive any direct light. The low vigor and poor crown condition of a suppressed shade intolerant tree will be very different from that of an intermediate, and should be documented as such. Determining Live Crown Ratio 1. Never “eyeball” LCR without measuring. You will underestimate the crown ratio. Standing on the ground, we get a foreshortened view of the crown; it will look shorter to us than it really is. The closer one is to the tree, and the taller the tree, the more your eye is tricked. In fact, it is an interesting exercise to guess what you think the LCR will be, then measure it, and see how close you are. 2. Determine length of crown using the same measuring techniques and equipment that you use to estimate total height. 3. It is sometimes difficult to determine where the base of the crown is. Brush or limbs from other trees may obscure it, or one side of the tree may have limbs lower than the other side. Try to get to a spot where you can see the tree to take care of the first problem. The standard for handling an uneven tree base is to sight on a spot that is halfway between the lowest branches on each side of the tree – “split the difference” so to speak (Figure 5.8). Figure 5.8. Estimating LCR when crown base is uneven.Measure the base halfway between the lowest significant branches on each side of the tree. 4. Ignore a lone live branch that is by itself low on the tree, and clearly not part of the overall crown. 5. Live crown ratio is generally recorded as a whole number (%), not a fraction in decimal form. And as always, record to the precision of the instrument used. We cannot accurately measure to a tenth of a percentage. (Calculator reads 53.6? Record LCR as 54).	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/05%3A_Stand_Characteristics/05.3%3A_Live_Crown_Ratio.txt
5.5 Stand Growth and Development Over Time In addition to giving us a snapshot of current stand conditions, stand exams can also provide clues to stand development over time if conducted periodically on the same site. Tree density, species composition, crown class distinctions and live crown ratios are all interwoven, and their relationships evolve over time to paint a picture of stand development. Although this is the subject of future ecology and silviculture classes, a brief introduction here will give you a better understanding of the crown dynamics you observe as you are measuring in the forest. Evenaged stands typically originate after large-scale disturbances occur on a site – wildfire, harvesting, windthrow, etc. Resulting forest development tends to follow a pattern of progression through four or more identifiable stages as described by Oliver and Larson (1996): Stand initiation or open shrub stage: the open condition after disturbance allows colonization by a variety of plants. Forest floor herbs, shrubs and seedlings may have survived the disturbance, as well as new individuals and pioneer species that appear over a period of several years. This is generally a period of diverse species composition. Planted seedlings are part of this stage (Figure 5.9A below). Figure 5.9A. The open shrub stage is dominated by shrubs, grasses, and seedlings. Figure 5.9B. The stem exclusion stage is typified by low levels of understory vegetation. Stem exclusion stage: crown closure occurs as tree crowns touch and available growing space is occupied. Overstory competition for light and growing space intensifies, and roots compete for soil moisture and nutrients. Some species die out and understory seedlings become scarce. This is generally a period of low biodiversity (Figure 5.9B). Understory reinitiation stage: small gaps of light in the canopy are created by breakage or death of individual trees – those lost to suppression, pests, windthrow, etc. This creates an opportunity for new species or individuals to establish in the understory, or for shade tolerant saplings already established in the understory to grow quickly into the gap. This stage generally contains more plant and animal species than the stem exclusion stage, but fewer than the stand initiation stage (Figure 5.9C). Figure 5.9C. In the understory reinitiation stage, saplings occupy pockets of light that develop in the understory. Figure 5.9D. The old growth/complex stage is multistoried with woody debris on the ground. Old-growth stage: large overstory trees are replaced by younger understory trees. As the original cohort making up the crown gradually dies, very large gaps allow the trees in the lower forest layers to grow into the canopy. This happens in an irregular fashion, so a multilayered structure emerges. This is the stage of the greatest structural diversity, and is complemented by high species diversity (Figure 5.9D). During all stages of stand development, plants are competing for light, nutrients, water, and growing space. Different species have different strategies for maximizing their ability to accumulate these resources, but the reality is clear; there is only so much to go around. During the stand initiation or open shrub stage, the forest may be dominated by herbs, shrubs and small seedlings. During this time, shrubs may grow the fastest, often outcompeting trees for sunlight. Seedlings overtopped by shrubs will die out, but the trees that grow taller than the shrubs begin to dominate the light source. As they fill out their crowns and get big enough to touch each other, crown closure occurs. Trees generally have high LCR’s and nearly all occupy dominant crown classes as the stand enters the stem exclusion stage. Competition between trees for light becomes particularly intense during this stage, as nearly all the crowns are about the same height and size. Light to the understory is drastically reduced, as evidenced by the limited number and abundance of understory plants. As trees continue to grow, they require more physical space for branch and crown expansion, and differentiation into crown classes becomes evident. The healthiest trees, able to grow faster and occupy more space, become the dominant trees. Slower growing trees become codominant, and inferior trees lag behind, creating the intermediate crown classes. These trends become more and more pronounced with time. Large dominants remain dominant, while those that are not as competitive become codominant as their LCR’s shrink. Some codominants are outcompeted and become intermediates, while the weakest trees become suppressed and eventually die. This is called self-thinning, and continues throughout the life of the stand as the trees get larger and larger (Figure 5.10). Thus, an area initially supporting 600 seedlings per acre may only support 200 trees per acre when they reach 50 years, or 30 trees per acre by the time they reach old-growth. Figure 5.10. Trees differentiate into crown classes with time, as competition for growing space increases. (Emmingham and Elwood 1993) A direct relationship exists between a tree’s diameter and its leaf biomass. The greater the volume of space a crown occupies, the more foliage a tree can support, and the more light it can capture. The more sugar it produces from those leaves, the more energy it has available for growth and the more wood it can produce each year. On the other hand, the smaller a tree’s crown is, the less space it has for foliage, and the smaller its growth rings will be. Thus we arrive at the diameter distribution in Figure 4-5. There is a range of diameters from 6”-36”, even though all trees are in the same canopy layer or cohort. Subordinate crown classes in the overstory with low LCR’s account for the small diameter trees, and dominant trees make up the larger diameter classes. A fascinating exercise that demonstrates the interrelationships among neighboring trees as they compete for light and growing space over time, is to chart individual tree diameter growth from increment core samples. The growth rings reflect individual tree crown expansion, and can help explain why some trees become dominant, while others are classified as intermediate. The illustration below shows diameter growth of four Douglas-fir trees growing side by side in an evenaged stand (Figure 5.11). Cores were taken at dbh, so no data are available to chart how many years it took each tree to reach dbh or which year each tree germinated and began to grow. But as you can see, the tree classified as intermediate (Tree10), appears to be about 10 years younger than the other three trees, and although its growth rates are on par with the other trees for the first 15 years, its curve flattens off after 1973, revealing its inability to capture much crown space, even though it occupies the same canopy layer as the larger trees. (This tree illustrates why even-layered is not necessarily evenaged, and why the term “cohort” rather than “age class” is preferred by some when discussing forest structural layers.) The dominant tree (Tree 11) maintains its high growth rate throughout its lifespan, and really pulls away from the other trees after 1983. The codominants (Trees 14 and15) display early growth equal to dominant Tree 11, then taper off over the last 25-30 years. It is likely that the stem exclusion stage began around 1968, and the effects of the more intense competition for light and growing space become evident over the following 5 -10 years. Figure 5.11. Diameter growth of four neighboring trees over time, taken from core samples. Data collected in an evenaged stand on a west slope by MHCC Forest Measurements I students January 2004. There are two interesting sidelights to observe with the codominant trees. Look at Tree 14. Its growth is similar to dominant Tree 11 until a sharp decline starts in 1968. Was there an event between 1968 and 1973 that would have resulted in a sudden loss of growth during that period? Many trees in this stand showed crooks in the trunks at about the same height, indicating that perhaps the 1969 ice storm caused top breakage in the stand. However, the last 15 years show that this tree has recovered, and is again displaying fairly rapid growth. Codominant Tree 15 on the other hand, shows a gradual slowdown and relatively flat growth rate since 1983. Does this indicate lower vigor? Will this tree ultimately become an intermediate tree as the surrounding stronger trees garner more and more light and growing space? At this point, it certainly appears that it is losing ground to the other trees. It is amazing what you can learn from four cores samples!	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/05%3A_Stand_Characteristics/05.5%3A_Stand_Growth_and_Development_Over_Time.txt
5.6 Application of LCR and Crown Class in Forest Management Live crown ratio and crown class are descriptors of tree crown characteristics and indicators of tree vigor. One of the ways that foresters use these terms is to communicate decisions about stand management. For example, let’s say a forester wants to improve stand vigor by doing the following: • reduce incidence of mortality by reducing tree density • concentrate growth on the healthiest trees • remove trees with evidence of disease These are general concepts and overall directions for the stand. But how does one decide which individual trees to cut or leave, and how does one communicate that information, especially to a crew of people marking the trees? Each acre of ground and each individual tree in the forest are unique. Until one actually walks through the entire stand, decisions about individual trees cannot be made. So a set of specific directions describing cut and leave trees must be written to more clearly explain a forester’s intentions. Therefore, in writing a prescription for the stand management described above, a forester would use standard terms to describe the intended management outcomes. For example, the following directions might be part of the marking directions. • Reduce tree density to 75 Trees per acre. On average, space trees ≈ 24’ apart. • Leave primarily Dominant trees; second preference is for Codominant trees with LCR > 40%. • Favor trees with intact crowns. • Remove trees with evidence of disease or deformity. • Remove primarily Intermediate and Suppressed trees. • Remove primarily trees with LCR< 30%. In this way, the person making the cut and leave decisions on the ground has a much clearer idea of how to achieve the objective to “improve stand vigor.” 05.7: Summary Questions 5.7 Summary Questions 1. Assign a crown class to each tree illustrated below. 2. Where on this tree should the live crown be measured? 3. Determine LCR for each tree illustrated. 1. The data in Table 4-4 below are from an evenaged stand in the stem exclusion stage. They represent the average live crown ratios (LCR) of trees sampled in the stand by species. Data were collected by MHCC Forest Measurements I students in February 2010. • Do the LCR’s reflect a stand with high or low crown competition? Explain. • Do the LCR’s of each species seem reasonable given their shade tolerance? • These data were gathered in February. Does the time of year pose any problems for estimating LCR on deciduous species like red alder? • Which species would you expect to dominate this stand in the future? Why? Answers to Summary Questions 1. Trees on the ends of the illustrations are hard to determine, given that we do not know what is on the other side of them. I assume there are trees beyond what is shown, so am using crown size as a partial indicator of the amount of light they are receiving. Position in the crown is key. The following are what I would assign, but I think the starred one (*) is borderline, and could be assigned the next higher crown class. 1. Since LCR is simply a ratio, any scale can be used to measure. I used the 20 scale on my triangular engineer’s ruler to obtain fairly good precision. So your values may differ, but LCR% should be similar. Trees with slope measurements from left to right: Tree 1: (70-14) = 70% Tree 2: (70-38) = 40% Tree 3: (70-22) = 60% (70+10) (70+10) (70+10) 1. The following answers refer to the data presented in Table 4-4. • The bulk of the trees in this stand are Douglas-fir, with an average live crown ratio of 40%. This indicates to me a canopy experiencing high crown competition. As crown closure occurs, trees drop low branches that are being shaded (particularly shade intolerant or intermediate species like red alder and Douglas-fir). Foresters often refer to a lower limit of 30% LCR as their cut-off for vigorously growing trees. If I were managing this stand, I would seriously consider a thinning to increase light availability to the trees I wanted to maintain on the site. • We would expect the live crown ratios to be the shortest on the shade intolerant species, and longest on the shade tolerant. Our measurements show this pattern; red alder<Douglas-fir<western hemlock. However, since only one western redcedar was measured, we don’t have a representative sample for this species. • These trees were measured in the winter, with no leaves, and only buds to indicate where the bottom of the crown was. I would take the red alder LCR estimates with a grain of salt. • I would expect Douglas-fir to continue to dominate in the future, followed by western hemlock. Red alder is a short-lived species, and is already subordinate in the forest.	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/05%3A_Stand_Characteristics/05.6%3A_Application_of_LCR_and_Crown_Class_in_Forest_Management.txt
6.1 Forest Site Productivity Just as a farmer might wish to know how “good” his ground might be for various crops, so a forester will wish to know how “good” his forest land is. Since forests are dominated by trees, this generally translates to predicting how well trees will grow. Decisions about what species to grow, how intensely to manage the trees, or whether or not trees are the best crop for a particularly piece of ground, are all tied to how plants grow on a site. For example, temperatures may dictate a shift from Douglas-fir to noble fir (Abies procera) once a certain elevation is reached. Trees growing on a very productive site may be thinned more frequently over a rotation than trees growing on a less productive site. Marginal pine forestland may be more suitably managed for wildlife habitat than for timber. Site quality refers to the inherent ability of a forest to produce biomass (or grow trees). It is the composite expression of a variety of physical and chemical attributes of a forested area, including its soil, topography and climate. Site characteristics such as: • soil depth, texture, and fertility; • slope, aspect, and elevation; and • precipitation, temperature and length of growing season; all combine to influence how well trees grow (Figure 6.1). Figure 6.1. A number of site factors combine to influence site quality. (Note: many people use the terms site quality and site productivity interchangeably. Purists, however, prefer “site quality” as a baseline indicator, as the productivity of a site can be altered by fertilizing, irrigating, mulching or altering the soil makeup.) To obtain a measure of site quality, one might first think of examining these site variables and correlating them to tree growth. There have been some attempts at doing just that, but the amount of work and expense required to get meaningful data are generally too great for the range of conditions found in most forest ownerships. Some larger companies, such as Weyerhaeuser, have inventoried and classified their soils, and the Forest Service has developed plant associations to indicate site conditions, but neither may be available for the majority of land managers. Intuitively, if one is interested in tree growth, then one solution is simply to measure how trees grow on the site. When measuring the trees, correlations are not required; the summation of all variables that influence tree growth is expressed in the biomass itself. The “proof is in the pudding” so to speak. And although the causal reasons for the productivity are not identified, as would be the case if all the influential variables were measured, a reliable indicator for tree growth on the site can be obtained. The question then becomes, “What is the best way to measure tree growth?” Many measurable tree growth attributes are strongly influenced by stand density. If few trees are present on a site, the individual trees will have large crowns, and thus large diameters and wide growth rings. Conversely, trees of the same age in a denser stand will have narrower crowns, smaller diameters, and tighter growth rings (Figure 6.2). Figure 6.2. (A) Trees with ample crown space have larger diameters, while (B) those spaced close together have narrower crowns and thus smaller diameters. Since tree volume is a function of tree diameter and height, volume is also tied directly to stand density. Therefore, diameter, crown volume, tree volume or tree ring growth do not make good measures of overall forest productivity. Average tree height, on the other hand, is not confounded in this manner except at extreme densities. Tree height is relatively independent of tree density for most forest tree species. Simply put, trees grow taller on good sites; grow shorter on poor sites. Therefore, tree height is a more reliable measure of the site’s inherent productivity than most other measures. It is also a quick and easy measurement to take in the field, unlike parameters such as soil fertility or microclimate. 06.2: Overview of Site Index 6.2 Overview of Site Index To determine site quality using tree height as the indicator, appropriate “site trees” of each species are selected in a stand. The site trees’ heights and ages are measured in the field, and then plotted or indexed on species-specific growth curves or tables (see Figure 6.3). These tree height-to-age relationship curves are derived from historical growth and yield field data, and show how the best trees from a variety of sites have grown over time without intensive management or site quality intervention. For a given species, a tree that is 120 feet tall at age 50 typically has better growing conditions than a tree that is only 80 feet tall at age 50. And, as indicated by the growth curves, the shorter tree will most likely continue to grow at a slower rate as it ages (Figure 6.3). There are exceptions to these generalized trends of course, but for most sites the general trends are sufficiently reliable. Figure 6.3. Kings’ site index for Douglas-fir in western Washington. For a given age a tree 120′ tall will continue to grow at a faster rate than a tree 80′ tall. (From Smith et 1l. 1997.) Site indexes for some species are grouped together intosite classes, with Site Class I being the highest site, and Site Class V or VI being the lowest. In our first example above for Douglas-fir, the tree whose 50-year site index is 80 feet is in Site Class IV, while the 120 foot tree is growing on Site Class II ground (Figure 6.3). Trees growing on Site Class I lands are highly productive, typically growing on rich soil, with access to moisture, and protection from the wind. Alluvial sites at low elevations often fall into this category. Conversely, Site Class V trees are generally growing on poor soils, in droughty climates, or at the upper edge of their elevational range. Figure 6.4. Height of dominant trees of the same age on different slope positions. (A) Dark coloring shows depth of soil. (B) Dashed lines indicate water table. (After Spurr and Barnes 1980). Site Class may also vary on a single slope. The ridgetop, exposed to wind and erosion, may produce trees that fall into Site Class III, whereas the toe of the slope, with less exposed rock and deeper soils collecting that eroded material, is Site Class II (Figure 6.4: A). Further, trees growing midslope with good drainage and plenty of sun may grow taller than the same species at the base of the slope in a riparian area if rooting depth is restricted by a high water table (Figure 6.4: B).	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/06%3A_Site_Quality/06.1%3A_Forest_Site_Productivity.txt
6.3 How to Use Site Index Curves Site Index is defined as the height of a tree at some base age. Height is in feet. For young stands, a base age of 50 years is typically used; for mature stands a base age of 100 is used. As rotation lengths decline, more and more site index values are indexed to a base age of 50. In the literature of Pacific Northwest species, if the age is not referenced, a base age of 100 years is understood. In practice, most second-growth stands are indexed to age 50. For some short-lived species, such as red alder (Alnus rubra), a base age of 20 years may be used. Therefore, a stand with an average 50-yr site index of 110 would indicate that the trees are capable of reaching a total height of 110 feet at 50 years. By establishing a base age, stands of any age can be evaluated and compared, and thus the number “110” becomes an index to the site’s productivity. We know whether this is a high site or low site when compared with other tree heights at this age. Site index curves have been developed by plotting heights of different aged trees from study areas throughout a region. Best-fit lines are drawn through the plotted trees, and harmonic curves developed. The curves for King’s 50-yr site index for Douglas-fir, developed from stem analysis of trees in western Washington, are shown in Figure 6.5. Note that as site quality improves, the curves are steeper, particularly for young trees. Growth rates tend to level out as the trees mature. The growth curves also allow one to estimate a tree’s height at any age. By tracing along the curves, a tree that is 40 years old can be “grown” to obtain its estimated height at age 50 or 100 years. Likewise, a curve can estimate how tall a 90 year-old tree was at age 50 (see Figure 6.5). In this way, the growth curves can use current height and age data to predict the height of trees at a common or index age. Site index (SI), defined as the height of dominant and codominant trees at a base age (usually 50 or 100 years), puts trees of all ages on a relative basis so that the index number has meaning and comparisons can be made. The lower the index number, regardless of the tree’s current age, the poorer the site; the higher the index number, the better the site. Figure 6.5. Tracing height growth backward (top line) or forward (bottom line) to reach age 50. (From Smith et al. 1997.) 06.4: Characteristics of Suitable Site Index Trees 6.4 Characteristics of Suitable Site Index Trees “Site trees” are used to assess a site’s inherent ability to grow trees, and therefore should be the best trees on the site. We select trees expressing the full potential of the site, not those that have been subjected to damage, injury or disease. A tree with a broken top obviously is not as tall as it would have been without the breakage on any given site, and using such a tree would falsely indicate a lower site index than the site is capable of producing. Therefore, in selecting which trees to measure for obtaining site index, care must be taken to avoid those trees that misrepresent the true quality of a site. A site tree must meet all three of the following criteria: 1. It must be in the Dominant or Codominant crown class. 2. It must be free from past disturbance, injury or damage. A site index tree cannot have broken tops, scarred trunks, damaged or compacted root systems, insect injury and so on. These occurrences reduce a tree’s health and vigor so that it does not express the site’s full potential for growth. 3. It must be free from past suppression. Some trees can tolerate heavy shade when they are young, and then put on rapid growth when the canopy opens up, allowing full sunlight to shine on them. This pattern is not acceptable for a site index tree, since light availability dominated the tree’s ability to grow. The tree was not expressing the site’s full potential when shaded. Dominant and codominant trees should be examined carefully for outward signs of injury or defect before measuring for site index. In addition, each increment core sample used to estimate age should be checked for evidence of past suppression or injury. Dramatic shifts in the ring sizes, presence of rot, charcoal, and other abnormalities can indicate previous impacts (Figure 6.6). Figure 6.6. An increment core sample showing evidence of past suppression. “Normal” growth rings display a gradual decrease in ring width from pith to bark, as the wood is laid down over a larger and larger diameter. Small widths followed by large ring widths indicate a sudden shift in growing conditions. The following are illustrations of trees not suitable for site index determination, due to defect, injury or past suppression (Figure 6.7). Figure 6.7 Trees with abnormal growth or injuries do not reflect the full potential for growth on the site. From left: a tree with conks indicating internal rot; a tree with a deformed top indicating damage; a forked tree; a tree with a trunk scar indicating damage.	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/06%3A_Site_Quality/06.3%3A_How_to_Use_Site_Index_Curves.txt
6.5 Field Technique Tips for Determining Site Index In determining site index, we integrate the technician’s abilities to identify crown classes, measure tree height and estimate tree age. This is one of the few cases in which we choose a biased sample of trees to measure. We want to see how trees that were relatively unimpeded by neighboring trees or disturbances can grow on this site. We are trying to use the trees as an indication of the site. The objective is very different than a typical sampling scheme to get an average measure of stand volume, size or growth rates. Therefore, the sampling method is different as well. 1. Select trees to measure. The number of trees to measure will depend upon how variable the stand is, and the degree of accuracy desired. The greater the variability in size and species on the site, the larger the sample size needed to get an accurate estimate of site quality for each species present. For species that are grouped into Site Classes, a relative ranking is the objective, so a large sample size is not required. Criteria for selection: • Dominant or codominant crown class. Choose trees whose crowns are receiving full sunlight. • Check the outside—Free from past disturbance. Check all sides of the tree for signs of insect galls, conks, witches brooms, basal or trunk scars, breakage, etc. Check around the base of the tree for signs of root disease (e.g. Phaellus spp. or Heterobasidium spp.). There may be instances in which a stand severely hit by an ice or windstorm will have very few suitable site index trees to choose from. • Check the insideFree from past suppression. This may be difficult to assess on larger trees without looking at the increment core sample. Some people will core the tree first to make sure it is a usable site index tree before measuring the height to save time. On smaller trees, the distance between whorls can indicate general growth rate trends. 2. Extract a clean, intact core sample to estimate age. • Check core for evidence of rot, charcoal, past suppression or drought. • Make sure you can read the age – use a magnifying glass or hand lens on trees with tight rings. Look carefully at the regions indicating the center of the tree. Core samples more than a few of years from the pith are not reliable. Count the rings twice. 3. Measure total height. Obviously, this is a critical measurement. Measure your distance from the tree – do not pace. Make sure you can see the top. From a perspective that allows a clear view of the crown, look for evidence of breakage – flat tops, longer than expected side branches, etc. Also look for sucker limbs and forking in the crown. 4. Record your measurements. Record each tree as a pair of measurements – height and age. The two measurements are used together to obtain site index, so keep them as a pair. Always record breast height age in the field. This number can later be adjusted to total age by adding the number of years commonly needed for that species to reach breast height. This will vary by species and region. Typically, it is 4-8 years for most low elevation conifers. 06.6:. Determining Site Index from Field Measurements 6.6. Determining Site Index from Field Measurements Once height and age measurements are obtained for all site trees, site index can be determined. 1. Produce height and age measurements for suitable site index trees following the protocol from Section 6.5. Data for two Douglas-fir trees are listed below in Table 6.1. Table 6.1. Field Data for determining King’s site index for Douglas-fir. Tree Total Tree Height (ft.) Breast Ht. Age* (yrs.) Site Index (ft.) A 114 45 123 B 135 68 113 * King’s site index uses breast height age (from a core sample taken at dbh). 2. Plot each tree on the site index graph using the height and age as measured in the field. 3. Follow the curves forward or backward to the base age (50 years). In this case, we will “grow” Tree A to age 50, following the trends indicated by the nearest curves as we do so (Figure 6.6). Figure 6.6. Tree A is “grown” from 45 years to 50 years. Estimated height at 50 years is ≈ 123’. Site Index for Tree A is 123. Tree B is traced back to 50 years. Estimated height at 50 years is ≈ 113’. Site Index for Tree B is 113. Thus two trees of unequal age can be compared on a relative basis to indicate how capable the forest site is of growing Douglas-fir trees. (Adapted from Smith et al. 1997.) 4. Determine the height of Tree A at age 50. This height, 123 feet, is the Site Index for that tree. 5. Repeat this for each site tree. When a site index value for each tree has been determined, an average can be calculated for the stand. The average for our two trees is 118 feet, which puts our trees on low site Class II land. It is not correct to calculate the average age and average height of the measured trees, and plot that to determine site index.	textbooks/bio/Botany/Forest_Measurements_-_An_Applied_Approach_(DeYoung)/06%3A_Site_Quality/06.5%3A_Field_Technique_Tips_for_Determining_Site_Index.txt
Welcome to Plant Biology where all life is dependent on! This book’s main focus is learning plant biology. This diverse group of kingdom can go back to 470 million years ago. Green plants synthesize their own food using their special organelles, namely chloroplasts. Green plants demonstrate features including metabolism, $\mathrm{DNA}$, emergent properties, regulation, and interaction with environment. Plant growth is a genetically programmed process and is influenced by environment. There is a relationship between structure and function. Moreover, plants have large central vacuoles and cell walls made of cellulose and pectin. There are two phases of life in plants including diploid (2n) sporophyte and haploid (n) gametophyte. $1$. Student Learning Outcomes (SLOs) • SLO 01.01: Apply the best practices for learning and mastering plant biology. • SLO 01.02: Describe the reasons we study plants. • SLO 01.03: Distinguish between heterotrophs and autotrophs. • SLO 01.04: Define the 24 hour-(= 4.6 billion years) clock of the Earth. • SLO 01.05: Identify given plant species with their scientific names based on their key features. • SLO 01.06: Explain the differences between monocots and dicots classes. • SLO 01.07: Explain the differences between annuals and perennials. $4$. Test Your Knowledge • Assessment 01.3.1: Provide examples of plant species that provide medicines. • Assessment 01.3.2: What do plants, algae, and cyanobacteria have in common? • Assessment 01.3.3: Explain the suggestion you would give to feed the 10 billion world population by 2050. • Assessment 01.3.4: Explain the importance of green plants and why life is dependent on them. $6$. 1. Aloe vera, Neem, Garlic, Nettle, and Lemon balm 2. They all can perform photosynthesis 3. We will need to improve food production $\sim 60 \%$ while increasing sustainability 4. Plants and animals are dependent on each other, while both photosynthesis and sun energy makes life possible 1.02: Plant Cells and Tissues As the building block of living organisms, plant cells were discovered in 1665 by Robert Hooke. Like animals, plants are made of millions of complex eukaryotic cells. Cells make up tissue, and tissue makes up organs, including root, stem, and leaves. Specifically, roots help anchor plants in soil and take up nutrients and water from the soil. The stem is the pathway between the root and leaves, and supports leaves and flowers. Leaves are the main organs that carry out photosynthesis and respiration reactions. A meristem is the location where the plant grows and differentiates into mature tissue afterward. Therefore, meristems have continuously dividing unspecialized cells. Meristems can be classified under two main groups: 1. Apical Meristems (primary growth = length increase via shoot and root tip) [Protoderm / Ground Meristem / Procambium] 2. Lateral Meristems (secondary growth = girth increase) [Vascular cambium / Cork cambium] Finally, tissue growth is very important for root and shoot growth in plants and therefore plays a critical role in agricultural yield. $1$. Student Learning Outcomes (SLOs) • SLO 02.01: Apply the best practices for learning and mastering plant cell • SLO 02.02: Identify all organelles (15) of plant cells and their function • SLO 02.03: Distinguish between plant, animal, and bacteria cell • SLO 02.04: Distinguish different plastids such as chloroplasts and amyloplasts • SLO 02.05: Identify given plant species with their scientific names based on their key features • SLO 02.06: Explain the differences between various plant cell types • SLO 02.07: Define the “Cell Theory” $4$. Test Your Knowledge • Assessment 02.3.1: Provide the name of organelles plant cells have but animal cells not. • Assessment 02.3.2: What animal cell part has similarities to plant cell plasmodesmata? • Assessment 02.3.3: State the differences between primary and secondary growth. • Assessment 02.3.4: What are plant cell walls made of? $6$. Check Your Answers 1. Cell walls, chloroplasts, and central vacuole 2. Gap junctions 3. While primary growth is in lengths (elongates), secondary growth is in girth (thickens) 4. Cellulose and pectin	textbooks/bio/Botany/From_Growing_to_Biology%3A_Plants_(Hacisalihoglu)/01%3A_Chapters/1.01%3A_Plantae_Kingdom.txt
Due to the fact that they are underground, roots don’t necessarily get as much appreciation. Root is the underground part of the plant body that provides anchorage and absorption of water and mineral nutrients. Roots originate from the “radicle” part of an embryo in seed. Epidermis is the outermost layer of the root, which is followed by cortex for storage and endodermis. Underneath the endodermis, the next layer is pericycle, which produces lateral roots. The next layer is the vascular tissue, which includes xylem and phloem as innermost parts of the root system. The three regions of the root tip are the meristematic region, the elongation region, and the maturation region. The maturation region is marked with root hairs, whereas the meristematic region is protected by a root cap. Finally, root tips continuously grow and push through soil throughout plant life. Let’s get to the root of plant root system. $1$. Student Learning Outcomes (SLOs) • SLO 03.01: Apply the best practices for learning root system • SLO 03.02: Draw and label three major root systems of Angiosperms • SLO 03.03: Compare the roots of monocots and dicots • SLO 03.04: Explain the differences between apoplastic and symplastic pathways • SLO 03.05: Identify given plant species with their scientific names based on their key features • SLO 03.06: Explain where lateral roots originate • SLO 03.07: Explain how rhizobia works with select plants for providing nitrogen $4$. Test Your Knowledge • Assessment 03.3.1: Provide specific examples of the best plant growth method in Mars • Assessment 03.3.2: TRUE or FALSE-- Hydroponics increases crop yield 5-fold? • Assessment 03.3.3: Which plant growth method is more sustainable? • Assessment 03.3.4: State the differences between soil and hydroponics. $6$. Check Your Answers 1. Although this is still unknown and under research, this may happen in the near future 2. TRUE 3. The growing method that could use more renewable sources together with high yields and environmentally friendly 4. With hydroponics, growers can save water as well as control everything. On the other hand, soil is very important and has much less initial costs 1.04: Shoot System What is the function of plant shoot system? Plant shoot system of Angiosperms (a.k.a., flowering plants) are composed of stem and stem-attached organs such as leaves, buds, and flowers. The stem of a plant is the primary axis that supports plant leaves and reproductive structures. Furthermore, the stem provides water and minerals to above-ground parts, whereas roots transport photosynthates from source to sink tissues. 1. Primary Xylem [has vessels and tracheids]: produced by procambium then protoxylem and then metaxylem. Transports water and solutes. Their cells are non-living. 2. Primary Phloem [has sieve tube elements and companion cells]: produced by procambium. Transports sugars, hormones, and aminoacids from source to sink. Their cells have nucleus. Leaves are the greenish organ that are considered plant’s primary food manufacturing location. Leaves are very diverse in terms of their morphology and architecture. Moreover, leaves are used often in plant identification because of their unique patterns of leaf shape, color, and architectural patterns. $1$. Student Learning Outcomes (SLOs) • SLO 04.01: Apply the best practices for learning plant shoot system • SLO 04.02: List basic function of shoot, stem, and leaf • SLO 04.03: Explain why leaves change color • SLO 04.04: Define shoot apical dominance in plants • SLO 04.05: Identify given plant species with their scientific names based on their key features • SLO 04.06: 9. List six major groups of modified stem and modified leaves with examples • SLO 04.07: Draw and label C3, C4, and CAM leaves according to the photosynthesis type $4$. Test Your Knowledge • Assessment 04.3.1: TRUE or FALSE: The biggest leaf known belongs to Raffia palm. • Assessment 04.3.2: TRUE or FALSE: Carnivorous plants have modified leaves for capturing small animals to digest and get N. • Assessment 04.3.3: Compare and contrast monocot leaves and dicot leaves. • Assessment 04.3.4: Explain how p-proteins protect phloem as damage control. $6$. Check Your Answers 1. TRUE 2. TRUE 3. While monocot leaves have parallel arrangement, dicot leaves have web-like arrangement 4. P proteins are also known as “phloem-specific proteins” seal off by plugging damaged sieve element location 1.05: Systematics How can we best conserve plant biodiversity? Systematics, a combination of taxonomy and phylogenetics, is critically important in plant biology. It helps us to categorize plants and understand natural diversity. Each plant species has a common name and a scientific name. Scientific names are in Latin and binomial, as follows: Common name: Pea Scientific name: Pisum sativum Family: Fabaceae Class: Dicot Varieties: garden peas, snow peas, snap peas Systematics uses cladograms (mostly morphological characteristics) and phylogenetic trees (morphological plus genetic characteristics). Phylogenetic trees (a.k.a., evolutionary trees) are used in comparing plant species in evolutionary time and distance. Finally, two plant species are considered more related if the phylogenetic tree shows a more recent ancestor. $1$. Student Learning Outcomes (SLOs) • SLO 05.01: Apply the best practices for learning systematics • SLO 05.02: Explain binomial system • SLO 05.03: Distinguish between phylogenetic trees and cladograms • SLO 05.04: Distinguish between homologous vs analogous characters • SLO 05.05: Identify given plant species with their scientific names based on their key features • SLO 05.06: Explain the differences between ancestral and derived features • SLO 05.07: Diagram a typical plant cladogram $4$. Test Your Knowledge • Assessment 05.3.1: TRUE or FALSE: Carl Linnaeus first proposed the systematics. • Assessment 05.3.2: TRUE or FALSE: Clades arose before are named “basal”. • Assessment 05.3.3: Provide similarities between cladogram and phylogenetic tree. • Assessment 05.3.4: List specific characteristics of model plant Arabidopsis thaliana for plant biology. $6$. Check Your Answers 1. TRUE 2. TRUE 3. They are used interchangeably. While phylogenetic tree’s branch length may be considered important indicator of time / change, cladograms missing this 4. Short generation time. Small genome and mapping completed. Availability of many variants. Easy to grow in the lab	textbooks/bio/Botany/From_Growing_to_Biology%3A_Plants_(Hacisalihoglu)/01%3A_Chapters/1.03%3A_Root_System.txt
How would algae contribute to the future of food? There is an increasing interest in seaweed, a common name for macro marine algae such as brown, red, and green algae. Moreover, algae may be able to help to future food security since they are rich in nutrients as well as protein content. They could be used in many human diet areas including snacks, sushi, salads, soups, and vegetarian protein source. One example is red algae species Porphyra yezoensis that is commonly used in sushi rolling and contains about 47% protein content. $1$. Student Learning Outcomes (SLOs) • SLO 06.01: Apply the best practices for learning algae • SLO 06.02: Describe the main characteristics of Kingdom Protista • SLO 06.03: Distinguish between macro and micro algae • SLO 06.04: Distinguish between Chlamydomonas and Euglena • SLO 06.05: Identify given plant species with their scientific names based on their key features • SLO 06.06: Describe the main characteristics of heterotrophic fungi-like protists • SLO 06.07: Provide examples to phylums of Chloro-, Phaeo-, and Rhodo-phyta $4$. Test Your Knowledge • Assessment 1: TRUE or FALSE: The part that attach algae to its substrate is called “holdfast.” • Assessment 2: TRUE or FALSE: Gel-like lab product that originally comes from red algae is called “agar.” • Assessment 3: Provide evidence that green algae is the ancestor of green plants. • Assessment 4: List the potential of algae as future super-food. $6$. Check Your Answers 1. TRUE 2. TRUE 3. This can be explained by the similarities between green algae and plants 4. Algae definitely has a great potential for future food because of many reasons including high content of protein, minerals, vitamins, as well as its resilience to environmental stress 1.07: Bryophytes Bryophytes are low key plants with one major requirement, which is water due to their non-vascular anatomy. In return, bryophytes play an important role in soil biodiversity including erosion prevention and water absorption from heavy rainfalls. By going back to over 450 million years, bryophytes are considered the most ancient Plantae group with no true roots. Furthermore, bryophytes are considered great pioneer plant species together with lichens. $1$. Student Learning Outcomes (SLOs) • SLO 07.01: Apply the best practices for learning bryophytes • SLO 07.02: Describe the characteristics of phylum Marchantiophyta • SLO 07.03: Describe the characteristics of phylum Anthocerotophyta • SLO 07.04: Describe the characteristics of phylum Bryophyta • SLO 07.05: Identify given plant species with their scientific names based on their key features • SLO 07.06: Explain the differences between archegonium and antheridium • SLO 07.07: Identify gemma cups $4$. Test Your Knowledge • Assessment 1: TRUE or FALSE: Bryophytes have alternation of generations. • Assessment 2: TRUE or FALSE: Bryophytes are small plants with 1-2cm height. • Assessment 3: TRUE or FALSE: Asexual reproduction is carried out by gemmae cups. • Assessment 4: TRUE or FALSE: Mosses can grow in acidic and high salinity soils. 1. TRUE 2. TRUE 3. TRUE 4. TRUE 1.08: Seedless Plants Before seedless citrus or grapes, there were seedless vascular plants existed over 360 million years ago. They use spores for reproduction instead of cones or flowers. For example, whisk ferns (Psilotum nudum) are seedless, rootless, leafless ancient vascular plants that carry out photosynthesis via their green stems. Ferns are perennial seedless vascular plants and good at purifying air around them as well as accumulating heavy metals. Ferns are seedless but they do have sexual reproduction using underside sori spots that are packages of spores. On behalf of flower, they use a large heart-shaped gametophyte with eggs and sperm. $1$. Student Learning Outcomes (SLOs) • SLO 08.01: Apply the best practices for learning seedless vascular plants • SLO 08.02: Describe the characteristics of phylum Lycophyta • SLO 08.03: Describe the characteristics of phylum Sphenophyta • SLO 08.04: Describe the characteristics of phylum Psilophyta • SLO 08.05: Describe the characteristics of phylum Pterophyta • SLO 08.06: Identify given plant species with their scientific names based on their key features • SLO 08.07: Explain how seedless plants reproduce $4$. Test Your Knowledge • Assessment 1: TRUE or FALSE: Leaves of lycophytes are microphyll. • Assessment 2: TRUE or FALSE: The fern sporangia cluster is named sorus. • Assessment 3: Explain the usage of ferns for phytoremediation. • Assessment 4: TRUE or FALSE: There are shade-loving tree ferns can grow 30 ft. tall and live 500 years in Australia. $6$. Check Your Answers 1. TRUE 2. TRUE 3. It has been shown that certain fern varieties can remove heavy metals from soil such as arsenic 4. TRUE	textbooks/bio/Botany/From_Growing_to_Biology%3A_Plants_(Hacisalihoglu)/01%3A_Chapters/1.06%3A_Algae_%28Protista_Phylum%29.txt
Gymnosperms are one of the ancient plant groups with seed production. They are a group of vascular plants with naked (without ovary) seeds. Gymnospems are also heterosporous. Furthermore, gymnosperms produce two different types of cones, namely, large female cones and small male cones. Four groups of gymnosperms are known: 1. CYCADOPHYTA: 100 cycad species (cycad, sago palm) 2. GINKGOPHYTA: 1 plant species (ginkgo) 3. GNETOPHYTA: e.g., ephedra 4. CONIFEROPHYTA: 500 species (pine, fir, cedar, juniper, redwoods) They date back to 250 million years ago. Coniferophyta consists of largest, tallest, and oldest living trees. $1$. Student Learning Outcomes (SL • SLO 09.01: Apply the best practices for learning Gymnosperms • SLO 09.02: Describe the characteristics of phylum Coniferoophyta • SLO 09.03: Describe the characteristics of phylum Cycadophyta • SLO 09.04: Describe the characteristics of phylum Ginkgophyta • SLO 09.05: Identify given plant species with their scientific names based on their key features • SLO 09.06: Describe the characteristics of phylum Gnetophyta • SLO 09.07: Explain the differences between spores and seeds? $4$. Test Your Knowledge • Assessment 1: TRUE or FALSE: Cycads are diecious plants. • Assessment 2: TRUE or FALSE: Discovery of seed increased success of land plants. • Assessment 3: Provide specific function for sunken stomata of pine needles. • Assessment 4: TRUE or FALSE: Most common gymnosperm phylum is conifers. $6$. 1. TRUE 2. TRUE 3. Sunken stomata can help with plant water conservation in pine trees 4. TRUE 1.10: Flowers Fruits and Seeds (Flowering Angiosperms Dating back to 140 million years ago, flowering plants (angiosperms) evolved and make 80% of today’s plants including Arabidopsis. Flowers are the colorful reproductive components of angiosperms (flowering plants). Complete flowers consist of four parts, namely: sepals, petals, stamens, and carpel(s). Pollination is the movement of pollen from stamen to stigma. If pollination occurs with the plant’s own stigma, it is called self-pollination. On the other hand, if it occurs with a different plant stigma, it is called cross pollination. Pollen grains are male gametophytes, while the embryo sac is the female gametophyte. Pollinators most commonly used are insects, birds, and the wind. Rafflesia arnoldii, as well as A. titanium (Titan arum), are considered the largest single flowers found in any plants. $1$. Student Learning Outcomes (SLOs) • SLO 10.01: Apply the best practices for learning angiosperms • SLO 10.02: Describe the characteristics of phylum Anthophyta • SLO 10.03: Distinguish between monocot and edicot (dicot) classes • SLO 10.04: Explain how annuals, biennials, and perennials differ • SLO 10.05: Identify given plant species with their scientific names based on their key features • SLO 10.06: Explain the differences between monocots and dicots classes • SLO 10.07: Distinguish between ovary positions of flowers $4$. Test Your Knowledge • Assessment 1: TRUE or FALSE: Sunflowers moves their head from east to west daily to point to the sun. • Assessment 2: Compare and contrast pollination and fertilization. • Assessment 3: Compare and contrast the gametophytes of male and female in angiosperms. • Assessment 4: Compare and contrast the flowers of monocots and dicots. $6$. 1. TRUE 2. While fertilization is a cellular process of fusion of gametes, pollination is limited with transfer of pollen to stigma only 3. While male gametophyte has 3 cells, female gametophyte has 7 cells 4. While monocot flowers parts are in 3s, dicot flower parts are in 4s / 5s 1.11: Plant Hormones Plant growth regulators (phytohormones) are small organic molecules that occur naturally in plants. Phytohormones can regulate plant physiological growth processes such as flowering, germination, stem elongation, seed dormancy, fruit ripening, and gene expression. There are several phytohormones such as gibberellic acid ($\mathrm{GA}_{3}$) can increase stem growth parameters. Moreover, ethylene can affect fruit ripening in bananas. $1$. Student Learning Outcomes (SLOs) • SLO 11.01: Apply the best practices for learning phytohormones • SLO 11.02: Describe the characteristics of Auxins and Cytokinins • SLO 11.03: Describe the characteristics of Gibberellins and ABA • SLO 11.04: Describe the characteristics of Ethylene and Salicylic acid • SLO 11.05: Identify given plant species with their scientific names based on their key features • SLO 11.06: Explain the differences between natural and synthetic phytohormones • SLO 11.07: Explain the reason why ABA is named as a stress hormone $4$. Test Your Knowledge • Assessment 11.3.1: TRUE or FALSE: Phytohormones affect plant development process [growth + differentiation] • Assessment 11.3.2: TRUE or FALSE: Brassinosteroids act locally. • Assessment 11.3.3: Define seed dormancy and provide a specific function for plants. • Assessment 11.3.4: TRUE or FALSE: GAs promote bolting (flowering and flower stalk) $6$. Check Your Answers 1. TRUE 2. TRUE 3. Seed dormancy causes not germination of viable seeds even under favorable conditions. Seed dormancy is survival mechanism of controlling germination. 4. TRUE	textbooks/bio/Botany/From_Growing_to_Biology%3A_Plants_(Hacisalihoglu)/01%3A_Chapters/1.09%3A_Gymnosperms_%28Cone_Bearing%29.txt
Phenotype such as plant yield is a combination of both genotype and environmental factors. Genetics help plant biologists to understand how it affects plant life and subsequently how to understand plant yield and quality. Furthermore, plant germplasm banks are critically important for increasing diversity and identifying and mapping superior traits in the fight with global climate changes. Finally, developing new plant varieties will help the feeding increasing world population (estimated 10 billion) by the year 2050. $1$. Student Learning Outcomes (SLOs) • SLO 12.01: Apply the best practices for learning genetics • SLO 12.02: 2. Explain how Mendel’s particulate mechanisms differed from blending hypothesis • SLO 12.03: 3. Explain homozygous, heterozygous, phenotype, genotype, dominant, recessive, monohybrid, dihybrid, incomplete dominance, and co-dominance • SLO 12.04: 4. Describe polygenic inheritance and give an example from plants • SLO 12.05: Identify given plant species with their scientific names based on their key features • SLO 12.06: 5. Explain linked genes and gene mapping in plants • SLO 12.07: 1. Draw and label 10 steps of meiosis $4$. Test Your Knowledge • Assessment 12.3.1: TRUE or FALSE: Mutations are changes in the DNA-sequence. • Assessment 12.3.2: TRUE or FALSE: Linked genes are on the same chromosome therefore inherited together. • Assessment 12.3.3: TRUE or FALSE: Snapdragon flower color shows incomplete dominance. • Assessment 12.3.4: TRUE or FALSE: “Red-and-white Camellia flower” is a good example of plant co-dominance. ($\text{White } \times \text{ Red } \rightarrow \mathrm{~F}1: \text{ White & Red}$) 1. TRUE 2. TRUE 3. TRUE 4. TRUE 1.13: Plant Nutrition Nutrition has a critical impact from soil to plants to people levels. Essential nutrients are required by life but cannot be synthesized by the organism. For plants, essential mineral nutrients can be divided into two distinct groups, and they are all required for growth and production: 1. Macronutrients (needed in larger amounts): nitrogen ($\mathrm{N}$), phosphorus ($\mathrm{P}$), potassium ($\mathrm{K}$), calcium ($\mathrm{Ca}$), magnesium ($\mathrm{Mg}$), and sulfur ($\mathrm{S}$) 2. Micronutrients (trace elements, needed in smaller amounts): zinc ($\mathrm{Zn}$), copper ($\mathrm{Cu}$), iron ($\mathrm{Fe}$), chloride ($\mathrm{Cl}$), manganese ($\mathrm{Mn}$), molybdenum ($\mathrm{Mo}$), boron ($\mathrm{B}$), nickel ($\mathrm{Ni}$), selenium ($\mathrm{Se}$), iodine ($\mathrm{I}$) Climbing of world population to 10 billion by 2050 will clearly require not only more food production but also higher enhanced efficiency of nutrient usage since they are critical limiting factors. $1$. Student Learning Outcomes (SLOs) • SLO 13.01: Apply the best practices for learning plant mineral nutrition • SLO 13.02: Describe the characteristics of $\mathrm{N}$ (nitrogen), $\mathrm{P}$ (phosphorus), and $\mathrm{K}$ (potassium) • SLO 13.03: Describe the importance of zinc ($\mathrm{Zn}$) in plants • SLO 13.04: Explain some of the common symptoms of nutrient deficiencies • SLO 13.05: Identify given plant species with their scientific names based on their key features • SLO 13.06: Define soil components • SLO 13.07: Describe mycorrhizae and Rhizobia for plant P and N $4$. Test Your Knowledge • Assessment 1: TRUE or FALSE: Essential nutrients are the most important for the plant life cycle. • Assessment 2: NAME THE DEFICIENCY: Old leaf chlorosis, necrotic spots, stunted plants, especially in maize, sorghum, beans, potatoes • Assessment 3: NAME THE DEFICIENCY: Old leaf yellowing, light-green whole plant, most common nutrient deficiency. • Assessment 4: NAME THE DEFICIENCY: Burnt leaf tips, purple/dark green old leaf, second most common deficiency. $6$. Check Your Answers 1. TRUE 2. $\mathrm{Zn}$ (zinc deficiency) 3. $\mathrm{N}$ (nitrogen deficiency) 4. $\mathrm{P}$ (phosphorus deficiency)	textbooks/bio/Botany/From_Growing_to_Biology%3A_Plants_(Hacisalihoglu)/01%3A_Chapters/1.12%3A_Genetics.txt
Aquaporins, water channels in plant cell plasma membranes, play an important role in plant survival and growth. In return, they can be important players from increased temperatures to photosynthesis in plant life. Moreover, solutes are also transported via plasma membranes and critical to plant growth and health. In recent years, substantial research has been carried out to elucidate highly complex transport systems of nutrients such as zinc ($\mathrm{Zn}$), iron ($\mathrm{Fe}$), and nitrogen ($\mathrm{N}$). Furthermore, osmosis and diffusion help plant water and solute uptake, respectively. $1$. Student Learning Outcomes (SLOs) • SLO 14.01: Apply the best practices for learning plant transport • SLO 14.02: Describe the components of water potential • SLO 14.03: Describe the characteristics of passive and active transport • SLO 14.04: Compare plasmolyzed and turgid plant cells • SLO 14.05: Identify given plant species with their scientific names based on their key features • SLO 14.06: Explain the differences between hypertonic and hypotonic solutions • SLO 14.07: Explain the differences between diffusion and osmosis $4$. Test Your Knowledge • Assessment 1: TRUE or FALSE: Xylem is dead at maturity while phloem is alive. • Assessment.2: TRUE or FALSE: In phloem translocation, sugars move to organs that most needed. • Assessment.3: Compare and contrast osmosis, diffusion, and active transport. • Assessment 4: TRUE or FALSE: Guttation is loss of liquid droplets that contain substances [at night] while transpiration is loss of vapors of pure water [during the day]. $6$. Check Your Answers 1. TRUE 2. TRUE 3. While all three are movement of particles, diffusion and osmosis are passive transport only 4. TRUE 1.15: Secondary Growth Cambium growth layers are the main generators of dicot new wood cells (xylem) and inner bark tissues (phloem) in perennial plant species. Secondary growth is caused by secondary tissues in woody dicotyoledon and gymnosperm plant species getting wider stems, branches, and roots. Furthermore, almost no secondary growth is observed in herbaceous plants and most monocotyledons. Secondary growth, in general, is a result of two lateral meristems (cambiums): 1. Vascular cambium: produces secondary xylem and secondary phloem 2. Cork cambium: produces periderm (substitutes epidermis) Perennial trees can live for centuries including bristle cone pines, cypresses, and gingkoes. $1$. Student Learning Outcomes (SLOs) • SLO 15.01: Apply the best practices for learning secondary growth in select plants • SLO 15.02: Define vascular cambium and secondary growth • SLO 15.03: Explain what are tree rings, wood, and bark • SLO 15.04: Describe the characteristics of bark and its components • SLO 15.05: Identify given plant species with their scientific names based on their key features • SLO 15.06: Explain how to determine the age of a tree • SLO 15.07: Describe dendrochronology and its importance $4$. Test Your Knowledge • Assessment 15.3.1: TRUE or FALSE: World’s largest tree is General Sherman tree (Sequoia giganteum) that is located in California (H: 84m, W:30m). • Assessment 15.3.2: TRUE or FALSE: World’s tallest tree is Hyperion (Sequoia sempervirens) that is located in California (H: 116m). • Assessment 15.3.3: TRUE or FALSE: Sugar maple sap is used to make syrup. • Assessment 15.3.4: TRUE or FALSE: Briar wood is resistant to fire (used in pipes) 1. TRUE 2. TRUE 3. TRUE 4. TRUE 1.16: Photosynthesis (PS) Photosynthesis (PS) means oxygen production to sustain life on planet Earth. Moreover, PS is critically important for food crop yield and therefore future food security. Sunlight is the major source of PS together with chlorophyll in the food making process. Plants absorb carbondioxide ($\mathrm{CO}_{2}$) from atmosphere for PS at the optimal temperatures. Lastly, rubisco is both the most abundant enzyme in biosphere and carbon fixing enzyme to produce food. However, some plant species use another more PS-efficient enzyme namely PEP carboxylase via separating light reactions and Calvin cycle. For example C4 plants such as maize and CAM plants such as pineapples separates them in different tissues and different timing, respectively. Lastly, this process helps C4 and CAM plant species to minimize photorespiration usage of $\mathrm{O}_{2}$ instead of $\mathrm{CO}_{2}$. $1$. Student Learning Outcomes (SLOs) • SLO 16.01: Apply the best practices for learning photosynthesis • SLO 16.02: Describe the relationship between light and photosynthesis • SLO 16.03: Describe the relationship between chlorophyll and photosynthesis • SLO 16.04: Describe the relationship between $\mathrm{CO}_{2}$ and photosynthesis • SLO 16.05: Identify given plant species with their scientific names based on their key features • SLO 16.06: Explain the differences between C3, C4, and CAM photosynthesis • SLO 16.07: Explain the differences between light reactions and Calvin cycle? $4$. Test Your Knowledge • Assessment 1: TRUE or FALSE: Photosynthesis is the reverse of cellular respiration. • Assessment 2: TRUE or FALSE: Green plants, algae, cyanobacteria, some protists, and few animals can perform photosynthesis. • Assessment 3: TRUE or FALSE: While phytoplankton produces $70 \% \mathrm{~O}_{2}$, land plants produce $30 \% \mathrm{~O}_{2}$ of the world. • Assessment 4: TRUE or FALSE: Marine plants get some light from hydrothermal vents for their photosynthesis. 1. TRUE 2. TRUE 3. TRUE 4. TRUE	textbooks/bio/Botany/From_Growing_to_Biology%3A_Plants_(Hacisalihoglu)/01%3A_Chapters/1.14%3A_Water_and_Solute_Transport.txt
In our planet Earth’s 4.6 billion years of age, oxygen became available about 2.3 billion years ago. Therefore, there must have been fermentation used by early bacteria species since there was no oxygen availability. $\mathrm{ATP}$ (adenosine triphosphate) is the main energy resource of cells and product of cellular respiration and fermentation. Lastly, it will be critically important to study plant respiration since it may be enhanced under increasing carbondioxide levels and temperatures. $1$. Student Learning Outcomes (SLOs) • SLO 17.01: Apply the best practices for learning cellular respiration • SLO 17.02: Describe the characteristics of three main stages of cellular respiration • SLO 17.03: Explain the stage of cellular respiration that produces the most $\mathrm{ATP}$ • SLO 17.04: Describe the characteristics of mitochondria • SLO 17.05: Identify given plant species with their scientific names based on their key features • SLO 17.06: Explain the differences between cellular respiration and fermentation • SLO 17.07: Explain the differences between substrate level and oxidative phosphorylation $4$. Test Your Knowledge • Assessment 1: TRUE or FALSE: Mitochondria exist in all cells and originated by a bacteria engulfed by eukaryotes • Assessment 2: TRUE or FALSE: Plants also do respiration using glycolysis, Krebs cycle, oxidative phosphorylation mostly during the night as well as photo-respiration • Assessment 3: TRUE or FALSE: While anaerobic respiration produces $2 \mathrm{~ATP}$, aerobic respiration produces up to $32 \mathrm{~ATP}$ • Assessment.4: TRUE or FALSE: Lenticels pores in the stem / bark of trees involve gas exchange extensively 1. TRUE 2. TRUE 3. TRUE 4. TRUE 1.18: Indoor Vertical Farming and Cultivating Plants in Microgravity Is vertical farming future of sustainable crop production especially under suboptimal environment conditions such as drought and water shortage? 60% of US tomatoes and 35% of US total fresh produce are imported with considerable shipping carbon print. Vertical farms are automated / partially automated indoor hydroponic / aeroponic farming factories under LED lights. A variety of fresh plants are currently in vertical farms including lettuce, microgreens, leafy greens, tomato, cucumber, and pea shoots year around with zero pesticides / harmful chemicals. Moreover, plant growing in vertical farms uses no soil, sunlight and therefore not affected by climate stress conditions. Vertical farms may be the future of sustainable plant growing since land and water resources are getting more and more scarce to maximize yield as well as flavor. $1$. Student Learning Outcomes (SLOs) • SLO 18.01: Apply the best practices for mastering cultivating plants in microgravity • SLO 18.02: Assess the strategy of growing plants in simulated Martian soil mimics Mars • SLO 18.03: Distinguish between plant-available vs accessible format of nutrients • SLO 18.04: Assess the strategy of employing specific bacteria or fungi that are beneficial to plant growth in a Martian soil environment • SLO 18.05: Explain how vertical farming may cause majority of land and water use. • SLO 18.06: Assess the strategy of employing solar power for vertical farms • SLO 18.07: Explain the benefits of vertical farming $3$. Test Your Knowledge • Assessment 1: TRUE or FALSE: World food supply needs to increase 60% to feed 10 billion people by the year 2050. • Assessment 2: TRUE or FALSE: Hydroponics system uses 90% less water than soil growing. • Assessment 3: TRUE or FALSE: Hydroponics can increase tomato yield almost $6\times$. • Assessment 4: TRUE or FALSE: Microgreens (collard, arugula, basil, celery, lettuce, spinach) are nutrient packed that are $\sim 100\times$ more nutritious than regular greens. 1. TRUE 2. TRUE 3. TRUE 4. TRUE	textbooks/bio/Botany/From_Growing_to_Biology%3A_Plants_(Hacisalihoglu)/01%3A_Chapters/1.17%3A_Cellular_Respiration.txt
Superfoods are getting more and more popular due to their superior nutrient-rich characteristics. Many food plants including vegetables (e.g., lettuce, spinach, kale, cabbage), berries (e.g., blueberries), beans, nuts, and whole grains are rich in mineral nutrients and vitamins for human diet. Therefore, planting home gardens, renting garden plots, and visiting local farmers’ markets for locally grown are becoming popular worldwide. On the other hand, plant-based meat (beef, chicken, or fish alternatives) is also gaining popularity (estimated \$74 billion economy) by large restaurant chains worldwide. Lastly, there are also other future food alternatives including sea veggies such as sea lettuce, nori, and wakame with protein and nutritional content. In return, these new protein sources may be the answer for sustainable and eco-friendly protein supply for increasing world population. $1$. Student Learning Outcomes (SLOs) • SLO 19.01: Apply the best practices for learning plant-based nutrition • SLO 19.02: Describe the characteristics of plant-based proteins • SLO 19.03: Describe the characteristics of health benefits of human nutrition from plants • SLO 19.04: Describe the essential nutrients for human diet • SLO 19.05: Identify given plant species with their scientific names based on their key features • SLO 19.06: Explain the connection between heart health and plant-based diet • SLO 19.07: Explain the differences between carbohydrates, lipids, and proteins for human diet $3$. Test Your Knowledge • Assessment 1: TRUE or FALSE: Beans and lentils are protein rich plants. • Assessment 2: TRUE or FALSE: Broccoli is a cruciferous vegetable. • Assessment 3: TRUE or FALSE: Vegan diet eliminates all animal products and byproducts (dairy, meat, poultry, fish, eggs and honey). • Assessment 4: TRUE or FALSE: Vegetarian diet eliminates animal products except dairy and eggs. 1. TRUE 2. TRUE 3. TRUE 4. TRUE 1.20: Seed Germination and Seedling Establishment There is optimal temperature, light / darkness, and moisture requirement for seed germination of plant species. Days to germination varies from a few days (e.g., lettuce, cucumber, corn) to four days (e.g., cabbage, watermelon, kale) to five days (e.g., cauliflower, spinach) to six days (e.g., bean, carrot, eggplant, onion, pea) to seven days (e.g., celery) to eight days (e.g., pepper) to 13 days (e.g., parsley, parsnip) under optimal conditions of temperature and moisture. Crop rotation rotates crop species three year turn from leaf/stem crops (e.g. cabbage, broccoli, kale) to bulb/tuber crops (e.g., onion, potato, carrot) to fruit /seed crops (e.g., peas, corn, pumpkin, tomato, pepper). Lastly, there are perennial vegetable crops that come back every year such as rhubarb and chives, which have benefits with varying flowering time, extended seasons, and hardiness under suboptimal environment conditions. $1$. Student Learning Outcomes (SLOs) • SLO 20.01: Apply the best practices for learning germination and seedling establishment • SLO 20.02: Describe the characteristics of germination and dormancy • SLO 20.03: Describe the characteristics of basic plant growth requirements • SLO 20.04: Describe the characteristics of favorable conditions and duration for germination • SLO 20.05: Identify given plant species with their scientific names based on their key features • SLO 20.06: Explain how seed germination related to seed quality • SLO 20.07: Explain the nutritive value of seeds $3$. Test Your Knowledge • Assessment 1: TRUE or FALSE: A 2,000 year old date seed was found viable. • Assessment.2: TRUE or FALSE: Double coconut palm (coco de mer, Lodoicea maldivica) seed is considered the largest seed (44 lb). • Assessment 3: TRUE or FALSE: Flax seeds (linseed) are a great source of Omega-3 fatty acids, while pumpkin seeds are a great source of Omega-6 fatty acids. • Assessment 4: TRUE or FALSE: Sunflower, lettuce, Swiss chard, radish, Chinese cabbage, tomato, and pea seeds travelled to the International Space Station. 1. TRUE 2. TRUE 3. TRUE 4. TRUE	textbooks/bio/Botany/From_Growing_to_Biology%3A_Plants_(Hacisalihoglu)/01%3A_Chapters/1.19%3A_Human_Nutrition_from_Plants_and_Plant-based_Proteins.txt
Tea is one of the most consumed drinks in the world. Various tea categories (e.g., organic / conventional, powder, tea bags) and flavors (e.g., cinnamon, tapioca, lemon, jasmin, chocolate, original). Tea also is one of the acidic-soil loving plant species. Moreover, all varieties of green, black, oolong, and white teas come from the same plant species, Camellia sinensis. However, the best quality teas usually come from the top two leaves and bud of the each stem of tea plant that can be picked up to four harvests or flushes. $1$. Student Learning Outcomes (SLOs) • SLO 21.01: Apply the best practices for learning tea cultivation • SLO 21.02: Describe the characteristics of tea plant (Camellia sinensis) • SLO 21.03: Describe the characteristics of tea processing • SLO 21.04: Describe the characteristics of tea brewing • SLO 21.05: Identify given plant species with their scientific names based on their key features • SLO 21.06: Explain the differences between various tea types • SLO 21.07: Explain the differences between herbal, decaf, and regular tea $3$. Test Your Knowledge • Assessment 1: TRUE or FALSE: All tea types (black, green, white, and oolong) come from one plant: Camellia sinensis. • Assessment 2: TRUE or FALSE: Turkey is the top tea consuming country in the world (~7 lb / per capita). • Assessment 3: TRUE or FALSE: There are really only two words to say “tea”: te (by sea) or cha (by land). • Assessment 4: TRUE or FALSE: Herbal teas are not actually teas since they are derived from other plants (chamomile, rooibos, ginger, lemon, hibiscus, rose). 1. TRUE 2. TRUE 3. TRUE 4. TRUE 1.22: Coffee Growing Roast Grind and Beans How do you take your coffee–regular or decaf? Coffee is the most popular drink in the U.S. However, coffee plant species growing is dominantly around the equator countries such as Brazil, Colombia, Ethiopia, and Indonesia. Coffee plant (Coffea sp.), native to south west Ethiopia with very little genetic diversity, comes from beans of coffee fruit (a.k.a. berry or cherry). A combination of its susceptibility to extreme temperature changes and considering its low genetic diversity make breeders focus on developing more robust shade grown coffee cultivars worldwide. $1$. Student Learning Outcomes (SLOs) • SLO 22.01: Apply the best practices for learning coffee cultivation • SLO 22.02: Describe the characteristics of coffee plant (Coffea arabica) • SLO 22.03: Describe the characteristics of coffee processing • SLO 22.04: Describe the characteristics of coffee brewing • SLO 22.05: Identify given plant species with their scientific names based on their key features • SLO 22.06: Explain the differences between various tea coffees • SLO 22.07: Explain the differences between decaf, and regular coffee $3$. Test Your Knowledge • Assessment 1: TRUE or FALSE: Coffee is native to tropical East Africa highlands (Ethiopia). • Assessment 2: TRUE or FALSE: 40% of the world’s coffee is produced by Brazil. • Assessment 3: TRUE or FALSE: Finland drinks the most coffee per person in the world. • Assessment 4: TRUE or FALSE: U.S. is the world's largest coffee importer (2.5 Mil lb.). 1. TRUE 2. TRUE 3. TRUE 4. TRUE	textbooks/bio/Botany/From_Growing_to_Biology%3A_Plants_(Hacisalihoglu)/01%3A_Chapters/1.21%3A_Tea_Growing_Brew_and_Leaves.txt
How will planet Earth feed 10 billion people with less land and energy by the year 2050? It will clearly require sustainable approaches for crop cultivation and with enhanced resilience to environmental changes as well as reduced carbon footprint to protect the environment. There is an opportunity to promote sustainability as well as high yield, accelerated growth and minimized losses to environmental stress conditions. $1$. Student Learning Outcomes (SLOs) • SLO 23.01: Apply the best practices for learning sustainable agriculture • SLO 23.02: Describe the linkage between soil and plant growth • SLO 23.03: Describe the characteristics of sustainability including environment, economic, and community • SLO 23.04: Describe how crop species relates to the economy • SLO 23.05: Identify given plant species with their scientific names based on their key features • SLO 23.06: Describe how crop species relates to the environment • SLO 23.07: Explain the differences between different crop production methods such as organic and conventionally grown $3$. Test Your Knowledge • Assessment 1: TRUE or FALSE: USDA 100% organic certification criteria include not usage of synthetic fertilizers, prohibited pesticides, GMOs, and/ or hormones. • Assessment 2: TRUE or FALSE: In fruit / veggie labels: 9---- code indicates organic, 8---- code indicates GMO, and only four-digit (4---) code indicates conventionally grown. • Assessment 3: TRUE or FALSE: South Dakota grows the most sunflowers in the U.S. (5 Mil tones). • Assessment 4: TRUE or FALSE: One corn ear has an average of 800 seeds (kernels). • Assessment 5: TRUE or FALSE: Crayons are made of soybean oil. • Assessment 6: TRUE or FALSE: Florida is the top producer of orange, grapefruit, tomato, watermelon, cucumber, snap beans, squash, and sugar cane in the U.S. • Assessment 7: TRUE or FALSE: Pierson, Florida is known as the “Fern Capital of the World” • Assessment 8: TRUE or FALSE: Arabidopsis was the first plant (1982) and potato was the first food plant (1995) grown in outer space. • Assessment 9: TRUE or FALSE: California is the biggest peach producer. • Assessment 10: TRUE or FALSE: Georgia is the biggest peanut state and produces $\sim 50 \%$ of the U.S. peanut production. 1. TRUE 2. TRUE 3. TRUE 4. TRUE 5. TRUE 6. TRUE 7. TRUE 8. TRUE 9. TRUE 10. TRUE 1.24: Synthetic Biology and CRISPR Gene Editing in Crops One of the emerging fields in plant biology is developing crop plant cultivars with more stress resilient, disease resilient, nutrient efficient, and increased yield using new genome editing and design techniques. Some of the new products of synthetic biology (SynBio) include chemicals, biofuels, medicines, synthetic cells, plant genes, or promoters. Moreover, adaption of nitrogen fixation to major staple food crops could let non-legumes fix their own nitrogen fertilizer in the future. $1$. Student Learning Outcomes (SLOs) • SLO 24.01: Apply the best practices for learning Synthetic Biology, CRISPR Gene Editing • SLO 24.02: Describe the characteristics of CRISPR technology • SLO 24.03: Describe the characteristics of synthetic biology • SLO 24.04: Describe CRISPR/Cas9 tools for plants • SLO 24.05: Identify given plant species with their scientific names based on their key features • SLO 24.06: Explain how CRISPR could be used for improved nutrient usage • SLO 24.07: Explain how CRISPR could be used for improving crop yield $3$. Test Your Knowledge • Assessment 1: TRUE or FALSE: Dr. George Church (Professor of Genetics @ Harvard) is considered the father of Synthetic Biology. • Assessment 2: TRUE or FALSE: Self-fertilizing plants may be possible in the future with SynBio. • Assessment 3: TRUE or FALSE: Programmable plant seeds may be possible in the future with SynBio for colonization of Mars. • Assessment 4: TRUE or FALSE: Medicine producing plant seeds may be possible in the future with SynBio. 1. TRUE 2. TRUE 3. TRUE 4. TRUE	textbooks/bio/Botany/From_Growing_to_Biology%3A_Plants_(Hacisalihoglu)/01%3A_Chapters/1.23%3A_Sustainable_Agriculture_and_Food_Systems.txt
Plants are a very important source of food, feed, and fuel. Therefore, exploring their natural diversity and protecting their germplasm resources is key to future food security. Environmental interaction includes the defense of plant species against biotic and abiotic stress tolerance. There are a number of stress factors for plants including: temperature (cold, high), salt, nutrient deficiency, and metal toxicity. As a result, stress conditions can possibly inhibit the plant’s growth and development, and therefore, affect plant yield and quality. Furthermore, plant response to environmental stress (both biotic and abiotic) consists of several diverse mechanisms. For example, plant varieties can grow modified structures (e.g., spines) or modify their growth (e.g., shorter stems, modified leaf area) in response to environmental stress and to survive or adapt. The largest seed bank is the Svalbard Global Seed Vault (1000 m2) in the island of Spitsbergen, Norway that have 4.5 million seed accessions of total 6 million accessions worldwide. $1$. Student Learning Outcomes (SLOs) • SLO 25.01: Apply the best practices for learning resilience to environmental stress • SLO 25.02: Describe the characteristics of tolerance to high temperature stress • SLO 25.03: Describe the characteristics of tolerance to cold temperature stress • SLO 25.04: Describe the characteristics of tolerance to salt stress • SLO 25.05: Identify given plant species with their scientific names based on their key features • SLO 25.06: Explain importance of genetic variation in plant biology • SLO 25.07: Explain how diverse varieties affect survival of plants $3$. Test Your Knowledge • Assessment 1: TRUE or FALSE: You only need to plant these plants once and harvest for years because they are perennials: asparagus, chives, rhubarb, strawberries. • Assessment 2: TRUE or FALSE: Needle type of modified leaves are evolutionary adaptation to prevent desiccation and hold more moisture. • Assessment 3: TRUE or FALSE: All species lived in the sea until ~550 million years ago. • Assessment 4: TRUE or FALSE: Only 12 crops supply 80% of the world’s food supply: sugarcane, maize, rice, wheat, potato, soybean, cassava, tomato, banana, onion, apple, and grape. • Assessment 5: TRUE or FALSE: The more genetic variation is the better because it will increase survival of some varieties or species. 1. TRUE 2. TRUE 3. TRUE 4. TRUE 1.26: Fungi Kingdom Mushrooms belong to the fungi kingdom. They can provide proteins and many nutrients while minimal harmfulness to environment. Agaricus bisporus is an over \$24 billion economy with varieties such as portobella, cremini, and button mushrooms (both white and brown) in the U.S. $1$. Student Learning Outcomes (SLOs) • SLO 26.01: Apply the best practices for learning Kingdom Fungi • SLO 26.02: Describe the characteristics of fungi habitat • SLO 26.03: Describe the characteristics of phylum Ascomycota • SLO 26.04: Describe the characteristics of phylum Basidiomycota • SLO 26.05: Identify given plant species with their scientific names based on their key features • SLO 26.06: Describe the characteristics of phylum Deuteromycota • SLO 26.07: Describe the characteristics of phylum Glomeromycota $3$. Test Your Knowledge • Assessment 1: TRUE or FALSE: Truffles, rare underground edible fungi, found near chestnut, oak, pine, hazelnut, and pecan roots that exchange nutrients and sugars. • Assessment 2: TRUE or FALSE: White truffles (alba) can cost $\ 3,500 / \mathrm{lb}$. • Assessment 3: TRUE or FALSE: Antibiotic “penicillin” is derived from fungi Penicillium notatum. • Assessment 4: TRUE or FALSE: There are some fungi that glow in the dark just like fireflies when their luciferin reacts with $\mathrm{O}_{2}$. 1. TRUE 2. TRUE 3. TRUE 4. TRUE 1.27: Cyanobacteria and Viruses (COVID19 Pandemic Edition) Cyanobacteria is likely one of the bacteria species will help Mars colonization by sustainably growing in Mars soils and environment conditions. It is known that cyanobacteria helped oxygenation of our planet Earth atmosphere about 2.4 billion years ago. Furthermore, cyanobacteria can not only fix carbondioxide but also nitrogen as well. $1$. Student Learning Outcomes (SLOs) • SLO 27.01: Apply the best practicies for learning cyanobacteria and viruses • SLO 27.02: Describe the connection of cyanobacteria to nitrogen cycle • SLO 27.03: Describe the characteristics of photosynthetic cyanobacteria (most) • SLO 27.04: Describe the characteristics of viruses • SLO 27.05: Identify given plant species with their scientific names based on their key features • SLO 27.06: Explain the differences between viruses and their viral structure • SLO 27.07: Explain the mutation and genetic variation of viruses $3$. Test Your Knowledge • Assessment 1: TRUE or FALSE: COVID-19 is a term for “Coronavirus Disease 2019”, named after the year it was first identified (2019). • Assessment.2: TRUE or FALSE: Over 120+ “COVID-19” vaccine candidates have been proposed worldwide. • Assessment 3: TRUE or FALSE: COVID-19 has not currently been detected in Antarctica. • Assessment 4: TRUE or FALSE: SARS-CoV-2 as well as some plant viruses are made of RNA. • Assessment 5: TRUE or FALSE: A safe distance to stay apart from someone who’s sick is a minimum of 1 meter (3 ft). • Assessment 6: TRUE or FALSE: One COVID-19 infected person infects ~2.5 other people and 5% will need hospital care. • Assessment 7: TRUE or FALSE: Loss of smell (anosmia) and decreased sense of taste (ageusia) together with cough, fever and shortness of breath are symptoms of COVID-19 (+). • Assessment 8: TRUE or FALSE: COVID-19 spreads via respiratory droplets that pass from person to person. • Assessment 9: TRUE or FALSE: 60% alcohol can kill SARS-CoV-2. • Assessment 10: TRUE or FALSE: Increased risk of serious COVID-19 illness include diabetes as well as blood type A. 1. TRUE 2. TRUE 3. TRUE 4. TRUE 5. TRUE 6. TRUE 7. TRUE 8. TRUE 9. TRUE 10. TRUE	textbooks/bio/Botany/From_Growing_to_Biology%3A_Plants_(Hacisalihoglu)/01%3A_Chapters/1.25%3A_Mining_Plant_Superb_Varieties_for_Increased_Resilience_to_Suboptimal_Conditions.txt
How do cultivate growth mindset? Growth mindset individuals can develop their abilities compare to fixed mindset individuals. Moreover, growth mindset individuals have the attitude of constantly learning new things. Furthermore, there are increasing research interest in answering the question: Does growth mindset (also grit) help promote undergraduate student performance especially in STEM (science, technology, engineering, and math) field majors? $1$. Student Learning Outcomes (SLOs) • SLO 28.01: Apply the best practices for learning Growth Mindset and Grit • SLO 28.02: Describe teh characteristics of Growth Mindset • SLO 28.03: Describe the characteristics of Grit • SLO 28.04: Describe the characteristics developing growth mindset • SLO 28.05: Identify given plant species with their scientific names based on their key features • SLO 28.06: Explain strategies for fostering grit • SLO 28.07: Explain how to learn from failure $3$. Test Your Knowledge • Assessment 1: TRUE or FALSE: It's possible to grow new brain cells (neurogenesis). • Assessment 2: Do you have a BIOLOGY growth mindset? (hint: check your GM score). • Assessment 3: A pandemic such as COVID19 can help cultivate growth mindset. Why? • Assessment 4: TRUE or FALSE: Several celebrities who failed before succeeding built grit. Give examples. Stephen King, Walt Disney, JK Rowling (Harry Potter), and Bill Gates among others. $5$. Check Your Answers 1. TRUE 2. Strong growth mindset (45–60 points in Mindset Instrument) also create opportunities for growth and developing new techniques for resilience 3. Because of the fact that crisis like a pandemic 4. TRUE. 1.29: Student Learning What are the twenty-first-century learning skills that we can integrate in undergraduate education? There are at least four major skills as follows: 1. Critical thinking 2. Communication 3. Collaboration 4. Creativity Moreover, undergraduate students need to develop higher-order thinking skills such as creativity and synthesizing in order to be well-prepared for navigating the twenty-first century and success. $1$. Student Learning Outcomes (SLOs) • SLO 29.01: Apply the best practices for learning about student learning • SLO 29.02: Describe the characteristics of how learning works • SLO 29.03: Describe the characteristics of online learning • SLO 29.04: Describe the characteristics of in-person learning • SLO 29.05: Identify given plant species with their scientific names based on their key features • SLO 29.06: Describe the characteristics of hybrid learning • SLO 29.07: Explain classroom technology in the new era of learning $3$. Test Your Knowledge • Assessment 1: TRUE or FALSE: Growing plants help students learn valuable skills and concentrate. • Assessment 2: Multimedia tools such as videos improve learning. Why? • Assessment 3: TRUE or FALSE: US phone numbers are 7-digits because of the fact that human short-term memory can hold max 7 digits. • Assessment 4: TRUE or FALSE: Human can remember 65% info as image while 10% as a text. $5$. Check Your Answers 1. TRUE 2. Because of the fact that multimedia tools (videos, animation, picture) improve connections of content in both visual and verbal context, it helps brain improve learning. 3. TRUE 4. TRUE 1.30: How to Study STEM (Science Technology Engineering and Math) What are the best study skills for undergraduate STEM (Science, Technology, Engineering, & Math) subjects? Some effective study methods include as follows: • Attend every class lecture • Make flashcards and concept maps • Take your own good notes and repeat them daily • Read the textbook ahead and repeat • Use highlighters and colors when studying • Read it through before answering a question • Metacognition (MC): Learning how to learn Moreover, gaining mastery of content gradually help undergraduates to build more confidence, ownership of expertise, and appreciation for STEM fields. $1$. Student Learning Outcomes (SLOs) • SLO 30.01: Apply the best practices for learning How to Study Science (STEM) • SLO 30.02: Describe the characteristics of effective studying • SLO 30.03: Describe the characteristics of effective schedule • SLO 30.04: Describe the characteristics of effective note-taking • SLO 30.05: Identify given plant species with their scientific names based on their key features • SLO 30.06: Explain the differences between simply reading and active studying • SLO 30.07: Explain how explaining materials in your own words is an effective learning tool $3$. Test Your Knowledge • Assessment 1: TRUE or FALSE: Reading on hard-copy material is superior compare to screens. • Assessment 2: TRUE or FALSE: Active recall with closing the book is superior studying compared to re-reading. • Assessment 3: Teaching explaining the course material to somebody else is a superior learning technique. Why? • Assessment 4: TRUE or FALSE: A 30-minute exercise / per day increases brain cell growth and therefore learning. $5$. Check Your Answers 1. TRUE 2. TRUE 3. Because of the fact that memory need to be used regularly in order to perform optimally. Therefore, teaching someone else uses memory and improved learning the material better. 4. TRUE	textbooks/bio/Botany/From_Growing_to_Biology%3A_Plants_(Hacisalihoglu)/01%3A_Chapters/1.28%3A_Growth_Mindset_and_Grit.txt
(12 pts) (10 pts) (7 pts) Needs Help (5 pts) 1. TITLE (summarize conclusion in one sentence 1. AUTHOR(S) (summarize paper in one paragraph with breif intro, methods, results, and conclusion) 1. ABSTRACT (summarize paper in one paragraph with breif intro, methods, results, and conclusions) 1. INTRODUCTION (provide sufficient background info from literature with paraphrasing and citations) 1. MATERIALS & METHODS (clearly describe the materials and methodology) 1. RESULTS (present your data in tables and figures format) 1. DISCUSSION (discuss and explain your results with a clear conclusion) 1. REFERENCES (list all references cited in the paper) APA FORMAT (sources cited in parenthesis with authors' name and publication year) (4 pts) ------------ ------------------ ---------------- 2.02: List of Plant Species Covered in this Book 1 Abelmoschus esculentus Okra 59 Hypoestes aristata Ribbon bush 2 Abies fraseri Fraser fir 60 Ipomoea batatas Sweetpotato 3 Acer okagama Japanese maple 61 Iris germanica Iris 4 Agaricus bisporus Mushroom 62 Juniperus communis Juniper 5 Agave tequilana Blue agave 63 Lactuca sativa Lettuce 6 Alstroemeria aurea Peruvian-lily 64 Lilium candidum Lily 7 Alstroemeria aurea Pineapple 65 Malus domestica Apple 8 Anethum graveolens Dill 66 Mangifera indica Mango 9 Antirrhinum majus Snapdragon 67 Manihot esculenta Cassava (Yuca) 10 Arabidopsis thaliana Arabidopsis 68 Mentha spicata Mint 11 Asparagus densiflorus Asparagus 69 Mimosa pudica Sensitive plant 12 Asparagus officinalis Asparagus 70 Monstera adansonii Swiss cheese plant 13 Asplenium nidus Bird's-nest fern 71 Musa acuminata Banana 14 Aster amellus Aster 72 Nepenthes sp. Pitcher plant 15 Averrhoa carambola Starfruit 73 Nephrolepis exaltata Boston fern 16 Bambusa vulgaris Bamboo 74 Nerium oleander Oleander 17 Bambusa vulgari Begonia 75 Nipponanthemum nipponicum Daisy 18 Bambusa vulgari var.capitata Cabbage 76 Nymphaea alba Waterlily 19 Bambusa vulgari var.italica Broccoli 77 Oryza sativa Rice 20 Caladium bicolor Caladium 78 Pachira aquatica Money tree 21 Calluna vulgaris Heather 79 Pachystachys lutea Golden shrimp plant 22 Camellia japonica Camellia 80 Pelargonium hirsutum Geranium 23 Camellia sinensis Tea 81 Penusetum setaceum Fountain grass 24 Capsicum annuum Pepper 82 Persea americana Avocado 25 Capsicum chinense Habanero pepper 83 Petroselinum crispum Parsley 26 Carica papaya Papaya 84 Petunia atkinsiana Petunia 27 Carnegiea gigantea Saguaro 85 Phalaenopsis amabilis Moth orchid 28 Carya illinoensis Pecan 86 Phaseolus vulgaris Bean 29 Cattleya labiata Orchid Cattleya 87 Philodendron selloum Philodendron 30 Chlorophytum comosum Spider plant 88 Pisum sativum Pea 31 Chlorophytum comosum Pomelo 89 Prunus serrulata Sakura cherry 32 Citrus sinensis Orange 90 Quercus virginiana Live oak 33 Citrus sinensis Coconut 91 Rosa sp. Rose 34 Citrus sinensis Croton 92 Sabal palmetto Cabbage palm 35 Coleus solenostemon Coleus 93 Salvia hybrid Salvia 36 Crassula ovata Jade plant 94 Salvia officinalis Sage 37 Crotonanthus klotzsch Croton 95 Salvia rosmarinus Rosemary 38 Cucurbita pepo Pumpkin 96 Schefflera arboricola Dwarf umbrella tree 39 Curcuma longa Turmeric 97 Selaginella stellata Selaginella 40 Cycas revolata Sago palm 98 Senecio rowleyanus String of pearls 41 Cydonia oblonga Quince 99 Sequoia sempervirens Redwood 42 Daucus carota Carrot 100 Serenoa repens Saw palmetto 43 Dianthus caryophyllus Carnation 101 Setcreasea pallida Purple heart 44 Diospyros virginiana Persimmon 102 Solanum lycopersicum Tomato 45 Dracaena cinnabari Dragon blood tree 103 Solanum tuberosum Potato 46 Dracaena marginata Madagascar dragon tree 104 Sphagnum sp. Moss 47 Dracaena trifasciata Snake plant 105 Spinacia oleracea Spinach 48 Epipremnum aureum Golden pothos 106 Taxus brevifolia Pacific yew 49 Equisetum hyemale Horsetail 107 Thymus vulgaris Thyme 50 Euphorbia lactae Cactae 108 Triticum aestivum Wheat 51 Euphorbia pulcherrima Poinsettia 109 Tulipa sp. Tulips 52 Ginkgo biloba Ginkgo 110 Vaccinium corymbosum Blueberry 53 Hedera helix English ivy 111 Viola tricolor var. hortensis Pansy 54 Helianthus annuus Sunflower 112 Vitis vinifera Grape 55 Hevea brasiliensis Rubber tree 113 Zamia floridana Zamia 56 Hydrangea macrophylla Hydrangea 114 Zea mays Maize 57 Hylocereus undatus Dragon fruit 115 Zingiber officinale Ginger 58 Hypnum moss Moss 116 Zinnia elegans Zinnia	textbooks/bio/Botany/From_Growing_to_Biology%3A_Plants_(Hacisalihoglu)/02%3A_Appendix/2.01%3A_Rubric_as_a_Grading_Tool.txt
What is a Grass? Technically, the word grass refers to species in the Poaceae (a.k.a. Graminae) plant family. In this book, we have also included grass-like plants, sedges from the Cyperaceae family, and rushes from the Juncaceae family. The Plant Grasses, sedges, and rushes are in a botanical group referred to as monocotyledons, often called monocots for short. The name monocotyledon is derived from the single (mono) embryonic leaf (cotyledon) contained in the seed of a monocot. Graminoids and other monocots share this characteristic, along with narrow leaves, parallel venation, and fibrous root systems. Use the image on the below to learn the basic anatomy of a graminoid plant. An interactive or media element has been excluded from this version of the text. You can view it online here: https://open.lib.umn.edu/nativegrasses/?p=27 Inflorescence – The entire reproductive structure of a grass, sedge, or rush is called the inflorescence. Ligule – The ligule is where the blade and the sheath meet. The ligule may be hairy, smooth, or have some other identifying characteristic of the species. Blade – Term used to describe the leaf above the sheath. Culm – This term refers to the stem of a grass or sedge. Sheath – The sheath is the bottom of the leaf. It surrounds the culm like a tube. It splits open at the top to turn into the blade. Floret – The name for a grass flower. This drawing shows a mature floret. Spikelet – A unit made up of one or more florets, rachilla, and glumes. Rachilla – The structure on which the florets are borne. Glumes – Bracts that subtend the floret. Flowers Neither grasses, sedges, nor rushes have colorful, large, or showy flowers. All are wind pollinated and so do not need bright petals or nectar to attract animal pollinators. For this reason, the flowers are simplified and usually small in size. In grasses, the petals and sepals have been reduced to very small scales called lodicules that enclose the ovary, which contains one ovule. From the ovary rise two styles ending in feathery stigmas; adjacent are typically three anthers that open to shed pollen held on long, thin filaments. The ovary and anthers are usually protected and enclosed by two small papery bracts called the palea and the lemma. Outside the lemma and palea are two more larger, yet still small, papery bracts called glumes. When the anthers have ripe pollen, the very small lodicules help to open and close the papery bracts, thus assisting with wind pollination. All of these small parts make up the floret, an individual grass flower. A large seedhead or grass inflorescence usually contains hundreds of florets. The arrangement of the one or many florets and the branching patterns of these florets determines how grasses are identified, named, and classified. If there is only one floret subtended by the two glumes, the floret is called a one-flowered spikelet. If there are two or more florets above the glumes, it’s a multi-flowered spikelet. Different genera of grasses have specific numbers of florets in a spikelet. The arrangement of spikelets in an inflorescence is also characteristic of specific genera. To see these small flower parts, you need a hand lens or, ideally, a microscope. This is often where many people give up on learning grass identification! However, you can easily learn the differences in the large seedheads that will help you identify many grasses. Sedge inflorescences are simpler. However, they are just as small, and, again, the identification may require a hand lens or microscope. Sedges can be comprised of unisexual or bisexual flowers. Sedge female flowers are each enclosed by a small sack-like structure called a perigynium. The shape of the perigynium is often used in sedge identification. Many sedges have female flowers in one section (often lower on the flowering stem), with the male flowers that contain only the pollen in another section, (often on top of the stem). If you look closely at sedge flowers in early spring when they are shedding pollen, you can see the larger, more conspicuous female flowers growing below the male flowers. The flower (male or female) and bract is called a spikelet. Spikelets are attached directly to the axis that forms the inflorescence. Explore the image below to see the inflorescence of a sedge. An interactive or media element has been excluded from this version of the text. You can view it online here: https://open.lib.umn.edu/nativegrasses/?p=27 Spike – This is a Carex filifolia spike containing both male and female flowers. The male flowers make up the top half of the spike, distinguished by anthers. The female parts make up the bottom half of the spike, distinguished by the three feathery stigmas emerging from the perigynium. Female Flower – The female flower is enclosed by a sack called a perigynium. Three feathery stigmas emerge from the top of the perigynium. Male Flower – This male flower has the characteristic leaf-life scale which encompasses the three anthers emerging from the base. Rushes have the simplest inflorescence. The flowers are typically bisexual. From beneath each flower emerge six small green or brown, petal-like structures called tepals. Typically, there are many rush flowers held together in a cluster at the end of a stem. Stems and Leaves To quickly tell the difference between grasses, sedges, and rushes, look at the stem and leaves. Grass stems (culms) are normally round like a straw, and their leaves come off in two ranks, meaning one on either side of the plant—whereas the stems of sedges are usually triangular, and their leaves are three-ranked. It can be hard to feel the three edges when you roll the stem between your fingers. Rushes have round stems as well, but unlike grasses the leaves of rushes grow from the base of the plant, so the stems lack the nodes that arise from leaf joints and are completely smooth. This famous poem can help you remember the differences between the three: Sedges have edges; Rushes are round; Grasses have bumps all the way to the ground. In the poem, “edges” refers to the triangular stem of a sedge. “Round” refers to the smooth round stem of a rush. “Bumps” refers to the nodes or joints where leaves attach to the stem of a grass. Illustration credit for this section in order: American beakgrain: Hitchcock-Chase Collection of Grass Drawings, on indefinite loan from the Smithsonian Institution, courtesy of Hunt Institute for Botanical Documentation, Carnegie Mellon University, Pittsburgh, Pa. Angiosperm flower, grass flower, grass spikelet, inflorescence type: Clark, Lynn G., and Richard W. Pohl. Agnes Chase’s first book of grasses: the structure of grasses explained for beginners. Smithsonian Institution, 2012. Threadleaf sedge, rush flower, rush inflorescence: United States Department of Agriculture Forest Service Collection, courtesy Hunt Institute for Botanical Documentation, Carnegie Mellon University, Pittsburgh, PA.	textbooks/bio/Botany/Gardening_with_Native_Grasses_in_Cold_Climates_and_a_Guide_to_the_Butterflies_They_Support_(Narem_and_Meyer)/01%3A_Introduction_to_Grasses/1.01%3A_Parts_of_the_Plant.txt
Cool Season vs. Warm Season Grasses have evolved over centuries to take advantage of the environment around them. Depending on the climate where they originated, they have developed one of two different ways to produce sugars through photosynthesis. These ways are referred to as C3 and C4 photosynthesis. C3 plants have evolved in temperate climates and are called cool season plants because their photosynthetic pathway is most efficient in cooler temperatures. Hot temperatures slow the growth of C3 grasses and may induce dormancy until temperatures cool again. C3 grasses flower in late spring or early summer before temperatures get too high. C4, or warm season grasses, use an altered photosynthetic process that uses less water and takes advantage of warmer temperatures. Their optimum temperature range for growth and development is higher than C3 grasses. Warm season grasses flower at the end of the summer and reach their peak growth in September. Cool and warm season grasses will have very different growth rates and life cycles in a garden and prairie setting. Using these differences for design and function in the garden should be part of your overall use of grasses to maximize their benefit. The exact seasonal growth patterns of cool and warm season grasses differ slightly depending on the species and the climate. The above graph shows the general growth patterns of each type and how they overlap. Growth Habit Grasses have two general growth habits, clumping and running. Clumpers grow in tufts or bunches and are often referred to as bunch grasses. Grasses with a running growth habit spread rapidly by sending out horizontal stems called stolons if aboveground or called rhizomes if below ground. The type of growth habit is important to consider when deciding where and which grass to plant. Running grasses can be great for stabilizing banks and acting as good ground cover, but can also take over areas with less competitive plants. Most clumping grasses do not spread rapidly and instead grow slowly outward, making them easier to manage. Growth Form In addition to their growth habit, grasses grow in various shapes that are referred to in the design world as forms. Common grass forms are irregular, upright open, upright narrow, upright arching, mound, and open and spreading. IRREGULAR Culms are of varying length, often branched, and exhibit no regular pattern of growth, like the ‘Oehme’ palm sedge above. UPRIGHT OPEN Culms are multi-stemmed or branched, varying in height and spreading upward and outward, like the big bluestem above. UPRIGHT NARROW Culms are rarely, if ever, branched and usually perpendicular to the ground; mature height of each culm many times greater than width, like the Indiangrass above. MOUND Culms are usually short and hidden by long leaves that curve outward and downward, forming a dense plant that is more or less round in outline like the prairie dropseed plant above. UPRIGHT ARCHING Culms upright and spreading, with the inflorescence arching and/or nodding. Prairie cordgrass, pictured above, typically exhibits an upright arching form. OPEN AND SPREADING Culms and/or leaves spread more or less horizontally outward from the center of the plant and are rarely erect. Above, Pennsylvania sedge is exhibiting an open and spreading form. Annual vs. Perennial Most native grasses used for landscapes are long-lived perennials, going dormant in the winter and growing again the following spring. However, some grass species are annuals, completing their entire life cycle, and then dying in one year. Other grasses are perennials in warmer climates, such as in hardiness zones 6 or 7, but are grown as annuals in zones 3 and 4. Details on the perennial life-cycles of individual species can be found in Chapter 3. 1.03: Literature Cited Form definitions come from: Hockenberry, M. L. 1973. Landscape Characteristics and a key for selected ornamental grasses. M.S. Thesis. Cornell University.	textbooks/bio/Botany/Gardening_with_Native_Grasses_in_Cold_Climates_and_a_Guide_to_the_Butterflies_They_Support_(Narem_and_Meyer)/01%3A_Introduction_to_Grasses/1.02%3A_Growth.txt
Low Inputs Native grasses need little maintenance or input from gardeners. If they are planted in sites suitable to their native habitat, they rarely need water once established. They do well in tough sites that other plants may not be able to handle. Some native grasses are drought tolerant, able to grow in clay-soils, or standing water tolerant. Matching the native grass to its preferred site is key to a long-term sustainable planting. Native grasses rarely need fertilizer, and in fact too much fertilizer can actually be harmful, causing full-grown plants to grow weak and flop over. Native grasses are generally insect pest and pathogen free (see exceptions in Chapter 4). Because they are indigenous to the region, they have evolved to survive with larger animals that may be pests on other garden plants, such as deer and rabbits. In fact, some grasses with sharper leaves can be used as a barrier to protect vulnerable plants from deer (Darke 2007). Soil Benefits Grasses have deep, fibrous root systems that stabilize the soil, reducing erosion. The underground root system of many perennial grasses is larger than the aboveground plant. The fibrous or hair-like nature of grass roots enables them to take up large quantities of water and to increase organic matter in the soil as they decompose. Grasses, with their deep roots, helped produce the rich, fertile soils of the prairie. These root systems also act as absorption and filtration systems for water runoff, catching impurities and pollutants before they enter the ground water. For this reason, grasses have long been recommended as good plants for buffer strips, located along the edge of crop fields or along paved parking areas. Native grasses can be the workhorses for rain gardens and green swales in urban areas. Grass Root Depths In Tall and Mixed grass prairie (source: Weaver, 1958) PLANT ROOT DEPTH big bluestem 6-7 feet prairie cordgrass 6-10 feet switchgrass 8-11 ft little bluestem 4 -5 ft prairie dropseed 4-5 ft side-oats grama 4.5-5.5 ft Junegrass 15-20 in 2.02: Lepidoptera Relationships Grasses are important components in prairie ecosystems. Estimates on the components of the original North American prairie indicate that grasses composed up to 80% of the plants. Numerous species of grassland birds, mammals, and insects use grasses for nesting, cover, and food. As the prairie has declined across the Midwest, so have numerous native prairie species. Native grasses are especially important to certain plant-eating insects. In general, insect herbivores specialize in eating a specific species, genus, or family. These insects are called specialists, as compared to generalists, which can eat a wider variety of plants. A common example of this is the monarch butterfly, whose larvae feed only on plants in the milkweed genus. If there is a dearth of milkweed plants, the larvae do not start eating different species. Instead, they are simply left without food. Monarchs need milkweed species in order to survive and sustain their populations. This is the case with most other Lepidoptera (butterfly and moth) species, although there are exceptions. Groups of insects that have been comprehensively studied suggest that less than 10% of larvae feed on species from more than three families (Bernays and Graham 1988). Numerous species of Lepidoptera larvae have been noted in the literature to use native graminoids for food and shelter. In Minnesota alone, 36 species of Lepidoptera were recorded to feed on 17 dominant or common prairie grasses during their larval stage (Narem and Meyer 2017). When the range is expanded to include more states and more species of grasses, the number grows. Even more species, especially moths, are suspected of eating grasses, but as of yet do not have documented larval eating habits. As more research is done and more larval habits are documented, more species will be added to the list. Specific associations between native Lepidoptera of the northern Midwest and native grasses are listed in Chapter 3. Butterflies that feed on native grasses occur in two subfamilies: the Hesperiinae or grass skippers and the Satryinae or browns, stayrs, or nymphs. Grass skippers have short, thick bodies that grant them the ability to fly in bursts, making it look like they are skipping across the prairie. Larvae feed on grasses, sedges, and/or rushes. Many make and reside in shelters within or at the base of grasses during their larval life stage. They overwinter as larvae within the bases of bunch grasses at or just below the soil surface. The Satyrinae subfamily contains browns, satyrs, and nymphs. All species eat monocots during their larval stage; some eat grasses and/or sedges. The larvae pupate underground in silklined nests or hang upside down. They hibernate as larvae (Scott 1986). Many of the Lepidoptera that feed on grasses are endangered, threatened, or rare, like the Dakota skipper and Poweshiek skipperling. Often, these species depend on only a few species of grass to provide them with cover and/or food during their larval life stage. We should not be surprised that as the native grasses of the prairie disappear, the butterflies and birds dependent on this habitat have disappeared.	textbooks/bio/Botany/Gardening_with_Native_Grasses_in_Cold_Climates_and_a_Guide_to_the_Butterflies_They_Support_(Narem_and_Meyer)/02%3A_Benefits_of_Native_Grasses/2.01%3A_Soil_Benefits.txt
Native grasses provide habitat for other beneficial insects as well, such as ground beetles. Ground beetles are voracious predators. They prey on other invertebrates such as aphids, slugs, and grasshoppers, that can be pests on vegetable and row crops. For this reason, native grasses are being used in various agricultural schemes as a form of biological pest control. In England, farmers have been using beetle banks since the 1970‘s as a way to reduce chemical inputs. Beetle banks are rows of elevated earthen embankments that have been planted to native grasses and sometimes wildflowers. Predatory beetles take shelter in these strips over the winter, and dispatch in the spring into the fields where they prey on crop pests. Beetle banks have begun to catch on in the United States largely in the Pacific Northwest (Mäder et al. 2014). They are not commonly used throughout the country as of yet. Organizations like the Xerces Society are teaming up with federal agencies to research and promote this and other biological pest control measures. 2.04: Nativars Potential Indiangrass nativars planted for trials at the MN Landscape Arboretum. A cultivar is a plant that has been produced from human selection or breeding. A nativar is a cultivar of a native plant. Most native grass cultivars are nativars that have been selected from the wild and not bred in cultivation for many generations. Because they are propagated vegetatively, nativars are clones of each other. This ensures they have consistent size, shape, and color, but means they lack genetic variability. Plants grown from seed, however, have great genetic variability, as each seed is distinct and will produce a plant with different characteristics. This means that, appearance will vary between plants. While this is not optimal for a garden design, it is good for restorations. Plants grown from native seed will be better adapted to exist in native plant communities. For this reason, nativars are not equivalent ecological substitutes for plants grown from native seed and are not recommended for restorations (White 2016). However, native grass nativars provide many of the same benefits that grasses grown from seed provide. They both add organic matter to the soil, require few inputs, and require little maintenance. Benefits provided to wildlife are situational and nativar-specific, and have not been thoroughly studied yet. A study that looked at how well wildflower nativars attracted pollinators compared to the same species grown from seed found that plants grown from native seed outperformed their nativar counterparts more often, but sometimes no differences were found (White 2016). For one species, the nativar attracted more pollinators than the plant grown from seed. This demonstrates the need to evaluate nativars on an individual basis for the benefits they provide. In general, the farther removed a nativar is from the original plant, the less likely it will be to provide the same benefits (White 2016). Many native grass nativars are not far removed from their original species. For example, Blue HeavenTM is a nativar of little bluestem that was selected from a population of seed collected from Benton County, Minnesota. Blue HeavenTM was not bred with specific parents or used in a breeding program. It is simply a plant that was grown along with several other hundred little bluestem and literally ‘stood out in a huge field planting’ as a distinctively tall and darker colored little bluestem. All of the Blue HeavenTM plants have originated from this one original plant. Seed that comes from Blue HeavenTM will of course be little bluestem, but may not look exactly the same as the parent plant. 2.05: Literature Cited Bernays, E. and M. Grahm. 1988. On the evolution of host specificity in phytophagous arthropods. The Ecological Society of America. 69(4):886-892. doi.org/10.2307/1941237 Darke, R. 2007. The Encyclopedia of Grasses for livable Landscapes. Timber Press, Inc. OR. USA. Narem, D. M. and M.H. Meyer. 2017. Native Prairie Graminoid Host Plants of Minnesota and Associated Lepidoptera: A Literature Review. Journal of the Lepidopterists’ Society 71(4):225-235. doi.org/10.18473/lepi.71i4.a5 Scott, J. A. 1986. The Butterflies of North America. Stanford University Press, Stanford California. Weaver, J. E. 1958. Summary and Interpretation of Underground Development in Natural GrasslandCommunities. Ecological Monographs 28(1):55-78. doi.org/10.2307/1942275 White, A. S. 2016. From nursery to nature: Evaluating native herbaceous flowering plants versus native cultivars for pollinator habitat restoration. PhD dissertation, The University of Vermont and State Agricultural College.	textbooks/bio/Botany/Gardening_with_Native_Grasses_in_Cold_Climates_and_a_Guide_to_the_Butterflies_They_Support_(Narem_and_Meyer)/02%3A_Benefits_of_Native_Grasses/2.03%3A_Predatory_Insect_Relationships.txt
Andropogon gerardii Warm season; Perennial Characteristics: 4–8’; upright open; flowers purple; foliage blue-green; fall color Growing Conditions: average to wet soils; full sun; hardy zones 3–8 Big bluestem is one of the dominant grasses of the tallgrass prairie. An upright bunch grass, the foliage changes color from blue-green to rich bronze in the fall. The inflorescence is 3-branched and is commonly said to resemble a turkey foot. Each branch has a purple spike that turns bronze in the fall. Nativars: • ‘Blackhawks’: Foliage is darker purple than other nativars. Foliage starts dark green and takes on purple tones by midsummer, turning completely dark purple by fall. Can be susceptible to rust. • ‘Dancing Wind’: Reddish copper stems and flowers, turns purple and dark red in the fall. • ‘Indian Warrior’: Dark purple foliage and flowers, becomes open spreading with age. • ‘Rain Dance’: Foliage and flowers are purple with red tips. Foliage becomes maroon in the fall. • ‘Red October’: Red foliage in summer and fall Associated Lepidoptera: Species that feed on big bluestem according to the literature are Oslar’s roadside skipper (Amblyscirtes oslari), Delaware skipper (Anatrytone logan), Arogos skipper (Atrytone arogos), dusted skipper (Atrytonopsis hianna), wheat head armyworm (Faronta diffusa), Dakota skipper (Hesperia dacotae), cobweb skipper (Hesperia metea), Ottoe skipper (Hesperia ottoe), Indian skipper (Hesperia sassacus), Newman’s borer (Meropleon ambifusca), and byssus skipper (Problema byssus). 3.02: Sideoats grama Bouteloua curtipendula Warm season; Perennial Characteristics: 12–30”; upright open; flowers green, red; foliage gray-green Growing Conditions: average to dry soils; drought tolerant: full sun; self-seeder; hardy zones 3–8 Sideoats grama is a mid-height grass that grows upright and open, spreading out into a rounder shape. The pendulous seedheads hang from the stems and appear red when the stamens are shedding pollen. Nativars: Currently, no nativars are available. Associated Lepidoptera: Species that feed on sideoats grama according to the literature are Oslar’s roadside skipper (Amblyscirtes oslari), Arogos skipper (Atrytone arogos), Assiniboia skipper (Hesperia assiniboia), Dakota skipper (Hesperia dacotae), Pawnee skipper (Hesperia leonardus pawnee), Ottoe skipper (Hesperia ottoe), and Poweshiek skipperling (Oarisma poweshiek). 3.03: Blue grama Bouteloua gracilis Warm season; Perennial Characteristics: 8–24”; irregular; flowers green to yellow; foliage gray-green; self-seeder Growing Conditions: average to dry soils; drought tolerant: full sun; hardy zones 3–8 Blue grama has interesting seedheads that have been described as looking like tiny combs, eyebrows, or grasshoppers. Blue grama can handle hot and dry sites. It can be used for low maintenance or alternative lawns. Infrequent mowing, monthly or as little as twice a year, can maintain grasses, but broadleaf weed control may be necessary until grasses are established. Nativars: ‘Blond Ambition’: Seedheads are yellow-green and are borne on stems 3’, taller than blue grama plants from the Midwest. Selection is from New Mexico and may have limited hardiness in colder zones, can easily be grown as an annual. Associated Lepidoptera: Species that feed on blue grama according to the literature are Oslar’s roadside skipper (Amblyscirtes oslari), Simius skipper (Notamblyscirtes simius), Mead’s wood nymph (Cercyonis meadii), Blake’s tiger moth (Grammia blakei), Assiniboia skipper (Hesperia assiniboia), Common branded skipper (Hesperia comma), Leonard’s skipper (Hesperia leonardus), Ottoe skipper (Hesperia ottoe), Pahaska skipper (Hesperia pahaska), Uncas skipper (Hesperia uncas), Ridings’ satry (Neominois ridingsii), Garita skipperling (Oarisma garita), and Rhesus skipper (Polites rhesus). 3.04: Hairy grama Bouteloua hirsuta Warm season; Perennial Characteristics: 12–24”; upright open; flowers green to purple; foliage chartreuse Growing Conditions: average to dry; drought tolerant; full sun; hardy zones 3–8 Hairy grama is a smaller grass that has a very open growth habit, with leaves crowded near the base. The seedheads are similar in shape to blue grama, but are covered in fine hairs, giving them a fuzzy look. The seedheads can be green to purple, sometimes taking on a deep bronze color. Nativars: Currently, no nativars are available. The plant is not widely available, but can be found at native garden centers. Associated Lepidoptera: Species that feed on hairy grama according to the literature are Uncas skipper (Hesperia uncas), Ottoe skipper (Hesperia ottoe), and Leonard’s skipper (Hesperia leonardus pawnee). 3.05: Lake sedge hairy sedge Carex lacustris Cool season; Perennial Characteristics: 1–4’; open upright; foliage green; flowers yellow-green Growing Conditions: moist to wet soils; full sun to heavy shade; standing water tolerant; hardy zones 3–7 Lake sedge is a colony-forming sedge with strong rhizomes. For this reason, it is good for stabilizing river banks and lake shores, but may be aggressive. Nativars: No nativars are currently available. The plant is not widely available, but can be found at native garden centers. Associated Lepidoptera: Species that feed on lake/hairy sedge according to the literature are Dion skipper (Euphyes dion), Dukes’ skipper (Euphyes dukesi), sedge witch (Euphyes vestris), marsh eyed brown (Satyrodes eurydice), Appalachian brown (Satyrodes appalachia), and broad-winged skipper (Poanes viator).	textbooks/bio/Botany/Gardening_with_Native_Grasses_in_Cold_Climates_and_a_Guide_to_the_Butterflies_They_Support_(Narem_and_Meyer)/03%3A_Common_Native_Grasses_of_the_Northern_Midwest/3.01%3A_Big_bluestem.txt
Carex muskingumensis Cool season; Perennial Characteristics: 2–3’; upright open; foliage green to yellow; flowers tan; self-seeder Growing Conditions: full sun to medium shade; self-seeder; hardy zones 3–7 Native to wet areas along rivers and marshes, palm sedge is known for its stiff foliage and the three-ranking leaf arrangement typical of sedges. Easy to grow, it tolerates standing water at lake edges and soils that flood. In ideal sites, plants can be 36” wide, thick, and full. Chartreuse foliage when grown in sun, dark green in shade. Nativars: • ‘Little Midge’: very fine textured, 12-15” tall, stiff three-ranked foliage. • ‘Oehme’: has yellow margins, slower growing, very attractive. Named for Wolfgang Oehme. Associated Lepidoptera: No records of Lepidoptera feeding on palm sedge were found in the literature, but further research into Lepidoptera larval habits may discover associations in the future. 3.07: Pennsylvania sedge Carex pensylvanica Cool season; Perennial Characteristics: 6–12”; mound; foliage yellow-green to forest green; flowers brown to yellow Growing Conditions: average to dry soils; full sun to heavy shade; drought tolerant; hardy zones 3–8 This fine-textured sedge grows in a variety of sites, including dry shade. It can be used as a ground cover in landscaping situations, on steep slopes, and on other tough sites. Nativars: Currently, no nativars are available, but the species is widely available at garden centers. Associated Lepidoptera: While no records of Lepidoptera feeding or using Pennsylvania sedge were found in a search of the literature, there are records of Lepidoptera using sun sedge (Carex inops subsp. heliophila), which is closely related. Sun sedge occurs in dry prairie, whereas Pennsylvania sedge occurs in wooded areas. Lepidoptera that use sun sedge are Dakota skipper (Hesperia dacotae), Dun skipper (Euphyes vestris), Assiniboia skipper (Hesperia assiniboia), and Garita skipperling (Oarisma garita). 3.08: Tussock sedge Carex stricta Cool season; Perennial Characteristics: 1–4’; mound to open upright; foliage green; flowers brown Growing Conditions: moist to wet soils; full sun; standing water tolerant; hardy zones 3–7 Tussock sedge is a clump-forming sedge that can tolerate very wet sites. It is native to wetlands, wet meadows, fens, and prairie swales. It can tolerate flooding because it forms clumps above the water line, which allows water to get to its roots. This sedge can be aggressive in certain situations and develops a strong, deep root system. No nativars are currently available. The plant is not widely available, but can be found at native garden centers. Associated Lepidoptera: Species that feed on tussock sedge according to the literature are bog lithacodia moth (Deltote bellicula), black dash (Euphyes conspicua), Appalachian brown (Satyrodes appalachia), marsh eyed brown (Satyrodes eurydice), and mulberry wing (Poanes massasoit). 3.09: Tufted hairgrass Deschampsia cespitosa Cool season; Perennial Characteristics: 3–4’; mound; foliage dark green; flowers beige Growing Conditions: average to wet soils; sun to shade; hardy zones 3–9 This mound-forming grass requires moisture to establish. It is semi-evergreen, and one of the first grasses to grow in the spring. Foliage may show rust, but it is not fatal. Nativars: • ‘Bronzeschleier’: bronze veil hairgrass, flowers are darker, more bronze colored. • ‘Goldstaub’: gold dust hairgrass, shorter, only 1–2’, beautiful mound habit. • ‘Schottland’: Scotland hairgrass, yellow flowers, 2–3’, most common nativar. Associated Lepidoptera: No records of Lepidoptera feeding on tufted hairgrass were found in the literature, but further research into Lepidoptera larval habits may discover associations in the future. 3.10: Eastern bottlebrush grass Elymus hystrix Cool season; Perennial Characteristics: 30–36”; upright narrow; foliage chartreuse; flowers green to beige; self-seeder Growing Conditions: average to moist soils; full sun to heavy shade; hardy zones 3–7 This grass can be short-lived, but easily self-seeds. It is often found in wooded areas or at the edge of woods. The seedheads are unique and shaped like bottlebrush cleaners (hence the name), but shatter readily. Nativars: Currently, no nativars are available. Associated Lepidoptera: Species that feed on eastern bottlebrush grass according to the literature are the scythridid moth Asymmetrura graminivorella, golden borer moth (Papaipema cerina), the elachistid moths Elachista epimicta and Elachista orestella, the northern pearly eye (Enodia anthedon), and lanceolate helcystogramma moth (Helcystogramma hystricella). 3.11: Junegrass Koeleria macrantha Cool season; Perennial Characteristics: 28–36”; irregular; foliage blue gray; flowers light green to beige Growing Conditions: average to dry soils; full sun to light shade; hardy zones 3–8 Native to dry prairies, this grass grows in irregular tufts or bunches. It may be short-lived, especially in heavy soils. Good for septic mounds, dry gravely soils, dry slopes, and low maintenance lawns. Can tolerate foot traffic and mowing. Nativars: No nativars are currently available. The plant is not widely available yet, but can be found at native garden centers. Associated Lepidoptera: Species that feed on Junegrass according to the literature are tawny-edged skipper (Polites themistocles), Blake’s tiger moth (Grammia blakei), Assiniboia skipper (Hesperia assiniboia), Dakota skipper (Hesperia dacotae), and Garita skipperling (Oarisma garita). 3.12: Switchgrass Panicum virgatum Warm season; Perennial Characteristics: 3–6’; upright, foliage greenish purple; flowers bronze to beige; upright open; self-seeder Growing Conditions: average to wet soils; full sun; hardy zones 3–8 Native to the tallgrass prairie, switchgrass is competitive and can be aggressive. It is attractive through every season, even providing winter interest. Some nativars are prone to lodging, others self-sow large amounts of seed. Form and foliage color vary widely between nativars. Nativars: • ‘Cloud 9’: upright arching to 6’ or more, equally as wide; plant in the middle of a border with support for the huge 36” flowers. • ‘Heavy Metal’: upright, dense, thick foliage, 4–5’ • ‘Northwind’: very stiff and upright, wide olive green foliage with flowers borne partially in foliage, good for creating a vegetation screen when planted close together, 5’. • ‘Prairie Fire’: red and purple tipped foliage, 3.5–4’. • “Rehbraun’: red tipped foliage and red seeds, red-brown switchgrass, 3–4’. • ‘Shenandoah’: red and green foliage, 3–4’. • ‘Thundercloud’: very tall, upright, thick and massive, 6–7’. Associated Lepidoptera: Species that use switchgrass according to the literature are the noctuid moth Dichagyris acclivis, the tortricid moth Aethes spartinana, Delaware skipper (Anatrytone logan), the blastobasid moth Blastobasis repartella, pink-streak moth (Faronta rubripennis), Leonard’s skipper (Hesperia leonardus), silvered haimbachia moth (Haimbachia albescens), Texas mocis moth (Mocis texana), stalk borer (Papaipema nebris), and tawny-edged skipper (Polites themistocles).	textbooks/bio/Botany/Gardening_with_Native_Grasses_in_Cold_Climates_and_a_Guide_to_the_Butterflies_They_Support_(Narem_and_Meyer)/03%3A_Common_Native_Grasses_of_the_Northern_Midwest/3.06%3A_Palm_sedge.txt
Schizachyrium scoparium Warm season; Perennial Characteristics: 2–4’; upright; flowers purple; foliage blue-green; fall color; self-seeder Growing Conditions: average to dry soils; full sun; hardy zones 3–8 Native in tall and shortgrass prairies, little bluestem can grow in a variety of soils, but prefers well-drained to upland. It is beautiful throughout the season, with typically blue-green summer foliage turning to red and orange in the fall. Nativars: • ‘Carousel’: a rainbow of colors in blue-gray, bowl-shaped, 30” foliage. • Blue HeavenTM: University of Minnesota selection, upright blue foliage in summer, burgundy in late summer, red in fall, 3–4’. • ‘Prairie Blues’: blue foliage, but can be very open and prostrate, 3–4’. • ‘Standing Ovation’: Upright, blue-green turning orange, red, and yellow in the fall, 3–4’. • ‘The Blues’: light blue foliage, but can easily lodge in rich soil, 3–4’. Associated Lepidoptera: Species that feed on little bluestem according to the literature are Oslar’s roadside skipper (Amblyscirtes oslari), Arogos skipper (Atrytone arogos), dusted skipper (Atrytonopsis hianna), common wood nymph (Cercyonis pegala), the elachistid moth (Cosmopterix callichalca), Assiniboia skipper (Hesperia assiniboia), Dakota skipper (Hesperia dacotae), Leonard’s skipper (Hesperia leonardus), Pawnee skipper (Hesperia leonardus pawnee), cobweb skipper (Hesperia metea), Ottoe skipper (Hesperia ottoe), Indian skipper (Hesperia sassacus), swarthy skipper (Nastra lherminier), Poweshiek skipperling (Oarisma poweshiek), crossline skipper (Polites origenes), and the gelechiid moth (Stereomita andropogonis). 3.14: Indiangrass Sorghastrum nutans Warm season; Perennial Characteristics: 3–6’; upright to columnar; flowers bronze; foliage blue-green; fall color Growing Conditions: full sun; hardy zones 3–8 A dominant grass in the tallgrass prairie, Indiangrass is a large grass that grows very upright. The seedheads are long, feathery spikes that appear yellow when pollen is shedding and turn bronze as the season continues. Nativars: • ‘Indian Steel’: upright with numerous, shiny bronze flowers, 5–6’. • ‘Sioux Blue’: an excellent selection for gardens; showy yellow flowers, 5–5.5’. Associated Lepidoptera: Species that use Indiangrass according to the literature are pepper and salt skipper (Amblyscirtes hegon) and wheat head armyworm (Faronta diffusa). 3.15: Prairie cordgrass Spartina pectinata Warm season; Perennial Characteristics: 4–6’; upright arching; flowers green; foliage green to yellow green in fall Growing Conditions: average to wet soils; full sun; hardy zones 3–8 In native habitats, this grass is found in wet meadows and ditches, the edges of wetlands, and lakeshores. It prefers wet soils, and can tolerate sandy seashores and heavy clay soils. Its strong rhizomes can be aggressive in a garden, but are perfect for lakeshores and areas too wet for other plants. It provides a yellow fall color. Nativars: • ‘Aureo-Marginata’: variegated prairie cordgrass, yellow margins and stripes on the foliage, 4–6’ Associated Lepidoptera: Species that use prairie cordgrass according to the literature are the tortricid moth Aethes spartinana, the noctuid moth Chortodes enervata, the noctuid moth Mesapamea stipata, and the pyralid moth Peoria gemmatella. 3.16: Prairie dropseed Sporobolus heterolepis Warm season; Perennial Characteristics: 3–4’; mound; flowers beige with purplish hue; foliage deep to lime green; Growing Conditions: average to dry soils; full sun; hardy zones 3–8 This fine-textured mound-forming grass does well in upland or dry sites. The flowers are light and airy, creating a cloud-like mass. They have a unique fragrance and smell like hot buttered popcorn or coriander and cumin. Prairie dropseed can be used en masse to cover slopes and as an alternative lawn where foot traffic is minimal. Nativars: • ‘Tara’: shorter form, uniform and upright, flowers gold; 24–30”. Lepidoptera: Species that use prairie dropseed according to the literature are the noctuid moth Anicla tenuescens, the noctuid moth Dichagyris reliqua, Dakota skipper (Hesperia dacotae), Pawnee skipper (Hesperia leonardus pawnee), Ottoe skipper (Hesperia ottoe), and Poweshiek skipperling (Oarisma poweshiek).	textbooks/bio/Botany/Gardening_with_Native_Grasses_in_Cold_Climates_and_a_Guide_to_the_Butterflies_They_Support_(Narem_and_Meyer)/03%3A_Common_Native_Grasses_of_the_Northern_Midwest/3.13%3A_Little_bluestem.txt
Planting Grasses can be planted anytime starting from after the last frost in the spring to one month before the first hard freeze in the fall. However, planting in the spring in zones 3 and 4 provides the best chance of success. Only in the spring and early summer should you plant bare rooted grasses, like plugs or other small plants. In the fall, plant only large container plants with established roots and allow for at least one month of growth before winter. Nativars are only propagated as plants, not seed, in order to maintain their characteristic plant form and growth habit. Make sure to give plants plenty of water until they are properly established. Supplemental water may be needed if grasses are planted in the summer. Once they are established, additional irrigation or watering is unnecessary for most native species. Determine the spacing between plants according to the desired landscape effect and the plant’s setting. A good rule of thumb is to space plants equal to their mature height (plants 4’ tall are spaced 4’ apart), but you can plant farther apart if using them as specimen plants. To create a hedge or screen, plant grasses one-half their height apart from each other (4-foot tall grasses would be spaced 2 feet apart for a hedge). Seed vs. Plants If you are not concerned with specific plant placement, the planting is very large, or you are restoring a prairie, then establishing grasses from seed is the best option. Restoration projects that are a few thousand square feet or more should be seeded with native seed that will result in a diversity of genotypes and plants. Numerous resources are available to help with your specific needs and questions from the University of Minnesota Extension, The Nature Conservancy, and the Minnesota Department of Natural Resources. 4.02: Maintenance Removing Old Growth Grasses require the removal of old tops, or previous year’s growth, in early spring. This can be done by cutting back or burning grasses. The best time of year to remove old growth is very early in the spring before new growth has started. Grass plants add interesting shapes to the landscape and provide shelter for various kinds of wildlife during the winter, so it is important to wait to remove old growth until the spring. Cutting Back The type of tool you use to cut back grasses depends on the size of the planting. Hand pruning shears or an electric trimmer can be used for small to medium sized plantings. Larger plantings, like restorations, may require larger implements, like mowers or haying machinery. Burning Native prairie grasses evolved with periodic fires so they respond well to prescribed burns. Seed set and vigor often increase with annual burning. However, insects and mammals may be killed during burns, so it is recommended to burn only a portion of a prairie or planting at a time. The Minnesota Deparment of Natural Resources, and the Minnesota Department of Agriculture provide resources on prescribed burning. Crown Division As bunch grasses age and grow outward, the old growth in the middle often dies, which can give large bunch grasses an uneven, doughnut, or unhealthy appearance. A great way to invigorate these older plants is to divide them, discarding any dead centers or old growth, and transplanting the newly divided crowns. In early spring as new growth starts, you can determine the alive material and easily discard the dead portions. To divide the plant, use a sharp spade or knife to chop through the crown. Remove the old, dead growth, and replant the crown sections. After replanting, water generously until the grass is established. Lepidoptera-Friendly Management Many butterflies and moths that feed on grasses as larvae overwinter in the larval stage, and so are vulnerable to fire. If you suspect that you have skippers overwintering in your planting, consider cutting back grasses instead of burning. If fire management is a must, burn only a portion of the planting, leaving a refuge for skippers or other invertebrates that may be taking shelter in the grasses.	textbooks/bio/Botany/Gardening_with_Native_Grasses_in_Cold_Climates_and_a_Guide_to_the_Butterflies_They_Support_(Narem_and_Meyer)/04%3A_Planting_Maintenance_and_Management/4.01%3A_Planting.txt
But I thought they were low maintenance? In general, native grasses are low maintenance, but like any plant, they can have periodic issues that require management. This chapter covers the most common problems that can occur with native grasses. Lodging Sometimes completely healthy grasses will flop over, or lodge. Lodging can happen at the root or the stem level and is considered any displacement in the plant from a vertical position. It is a common problem in grasses and affects field grasses as well as ornamental grasses. Many factors can play a role in lodging, making it hard to pinpoint the exact cause. Factors include weather, soil type, sunlight, genetics, and topography. Lodging is often associated with high nutrient loads in the soil, such as excess nitrogen. Lodging is also partially genetic. Some cultivars are more prone to lodging than others. To help prevent lodging, make sure to plant grasses in appropriate sites. Manage your plants by dividing them and cutting back or burning them each year. This prevents grasses from getting too big and heavy at the top. Avoid planting in shade or low light conditions, which can increase lodging. Cold Hardiness Hardiness refers to the temperature range in which a plant can grow successfully. The USDA plant hardiness zone map gives the average annual minimum winter temperatures in 10 degree zones across the United States. If a grass is native to your region then it should be winter hardy. However, the distribution of many native grasses, especially prairie grasses, spans large geographical regions. For example, blue grama (Bouteloua gracilis) grows from Saskatchewan to Mexico. Because it occurs across such varied climates, there is variation within the species. For example, the nativar ‘Blonde Ambition’, which was selected from New Mexico, has limited hardiness in zone 4 and may not be hardy at all in zone 3 or 2. Keep this in mind when purchasing nativars from garden centers and make sure to double check the zones on the tag. If buying native seed, check the source of the seed, and make sure it comes from a local seed source (usually within 200–300 miles). Pests and Pathogens Pests and pathogens are rare in native grasses, but they are not entirely immune. Fungus in various forms, affects grasses. One such form, rust, can occur on many different grasses, but most commonly affects reed grass, reed canary grass, big bluestem, little bluestem, and switchgrass. Rust is not a fatal disease, but it does discolor foliage. Switchgrass and reed canary grass are prone to leaf spot and blight diseases, especially during wet growing seasons, and root and stem rot pathogens. Smut and head scab have also been known to affect switchgrass (Gleason et al. 2009). Fungal diseases are more damaging to some of the blue cultivars of switchgrass like ‘Heavy Metal’, ‘Warrior’, and ‘Prairie Sky’. Some sedges may develop Pythium root rot if overwatered. Weed Control Weed control can be a bit tricky in grass stands because it is difficult to identify weedy grasses from the grasses you planted intentionally at the beginning of the season. Additionally, many herbicides are made to kill grasses and monocots (Meyer 2012). You can prevent weeds in between plants by using mulch. Also, weedy cool seasons such as quack grass will start growing early in the spring. If quack grass seedlings sprout near a dormant warm season grass, nonselective herbicides can be applied in early spring to kill cool season grass weeds without harming the desired warm season grasses. However, weedy grasses, like quackgrass, may often start growing within an ornamental grass clump. Quackgrass has extensive rhizomes that are difficult to remove. In addition to removing any visible stems, quackgrass can grow from small pieces left behind after weeding. If the problem persists, digging the plants followed by careful examination of the different grass roots may be necessary. If the weedy grass roots are totally entangled with the desirable grass, you might have to discard everything and purchase new weed-free plants. Careful observation of your plants is the best defense against unwanted weeds. Weeds are always easiest to remove when they are small. Self-Seeding Some species and nativars of native grasses are competitive and self-seeding, and so require management in a garden setting. Two of the most aggressive are switchgrass and river oats. River oats may be marginally hardy in zone 4 gardens, but will often self-sow and grow from new seedlings each year. To manage self-seeders, keep an eye out for seedlings and control with hand weeding or selective herbicide. If any grasses become problematic from self-seeding, seedheads can be removed before the winter. Self-seeding characteristics of each grass are listed in the Chapter 3. For more information about self-seeders, check out this article in the University of Minnesota Extension Yard and Garden News by Mary Meyer. 4.04: Literature Cited Gleason, M. L., M. L. Daughtrey, R. Chase, G. W. Moorman, and D. S. Mueller. 2009. Diseases of herbaceous perennials. No. SB608. O7 G471. Meyer, M. H. 2012. Ornamental Grasses for Cold Climates: A guide to selection and management. University of Minnesota Extension	textbooks/bio/Botany/Gardening_with_Native_Grasses_in_Cold_Climates_and_a_Guide_to_the_Butterflies_They_Support_(Narem_and_Meyer)/04%3A_Planting_Maintenance_and_Management/4.03%3A_Management.txt
So, how do you decide which grass is the best for your landscape? When determining which native grass is right for your specific planting, you should first take into consideration the site conditions. Site considerations include the soil type, amount of sun, and the size and location of your planting. This will help narrow down the native grasses that you should choose for the site. Secondly, you should consider your design needs. What size, shape, and color fits best in your design? Thirdly, consider the temporal aspect of your planting. Do you want something that blooms mid-summer or in the fall? For a quick guide to species for tough sites, take a look at this list from Mary Meyer, made for the 30th anniversary of the Grass Collection at the Minnesota Landscape Arboretum. This list includes both native and non-native grasses, so be aware and double check the grass species at USDA plants to figure out if it’s native or not. Nativar vs. Plant from Native Seed Once initial considerations are narrowed down, you can make the decision between using a nativar or a plant grown from native seed. For the bonuses and drawbacks and nativars vs. plants grown from native seed refer to section 2.4. Even when selecting native seed, different regional ecotypes are available, so research the origin of the seed you will be using. Functional Gardens Native grasses are great plants for gardens that are designed with sustainable or ecological goals, such as pollinator gardens or rain gardens. There are numerous resources available for anyone interested in both pollinator and rain gardens. Organizations that have resources on pollinator gardens include the University of Minnesota Extension, the University of Minnesota Bee Lab, and the Xerces Society. Organizations that have resources on rain gardens include the University of Minnesota Extension, the Evironmental Protection Agency, and the Wisconsin Department of Natural Resources. 5.02: Wildflower and Grass Pairings As discussed in Chapter 2, native grasses benefit butterflies and moths during their larval stage. During this stage, these insects are small and earthbound, and so are not very mobile. Lepidoptera do most of their traveling during their adult stage, when they can fly and traverse longer distances. To attract Lepidoptera to a planting, grasses should be paired with wildflowers that provide food for their adult stage. There is a lot of information available on how to attract pollinators using floral resources. However, there is less information out there about grass skippers and other grass-feeding species. Generally, grass skipper butterflies feed on the nectar of flowers that grow in the same type of habitat where their host grasses grow, and that bloom during their butterfly life span. They seem to prefer composites and other flowers with easily available nectar, but as a group are moderately opportunistic in their choices for nectar. Many grass skipper species have short life spans as butterflies, sometimes only 3 5 weeks. They can only use the flowers that are blooming during the window of time that they are flying. Different species emerge as butterflies at different times during the spring and summer season, taking advantage of different floral resources. Complete Life Cycle Table To benefit Lepidoptera during their whole life cycle, plant both the nectar flowers for the adult stage and the host plants for the larval stage. The following table list combinations of nectar flowers and grasses that serve Lepidoptera species during both their butterfly and larvae life stages.This list was compiled by searching the literature (guidebooks and scientific journal articles) and taking note of adult nectar plants and larval food plants. GRASS + FLOWER = LEPIDOPTERA big bluestem bird’s-foot violet cobweb skipper little bluestem Carolina larkspur cobweb skipper big bluestem wild hyacinth cobweb skipper, dusted skipper little bluestem wild strawberry cobweb skipper, dusted skipper switchgrass viburnum spp. pepper and salt skipper sideoats grama penstemon spp. hilltop little skipper switchgrass dogbane tawny-edge skipper switchgrass purple coneflower tawny-edge skipper big bluestem common milkweed Delaware skipper, Ottoe skipper big bluestem pickerelweed Delaware skipper switchgrass swamp milkweed Delaware skipper big bluestem ox-eye Dakota skipper, arogos skipper prairie dropseed black-eyed Susans Dakota skipper, Poweshik skipperling little bluestem purple coneflower Dakota skipper, arogos skipper, Poweshik skipperling, Ottoe skipper prairie dropseed leadplant Ottoe skipper lake sedge Joe Pye weed northern/marsh eyed brown sideoats grama green milkweed arogos skipper, Ottoe skipper lake sedge blue vervain broad-winged skipper lake sedge swamp milkweed broad-winged skipper lake sedge pickerelweed Dion skipper lake sedge sneezeweed Dion skipper blue grama blazing star spp. common branded skipper blue grama goldenrod spp. common branded skipper blue grama New England Aster Leonard’s skipper tussock sedge swamp milkweed northern/marsh eyed brown little bluestem New Jersey tea crossline skipper Limitations and Possibilities of Butterfly Gardens While the addition of native nectar flowers into human dominated landscapes has shown to be successful in providing nectar to butterflies (Vickery 1995), there is debate surrounding the efficacy of butterfly gardens as breeding habitat. There have not been any studies on whether restorations or butterfly gardens function as successful breeding habitat for grass skippers. Many of the rare species that are grassland specialists have only been known to occur on native habitat and are not suspected to travel far from their established populations. However, other species of butterflies, such as the Monarch, have shown to be able to successfully use butterfly gardens as breeding habitat. Additional research is needed to fully understand the benefits of native landscaping in suburban and urban areas to Lepidoptera communities and rare species. A main benefit of residential butterfly gardens may be as stepping stones between larger natural areas, where Lepidoptera can obtain nectar before continuing on to permanent habitat (Vickery 1995; Di Mauro et. al. 2007). Hall et al. (2017) suggest new thinking as we continue to learn how to best design and use our man made environments to make them livable for not only us, but our critically important natural world. 5.03: Literature Cited Hall, D. M., Camilo, G. R., Tonietto, R. K., Ollerton, J. , Ahrné, K. , Arduser, M. , Ascher, J. S., Baldock, K. C., Fowler, R. , Frankie, G. , Goulson, D. , Gunnarsson, B. , Hanley, M. E., Jackson, J. I., Langellotto, G. , Lowenstein, D., Minor, E. S., Philpott, S. M., Potts, S. G., Sirohi, M. H., Spevak, E. M., Stone, G. N. and Threlfall, C. G. 2017. The city as a refuge for insect pollinators. Conservation Biology, 31: 24-29. doi:10.1111/cobi.12840. Di Mauro, D., T. Dietz and L. Rockwood. 2007. Determining the effect of urbanization on generalist butterfly species diversity in butterfly gardens. Urban Ecosystems. 10:427–439. doi:10.1007/s11252-007-0039-2 Vickery, M. L. 1995. Gardens: the neglected habitat. pp 123–134. In Ecology and Conservation of Butterflies. Chapman and Hill, London, England.	textbooks/bio/Botany/Gardening_with_Native_Grasses_in_Cold_Climates_and_a_Guide_to_the_Butterflies_They_Support_(Narem_and_Meyer)/05%3A_Grass_Selection_and_Butterfly_Pairings/5.01%3A_How_to_Begin.txt
This course is about organisms, biological things that most of us consider to be very familiar. The idea that life comes in packages called organisms is something that we all accept. And for most students, the study of biology, at least initially, is focused on organisms, most often humans or things that are much like humans (mammals). Like a number of biological concepts, organism is sometimes hard to pin down and there are certain situations where the concept of organism doesn't apply very well, especially for some of the forms of life covered in this course. An understanding of organisms is enhanced by viewing them comparatively and by viewing them from different perspectives. This course views organisms from four different perspectives, considering descriptions and comparisons of their (1) structure, (2) reproduction, (3) acquisition of matter and energy and (4) their interactions with each other and the conditions manifested in their environment. Our first task is to try to define what an organism is. Let us start by looking at things that might be considered organisms: The most obvious organisms are the moose. Their structure and development make their organismal nature easy to define. Other parcels of life, the grass, forbs, shrubs and trees may be more challenging to package as organisms. Defining an organism What are organisms? They are a manifestation of life, a 'living thing' . For most people organisms are the idea in their head when the term 'a living thing' is mentioned, but biologists appreciate that 'living things' don 't have to be organisms, they could be parts of organisms (fingers, cells, membranes) or groups of organisms (populations, communities) and maybe even something that mixes life and non-life (e.g., cell walls, soils). Life itself is hard to define and it is manifested at many scales of time and space. It is important to appreciate that there are' living things 'that aren' t organisms. Organisms are just one manifestation of living things. But what is special about the organism that sets it apart from other levels of biological structure? Can we pin the word down? 'When I use a word, ' Humpty Dumpty said in rather a scornful tone, 'it means just what I choose it to mean—neither more or less.' Words are essential to biology because they provide a means of communication and, without some conformity on definitions, communication can be difficult. At the same time, some words need to remain somewhat ambiguous because to pin them down too far renders them useless. Additionally, a word can shape thoughts and keep us from seeing phenomena. Organism is perhaps such a word!! Here are some attempts to define an organism, each followed by some limitations of the definition: • An organism is a fundamental unit of life: 'Fundamental' is a pretty vague term (which indeed might make this definition more useful!) but many would consider that a cell is the fundamental unit. It is important to realize that sometimes cells are organisms but sometimes they are just components of organisms. Most colleges teach a course on cell biology but (surprisingly!) courses on organisms are less common. • An organism is a unit of life that can reproduce: One of the characteristics of organisms is that they can replicate themselves, but they are hardly unique biological entities in this respect—cells, DNA, organelles and sometimes even communities can replicate themselves. And one might be able (depending on definitions) to come up with organisms that lack this ability (see the discussion of caterpillars below). • An organism is a cell or group of cells that is genetically distinct and genetically uniform. For familiar organisms (i.e., humans) this seems to work. Generally, a human organism is genetically distinct from its parents and from its offspring, and its cells are genetically uniform (except for sex cells). However, most unicellular organisms and many multicellular organisms produce 'clones' of themselves that are genetically identical but most would consider the offspring to be new organisms. Indeed, humans occasionally have identical twins, with two individuals that are identical genetically, and few (especially the twins!) would consider them one organism. Armadillos take this a step further and always give birth to genetically identical quadruplets. • An organisms is a cell or group of cells that is spatially separated from other cells, a spatially discrete unit of life. Thus, individual cells are organisms (unicellular organisms) when they are not attached to other cells but if they are in a cluster (i.e., attached to each other) then the cluster is considered an organism. This works pretty well but there are problems: • Sometimes what we consider to be separate organisms (e.g., aspen trees) are actually connected below ground by their root systems. Is the tree an organism or the cluster of trees an organism? • Pieces of (spatially discrete) organisms break off (e.g., leaves fall off a tree)—are falling leaves organisms since they are now spatially discrete? What about egg and sperm, they are spatially discrete bits of life, should they be considered organisms? • It is common to have spatially discrete structures (e.g., lichens, corals, mycorrhizae) that are composed of cells that have very different genetic constitutions (lichens consist of a fungus and an alga, corals [ often] consist of an animal and an alga; mycorrhizae contain a plant and a fungus). Generally, we consider associations of organisms to be a community, but maybe communities can be organisms? • What constitutes attachment? Mosses and lichens are attached to trees but most would not consider the combined entity to be an organism. Barnacles attach to whales but they are not considered a single organism. • An organism is a unit of life that is 'self-sufficient' , that can 'make it on its own' : Mosses and lichens don 't need the tree, they simply need to attach to whatever is available. In contrast, a liver need s the rest of your body in order to survive. Red blood cells circulat ing in blood are not considered organisms whereas Paramecium or an amoeba circulating in a pond would be because they can survive on their own. However, there really are very few organisms that are truly ' on their own ' and self-reliant: cows need grass, cows need a particular group of organisms in their digestive system, pine trees need fungi associated with their roots , and, as we will study, all plants need bacteria and fungi. Almost all organisms depend on other organisms for their livelihood and it is very hard to use ' self-sufficiency' to define an organism. • An organism is a unit of life that is distinct in time; it has a starting point and an ending point. For familiar (sexual, multicellular) organisms the start might be fertilization of an egg by a sperm and the end might be considered death. But organisms might start and end different ways. Consider a butterfly (the entity that can fly) : one might argue that it starts when it emerges from a chrysalis and ends with the death of the butterfly. Similarly, one could argue that a caterpillar is an organism that starts as a fertilized egg and ends as a chrysalis. This certainly isn 't death but it is the end of the caterpillar. Thus, we might say that the thing we generally call a butterfly exists in two different forms, both of them organisms : a caterpillar and a butterfly. Or consider a particular interesting form of life called a cellular slime mold . It sometimes exists as amoeba-like single cells. The cells engulf other bits of material, both living and dead, grow and divide to form more amoeba-like cells. When conditions are right the cells aggregate, forming a multicellular slug a few millimeters long that moves briefly in a manner reminiscent of a slug and then stops moving and undergoes a transformation into a stationary entity with a base connected to a thin stalk standing up to 10 mm in height with a ball at the top of the stalk. In time, the ball breaks open, releasing single cells that are dispersed and can grow into more amoeba-like cells. Like butterflies (and, as we will see, like some plants), cellular slime molds have multiple forms, in this case three: one form that specializes in eating (the amoeboid cells), one specialized for moving (the slug) and another that specializes in reproduction (the fruiting body). Thus, some ' living things ' exist multiple forms, and each of them might be considered ' an organism'. And each form has a starting point and an ending point but they may not be the familiar ones of fertilization (forming a zygote) and death. • O rganisms change through time, that is, they develop , changing in structure and in function. The simplest life-cycle pattern is a single cell that 'begins' when it is produced by the cell division of an existing cell and 'ends' when that cell divides to produce two daughter cells. Aside from growth, the basic structure (form) remains the same but internally (physiologically) there are a host of transformations (i.e., development) that allow for the acquisition of the materials necessary to form a new cell as well as changes that allow for division to take place. Multicellular organisms generally start with a single cell that proliferates to many cells , and the cells stay together after divid ing to produce a multicellular form that generally changes structure substantially, especially at the early stages of development. As we will see when we study reproduction and sex, in some organisms the cells that are 'passed on' (i.e., that can initiate the next generation) are of two types (e.g., egg and sperm) and they need to find each other and unite in order to form a cell that is capable of dividing to produce a new multicellular form. For other organisms a single cell released from a parent organism may undergo the developmental process to form a multicellular organism. • The development of familiar (animal) organisms is usually quite regimentedand resultsin a fairly consistent 'final' form. We will see that the development of some 'inanimate' (i.e., non-animal) organisms is not as rigid. In fact, many of the organisms that we will consider don 't produce a ' final 'form(an endpoint), they keep growing and growing. How do organisms end? The end of an organism doesn' t have to be deathby 'old age' ( 'wearing out) or by being ravaged by environmental conditions (e.g., cold weather) or biotic interactions(a disease or a predator). The end of some organisms is an aspect of development, e.g., the end of a caterpillar is the formation intoa chrysalis, the end of the ' slug 'stage of a cellular slime mold is its transformation into a stalked structure. This brings us back to the question of reproduction. As was mentioned above, one could argue that some organisms don' t reproduce themselves: caterpillars don 't make more caterpillars, they make butterflies; and butterflies don' t make more butterflies, they make caterpillars. We will study a number of 'biological things' that exhibit life cycles that include multiple forms, each of which could be considered an organism and each of which 'passes on' (produces) a cell or a group of cells that develops to form the next stage(organism), eventually repeating the cycle. Organismal life is perpetuated through time but is manifested in different forms(each an organism).If we consider the individual stages to be organisms than what might we call the entity that includes all stages? Usually it is also considered 'an organism' —monarch butterflies are both the caterpillar and the butterfly. This perhaps unfortunate because it obscures some interesting biology and it certainly makes defining 'organism' more challenging. In an organismal sense monarch butterflies are clearly not the same as caterpillars, their structure and function are very different although they are connected to each other not only through developmental patterns and also in a genetic, evolutionary and taxonomic sense. • Organisms might be defined by their ability to grow. This requires the acquisition of material and the use of that material to make the organism bigger. Although generally this is the case, there certainly are some things that one might consider an organism that are not capable of growth: consider mayflies (the ones with wings, not the aquatic form). These organisms aren 't capable of growing because they aren' t capable of eating, their mouths are permanently closed! The same thing is true of the 'slug' form and the 'stalked' form of the cellular slime mold and, as we shall see, many plants transform from a form that is capable of growth to one that is not. Caterpillars grow but don 't reproduce, butterflies don' t grow but they do reproduce. The ability to grow is essential somewhere in the life cycle but does not have to be present in all forms of the organism. • One final aspect of organisms is that they are considered to be the unit of selection in Darwinian evolution, although occasionally arguments are made for selection at other levels of biological organization (genes, populations). One of the purposes of this course is to give students a new perspective to understand life. Understandably, we all think that living things (i.e. organisms) are like humans. While all life is fundamentally the same in its chemical composition and in how it functions, there are substantial differences in the way they go about the business of living. We will examine a variety of organisms, some very familiar like pine trees and dandelions, some very unfamiliar like cellular slime molds, with an emphasis on comparing and contrasting a variety of features. This study should give students a new vantage point from which to study life's organization and behavior. So, what are organisms? They are biological entities that can be defined in space (i.e. they have a boundary and a form–a structure) and can be defined in time (i.e. they have a beginning and an ending and a pattern of development between these times). They function in a way that ultimately results in their reproduction, i.e., making more of themselves. Reproduction necessarily requires the acquisition of materials so that growth can occur. Occasionally organisms have multiple forms and each of these forms can be considered an organism (e.g., caterpillar and butterfly; amoebae, slug and fruiting stages of a slime mold). In situations like these, an individual stage might not both grow and reproduce, but collectively, as result of the action of all the stages, both growth and reproduction are accomplished. As a result of their structure and their activities, organisms interact with their environment and with other organisms. This course will be studying a diverse group of organisms that at one point were considered plants, considering their structure and how it develops, their ability to reproduce, their acquisition of matter and energy, and interactions with conditions and with other organisms.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.01%3A_Organisms.txt
While it is uncommon, people sometimes give names to individual plants. For example, i n Sequoia National park stands 'General Sherman' , considered to be the largest organism living on earth. Because organisms are discrete packages (i.e., with boundaries in space and time) it certainly possible to name them. But there are an awful lot of them and it is simply impractical to name them all. However, if one observes organisms, it is quickly apparent that they occur in groups, i.e. there are groups of them that look similar and thus the group can be considered an entity itself. Moreover, additional study will usually reveal that identified (i.e., defined) groups of organisms can often be: (1) subdivided into smaller groups and (2) lumped together into bigger groups; that is, that the diversity of organisms is organized into clusters of similarity and there are clusters of the clusters. These biological patterns seek an explanation: why do organisms come in groups and why are there groups of groups? Even if organisms did not 'naturally' occur in groups it would be important for biologist to define groups; there is simply so much biological diversity that some sort of 'filing system' is required to organize it all. Thus , there are two aspects to organizing organisms into groups: (1) a practical aspect, producing a way to manage all the variety of organismal life, to arrange its vast diversity, (2) a mechanistic (process) aspect, producing a system that will allow biologists to understand mechanisms that result in the patterns of diversity , e.g., why there are groups. To a large extent these two aspects can be satisfied simultaneously, i.e., there are systems that categorize life easily and also allow users to study the processes (evolutionary mechanisms) that lead to the categories. However, the biological landscape is vast ; clusters range from groups (species, or perhaps subspecies) that might have less than 1000 organisms that all 'look' very similar to groups (families, orders) that are comprised of millions of individuals , with members that do not 'look' very similar yet do possess some 'fundamental similarities.' With such a span in scale one should appreciate that there may be situations where a system that is useful to consider the evolutionary relationships (i.e., the phylogeny ) between groups of organisms may not very handy as a filing system. O r, looking at it from a different perspective, classification schemes that easily organize life 's diversity may not do so in a way that reflects the phylogeny of different groups. An example familiar to most biology students would be ' reptiles ', a handy group in terms of classification (reptiles are vertebrates that aren' t amphibians, birds or mammals), but a group that does not represent phylogeny. This book is primarily about organisms. A nd while i n general it will use a phylogenetically based classification scheme , occasionally it will consider groups that are 'artificial' and do not reflect a phylogenetic entity , examples would be 'green algae' and 'gymnosperms' . We will be dealing with scientific names, and the groups that they describe, throughout the book and it is important to appreciate the basis and the limitations of the naming. Shakespeare asks “ what 's in a name? ” and answers with the implication that names are basically trivial. But names are profoundly significant in ways that often are not appreciated. Like water to a fish and air to humans, we are so immersed in names that we rarely stop to consider them. But names say much about humans, about how we think and what we think. Indeed, it is probably the case that names not only reflect how we think, they may actually dictate how we think. Names reflect the organization by which we view things and the way we process the information that we receive. While classification is useful whenever one is faced with a large number of variable entities, we need to consider to what extent our classification is a reflection of our thought (i.e., we are imposing order on something that isn' t really ordered) , or a reflection of reality (i.e., there is an order that we are describing) , or something in between. Stated another way, names reflect an organization and it is important to consider whether the organization is inherent to what is being named or inherent to our minds. Keep in mind that naming is a grouping process, i.e., it is a mechanism to put 'things' (in our case biological things) together. Faced with diversity , humans lump things together into categories, putting similar things together into groups; this makes the diversity more manageable and this is what classification (naming) is all about. At the same time, one should appreciate that any classification, in fact, the very process of 'naming' , results in a loss of information to the extent that any organism varies from the norm that characterizes the group. The name 'tree' sets up a classification of living things, one that is both useful and arbitrary; not all trees are the same and describing something as a tree strips an organism its individuality. The same could be said for the terms 'sequoia' , 'Sequoiadendron ' , and ' Sequoiadendron giganteum ' . For any named biological group, it is important to consider how 'real' the group is: do the entities naturally fall together or are we just putting them together as a means to simplify the system. If the groups are 'real' ( valid ) one might consider what biological processes might relate to their validity ; what biological process forms the group? Thus the fundamental question to address when naming groups of things is what criteria will be used to group them. For instance, if you are classifying motor vehicles one might group them based on color, on manufacturer , or on type of vehicle. When considering organisms deciding what criteria to group them on is a tough question: organisms are exceedingly diverse and they differ in myriad ways. Because living things have many, many characteristics, there are many different ways that they can be grouped. Moreover, until some goal has been attached to the classification, there is not 'right' way for it to be done; it is simply an arbitrary way to simplify a diverse system. Classifying cars based on color is certainly easy and, in some cases, might be useful, but it is not very useful if one's goal is to explain the overall patterns in car variation. Two features make a classification easier to develop and make the entities thereby defined more 'real' , i.e., an accurate representation of the reality. One feature relates to the pattern of variation. Consider a group of organisms that has only one characteristic, or perhaps only one characteristic that might distinguish one organism from another, for example, a group of organisms that are all the same except for length. Figure 2 (a) and (b) show two such groups of organisms, one where a classification (naming) is an accurate reflection of reality and one where it is not. Both plots are 'frequency histograms' , showing the distribution of individuals of different sizes. The difference between the two is in the pattern of variation. The group of organisms in 1(a) is easy to classify into three groups because the there are 'gaps' in the distribution. A statistical way of describing what is shown in 1(a) is that one can define groups ( 'small' , 'medium' , 'large' ) so that the variation within a group is small compared to the variation between groups. The group of organisms in figure 1(b) is less easily classified because there are no gaps in the distribution of organisms of different sizes; there are no obvious groups, and whatever group you might define has as much variation within it as there is between that gr oup and the remainder of organisms. Note that it certainly is possible to classify the organisms shown in 1(b); we could divide them into that are 'small' (less than 6 units in length), 'medium' (greater than 6 but less than 16 units in length) and 'large' (16 units or more in length). Although such a classification is arbitrary and not an accurate reflection of reality, this does not mean that it might not be useful. Figure 2 Two examples of variation within a group of organisms. Both plots are frequency histograms, showing the number of individuals within a series of size classes. A second factor that makes classification more 'real' is a correlation between different characteristics. If all the small organisms of figure 1(a) were round, the medium sized one 's square and the large ones cylindric there would be a correlation between size and shape. This would make the categories (small, medium and large) more justifiable; it would make them more ' real'. Alternatively, if all the size groupings had all three shapes it would make the categories based on size (or based on shape) less real. In general , organisms show variation that is discontinuous and they exhibit correlation in variation of different characters, and both these features make classification easier. These pattens of nature not only make classification of organisms simpler, by reducing the number of characters that one needs to consider, it also hints that there are better, or perhaps even a 'best' , way to classify living things. This might be described as a 'natural' classification, one that is based on 'fundamental similarities' . This idea was apparent to early naturalists. Carl Linnaeus, who developed one of the first classification schemes, recognized that his technique of classification, although useful, was flawed because it was not 'natural' , i.e., it put things together based on features that did not correspond to many other features. His categories were useful because they put organisms into bins and made their diversity much more manageable, but Linn ae us appreciated that there was an organization to the diversity of living things and that this organization was not always reflected in his categories. If there was an organization to the diversity of living things, there should be a reason for this. Three hundred years after Linnaeus, Charles Darwin, who was an excellent student of classification (of organisms as varied as beetles, orchids and barnacles) , came up with an explanation for the correlated variation and for the observation that living things appeared to fall into 'natural' groupings: it was consequence of the process of evolution , the changes in the characteristics of groups of organisms through time. The fundamental similarity of groups of organisms was due to the fact that together they shared a common evolutionary ancestry. Indeed, Darwin's taxonomic acumen was highly significant to his elucidation of the process of evolution. He made two key observations that were connected to his understanding of taxonomy : 1. in widely separated parts of the world where conditions are similar, for example, deserts in South America and in Africa, organisms often look similar even though they are not 'fundamentally similar' ; 2. in one region of the world where conditions varied considerably within a relatively small geographic area, e.g., going from plains to mountains in southern South America, organisms that on first examination seem very different, upon closer study are 'fundamentally similar' . The process of organic evolution explained both of these patterns; in the first instance , convergent evolution could cause organisms that are fundamentally different (i.e., not closely related) to look superficially similar; in the second case divergent evolution (adaptive radiation) could cause fundamentally similar (i.e., closely related) organisms to diversify and look different. It can be seen that although evolution explains different reasons why things might look alike, it does NOT, at least initially, explain how one might group things : should it be on the basis of 'basic, i.e. fundamental, similarity' and thus combine things that may not look that similar until 'closely examined' (see figure 3 which shows two different members of the cactus family, a leafy cactus and a more 'normal' looking cactus); or should things be grouped on the basis of 'superficial similarity' , i.e. group things if, on the surface, they look similar (see figure 4 which shows two plants that look superficially similar yet are 'fundamentally' different). The distinction may seem petty (i.e. what is the difference between superficial similarity and fundamental similarity), but it has real consequences because perceptions vary. For example, people commonly group flowers on the basis of flower color, which is one of the most easily perceived characteristics of plants, but it turns out to also be one of the most superficial. Figure 3 These two plants are closely related and both in the cactus family, yet they 'look' very different, with the Pereksia (on the left) having a more typical plant form with typical leaves and branches, while the saguaro cactus on the right has evolved a very different form with no obvious leaves, an unusual branching pattern and an abundance of spines. Figure 4 Convergent evolution in plant form. The plant on the left is a euphorb that is not at all closely related to the cactus on the right. Although similar in form (unbranched, lacking typical leaves, having spines), this is not the result of a close evolutionary ancestry, but is the result of convergent evolution, two groups of plants 'converging' on a form that presumably is useful under arid conditions. For one particular group of people, biologists, Darwin 's theory of evolution did provide a rationale for grouping and naming living things, organisms should be classified based on their phylogeny, their evolutionary ancestry, i.e., their fundamental similarities. For those who are studying organic diversity it would desirable to group things based on ' fundamental similarities ' (= evolutionary ancestry) because, among other things, it allows us to view the consequences of evolution. But we are still left with the question of how to recognize phylogenetic groups. From pre-Linnaean times through Darwin and up until the middle of the last century, sci entists searched for features that they thought reflected ' fundamental similarities '. After Darwin' s ideas were accepted , scientists realized that what they were looking for were features that reflected the evolutionary past of organisms. But these characteristics are elusive entities and no one really knew if they had found one because most evolutionary history is impossible to trace—the fossil record is grossly inadequate except for large-scale overviews. Over the last fifty years molecular biology brought new approaches to taxonomy. It allows organisms to be compared on the basis of similarities in the sequences of amino acids in proteins or sequences of nucleotide bases in nucleic acids (DNA, RNA). These are more than just new features to be compared; they are features that one can argue do reflect evolutionary lineage. Through time, changes accumulate so that the longer the time since two lines diverge the more differences that accumulate in the sequence of amino acids in proteins or nucleotide bases in nucleic acids. One might argue that this is how classification has always been done, that the assumption has always been that groups 'accumulate' more and more differences through evolutionary time and that you separate groups as they diverge in characteristics. Although this is true in a very general sense , it does not strictly apply—classification has always involved 'character weighting' , i.e., observers have always felt that some characteristics , ones that are less easily modified by natural selection should have more 'weight' in a classification than others, characteristics, e.g., flower color, that are readily shaped by evolution and thus might occur independently in two lines that are not phylogenetically related. The formation of groups is based not just on the accumulation of differences but rather the acquisition of key differences , the differences that reflect phylogeny. Molecular biology provides a tremendous increase in characteristics that can be compared. And, significantly, it provides characteristics that are unlikely to be selected for by natural selection. This is significant because if two organisms share a feature this can be explained two ways: (1) it may reflect a common ancestry ( 'fundamental' similarity) , or (2) it may reflect a common selective force ( 'superficial' similarity). However, if two organisms share a feature that is unlikely to be selected for then the only explanation involves a common ancestry. Assuming that one wants a classification based on ancestry, then using molecular data provides a way to trace ancestry. One feature of b iological classification from the time of Linnaeus to now, and a feature of most (but not all) classification s , is that they are hierarchi c al , with species grouped into genera, genera into families, families into orders, orders into classes, classes into phyla and phyla into kingdoms (and, some would add, kingdoms into domains). However, with the exception of species (whose definition we will consider later in the course) , none of these levels is defined— a genus is a group of related species, but how closely related is never specified. Thus, although it is often the case that there is agreement that a group of living things represents a taxonomic entity, exactly what level that group should be placed at, and how this group relates to other groups, may be quite controversial. Moreover, the seemingly logical idea that groups should be organized on the basis of evolutionary ancestry doesn 't mesh very well with a classification that has levels–evolution doesn' t necessarily operate in a way to produce levels; and there is no reason to assume that the levels produced on one branch might coincide with levels on another branch. One certainly can devise classification schemes that match more closely the way that we believe evolution operates; but these schemes will not be as useful in pigeon-holing (categorizing) living things. As is the case with many concepts (and in fact with words themselves!) one must balance between utility and accuracy; useful concepts often distort reality; making them more real often renders them less useful. Most biologists approach classification from a 'cladistic' viewpoint which is centered on the idea that evolution produces 'clades' (groups) as a result of the splitting of a previous ly existing clade. Seen through time one would see a branching diagram. In general, this probably reflects the general pattern of evolution and the development of diversity. But we have good evidence that groups not only split but sometimes merge (e.g., the endosymbiont theory for the appearance of eukaryotes; secondary endosymbiosis and the origin of multiple algal groups) and neither cladistic approaches or a hierarchical system deals well with this possibility. For most of this course we will speak of groups that are generally considered 'real' , that is, a group of organisms that are set off, in terms of phylogeny and in terms of characteristics, from other living things. Because our focus is on organisms and their diversityand we will be less concerned with the exact placement of the group in a taxonomic scheme or the exact phylogenetic relationship between this group and other groups. This information is covered in the 'fact sheets' for specific groups in the Organisms section of the book, but note that the text as a whole is NOT organized along phylogeny/taxonomy lines. In fact, I will refer to a number of 'artificial' (i.e., non-phylogenetic) groups, these are listed below and serve as examples of groupings that are known to be artificial yet are useful for reasons of history, ecology or convenience. • 'inanimate life' — living things that are not animals (i.e., in the Animal Kingdom). Using a five-kingdom classification this would include Monera (i.e., prokaryotes), Fungi, Plants and Protists. • algae — aquatic photosynthetic organisms. This category spans most of the phylogenetic universe! Yet for ecological reasons, it is useful! • macroalgae — multicellular or large colonial algae • green algae — aquatic, photosynthetic organisms with multiple similarities to plants (pigments, cell wall chemistry, storage carbohydrates). This group is useful to know about but for a host of reasons is difficult to define rigorously in a phylogenetic sense. • gymnosperms — plants that have seeds but don't have flowers. This is a historical category that is still in common use and worthwhile to be aware of. It is an example of a grouping based on the lack of a particular characteristic, which generally is not phylogenetically sound. Other examples of artificial groups based on what they lack are: • prokaryotes — cells without nuclei • protists — eukaryotic organisms that are not animals, fungi, plants or prokaryotes • bryophytes — plants without vascular tissue (mosses, liverworts and hornworts) • fern 'allies' — vascular plants without seeds	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.02%3A_Taxonomy_and_Phylogeny.txt
Significance of boundaries A coccolithophore, which has an outside coating of overlapping plates of calcium carbonate We have defined organisms as living material that are discrete (i.e., bounded) in space and time. Being distinct in space requires a boundary that separates the organismsfrom the 'outside' . For single-celled organisms the boundary is the outermost component of that cell, and for most of the single celled organisms studied in this course that outermost componentis a cell wall, but the chemical and physical nature of the wall varies considerably. For some unicellular organisms there is no cell wall and the outermost layeris a structure called a cell membrane. For multicellular organisms, the boundary is the collective of all the (generally specialized) cells on the organism's perimeter, its dermal tissues. For most of the organisms studied here the dermal cells have a cell wall and also a specialized coating on the outside. This chapter examines the physical and chemical nature of organism boundaries and also considers the significant functions of the boundary, starting with its influence on flux, the movement of materials in and out of the organism. TOPICS • Boundaries and flux • Structural, chemical and physical nature of boundaries • Membrane • Walls • Polysaccharide cell walls • plants, fungi, bacteria, archaebacteria • Inorganic cell walls • Internal cell walls • Dermal tissue • Coatings • Boundaries and structure • Boundaries and movement • Boundaries and communication Boundaries and flux One reason t he boundary is significant because it represents a barrier to movement into and out of the organism. This movement can be described as a 'flux' and flux can be modeled as being a function of three parameters present in the following formula (which is actually a model of what causes materials to move): Flux = (driving force * surface area) / resistance While in many ways this equation is a simplification, it does point out the three fundamental properties that determine the flow of materials into and out of the cell: • Driving force—this is generally approximated by the difference in the concentration of something on the inside vs. the outside , but in the case of heat flow the driving force is the difference in temperature; considering the movement of fluids (e.g., air, water) the driving force can be pressure differences; in all these situations, the bigger the driving force, the more flux there is. • Resistance—the resistance can be described as the difficulty with which materials can move from the outside to the inside, or vice versa. Some materials readily allow the movement of molecules (or heat) through them , i.e., they have a low resistance. Other materials only reluctantly allow materials (or heat) to move through them, i.e., they have a high resistance. It is important to appreciate that resistance depends on the substance/ molecule one is keeping track off; a boundary may have a very high resistance to some molecules and a very low resistance to others. (related terms are conductance and permeability, which , for our purposes, are the reciprocal of resistance) • Surface area — the more surface area through which materials can flow, the more flux. As will be discussed in the next chapter , the surface area is determined by the shape and size of the organism. The driving force is determined by where the organism is and what is going on inside and outside of the organism. Organisms can manipulate fluxes by manipulating the driving force. Most of the discussion of these mechanisms is beyond the scope of this book but we will mention some in Chapter 22 . In the case of the flow of materials or heat into and out of cells, t he resistance to flux is determined by the chemical and physical characteristics of the boundary between the organism and its environment. Besides being important in influencing the flux of materials into and out of organisms, boundaries serve other important functions that will be discussed after describing different types of boundaries. Structural, chemical and physical nature of boundaries Cell membrane The chemical nature of the cell membrane should be familiar to biology students : a phospholipid bilayer with proteins imbedded in and through it. The two sides of this membrane are 'w et' (i.e., hydrophilic) due to the attraction of polar water molecules to the charged phosphate groups. The interior of the membrane is dry (i.e., hydrophobic) because lipid molecules carry no charges and have no regions that are even partially charged and to which a polar (= partially charged) water molecule might be attracted. However, there are tubular proteins passing through cell membranes. These tubular proteins may have a 'wet' in interior, providing for water filled channels running from the outside to the inside. Some of these channels allow selective passage of ions and many of them can be manipulated (opened or closed). Although the chemical nature of the hydrophobic layer is different in the Archaea, the basic structure of membranes is fundamentally the same for all organisms. Significant to organism function is that the membrane is quite permeable (low resistance) to small, uncharged molecules ( significantly O 2 , CO 2 and H 2 O) but not very permeable (high resistance) to charged molecules (ions) and to larger molecules, especially if they are not soluble in lipids. The cell membrane generally has little strength and readily yields to internal and external forces, causing the cell to change shape. Organisms lacking a cell wall in terrestrial environments cannot be very tall because the force of gravity flattens them. This can be overcome with an internal skeleton (vertebrates) or an external one (exoskeleton), which is a rigid boundary. Cell walls In contrast to the consistent presence and composition of the cell membranein organisms, cell walls show much greater variability. Many organisms (e.g., almost all animals) have no cell wall. For the organisms that possess walls, its composition is quite variable (Table 1), although some of its structural features are more consistent. Polysaccharide cell walls The cell walls plants, fungi, water molds, brown algae, red algae and (most)green algae have a similar structure and chemistry. Thesecell walls are composite structures, and can be considered to be gels. They consist of fibers made of elongate carbohydrate polymers that resist being stretched. These are imbedded in a matrix of different carbohydrate polymers that are highly hygroscopic (water absorbing) (Figure 4). Two common fiber materials are cellulose (found in plants, water molds and green algae) and chitin (found in fungi). Cellulose is a polymer made up of glucose monomers, as is the more familiar polysaccharide, starch, but the two have very different roles, one structural and one energy storage. Chitin is also a polysaccharide polymer but the subunits (N-acetylglucosamine) are hexoses with a nitrogen attached (Figure 5). Both cellulose and chitin occur in fibers, strands of multiple (20-100) individual polymer molecules interacting with the neighboring molecules to form a crystalline structure. These fibers are significant in multiple ways: (1) because there are multiple molecules and they are bound to each other , the fibers, and the wall they are present in, are considerably 'stronger' (see below) than would be the case if the individual molecules did not interact to form fibers ; (2) the fiber is difficult to digest because the component polymer molecules are not very accessible to enzymes and the fiber itself is not soluble in water, in spite of the fact that the monomers, e.g. glucose, are very soluble in water. The fibers of chitin and cellulose are deposited in a matrix of other polysaccharide polymers whose composition is much more variable, meaning both that the polymer 'chain' consists of several subunits, not just one, and the linkages between subunits are more variable, not always the same and not always 'end to end' but with branching (one subunit connected to three other subunits, not just to the ones 'in front and behind' it). While these polymers are given names (hemicellulose, pectin, agaropectin), the names refer to groups of chemicals and not to a specific chemical structure and composition. Some of these chemicals bind to cellulose or chitin fibrils, connecting them to each other and providing more structure to the cell wall and also allowing the cell walls of adjacent cells to be bound to each other. Although they are made primarily of polysaccharides, these cell walls contain some protein molecules. The function(s) of the proteins are not known with certainty. They are probably not particularly significant structurally in the way that the chitin and cellulose are and the way that the intracellular proteins tubulin and actin are. The protein component of the cell wall is probably significant in being able to change, through enzymatic action, the structure of the rest of the wall, e.g., during cellular growth when the wall 'relaxes' and allows the internal pressure of the cell to bring about growth (Chpt 25). Wall proteins are probably also significant in allowing material to get through the cell wall (both inward or outward). Generally, carbohydrate cellwalls readily absorb water and can be considered to be a hydrogel. The absorption of water comes from the adhesionofwater molecules to the carbohydrate components of the cell wall, in particular the 'matrix' polymers (e.g., pectins, hemicellulose) plus the cohesion of water to itself. The hydrophilic nature of the cell wall makes it highly permeable (low resistance) to the movement of water (as a result of either diffusion or as a result of pressure differences, i.e., mass flow (more discussion on this when discussing material movement, Chpt 24). Small water-soluble molecules also move readily through the wall both as a result of diffusion and as a result of the water that it is dissolved in moving via mass flow. However, dissolved cations may be slowed by being bound to negatively charged components of the polysaccharides. Under some circumstances, the cell wall of plants can shift from being hydrophilic to being hydrophobic as the result of the deposition of 'water-proofing' materials called cutin and suberin in the wall. These materials are found in cell walls of certain plant tissues where their ability to retard the movement of water is significant. Both suberin and cutin are mixtures of multiple compounds including polymers with hydrophobic subunits and wax molecules. Like the lipid portion the cell membrane, these chemicals are 'dry' (hydrophobic) and water movement through walls with these materials is much retarded. While there are some chemical differences between the two, the primary distinction between cutin and suberin is location. Cutin is deposited in a coating called cuticle, present on the external walls of cells located on the outside of the aerial portions of plants. Suberin is deposited in the walls of certain cells as they are produced. Suberin is found in the above-ground portion of the plant in places where growth or mechanical damage has eliminated the cuticle. Suberin is also found in the below-ground portion of the plant in a cylindrical tissue called the endodermis, whose significance will be discussed later. A final component of found in some polysaccharide cell walls is lignin, a material absent in non-vascular plants (e.g., mosses) but found in the cell walls of most vascular plants, and a material that is highly significant to their evolutionary success, i.e., their prevalence in today's flora. Similar to pectins and hemicellulose, lignin is a matrix that surrounds cellulose fibrils. Lignin is produced in what is described as the secondary cell wall, a component of the cell wall only in certain cells. The secondary cell wall is laid down after cells have stopped growing, necessarily so because lignin is a rigid material that will not yield readily, therefore preventing the cellular expansion needed for growth. Lignin is the material that makes wood tissues woody. It is stiff and rigid and allows plants to be tall by resisting the compressive force of gravity. Like hemicellulose and pectin, lignin is a complex polymer with subunits that are not all the same and are not always connected the same way. Moreover, the subunits of lignin are not sugars, they are phenolic molecules chemically quite different from sugars. Lignin polymers extend in three dimensions, forming a solid material. Lignin is hard to digest and its breakdown products are phenols, chemicals that are poisonous to many organisms. Hence, lignin is resistant to degradation. The secondary cell wall is deposited inside of the primary cell wall and it necessarily shrinks the space available to the membrane bounded cytosol, sometimes eliminating it almost completely. Most cells with secondary cell walls are short-lived and are structural, providing function to the plant when they are dead. Bacterial cell walls Not all bacteria possess cell walls but the ones that do possess a wall material unique to bacteria called peptidoglycan. As the name implies, peptidoglycan has components that are peptides (sequences of amino acids) and components that are sugars (carbohydrates). Unlike the polysaccharide wall materials described above (e.g., cellulose) which are chains of monomers, peptidoglycan polymers form a mesh, a three-dimensional molecule (like lignin) with units linked not just end-to-end but also above-and-below and side-to-side. Also significant is the fact that many bacteria, including 'gram-negative' bacteria and cyanobacteria , have an 'outer membrane' , a second phospholipid membrane that occurs outside of a (thinner) peptidoglycan cell wall. Some bacteria possess one additional layer, a 'S-layer' , a protein layer on the very outside of the cell, outside the outer membrane of gram-negative bacteria and the peptidoglycan cell wall layer of gram-positive bacteria. Archaea cell walls Archaea do not produce a peptidoglycan cell wall, although a few have a cell wall composed of a similar carbohydrate/peptide compound. Most archaea are bounded on the outside by an S-layer, a self-assembling structure composed of globular proteins or glycoproteins. 'Inorganic' cell walls' All of the cell wall materials discussed so far would be considered 'organic' , a flexible term whose exact meaning wanders considerably. In this context it refers to 'biological materials' , molecules found in living things, as opposed to inorganic molecules, those commonly found in non-living things. There are two important cell wall materials, calcium carbonate and silica dioxide, that are considered inorganic because both are very commonly found in non-biological situations, both commonly occurring as minerals in rocks. However, these minerals are in some sense 'organic' because they can be produced by biological processes, i.e., cells produce conditions whereby calcium carbonate or silicon dioxide is precipitated out of solutions. In fact, their presence in some rocks is completely due to their manufacture by marine organisms whose remains became deposits at the bottoms of oceans and eventually in rocks. The 'White Cliffs of Dover' are formed from a massive deposit of coccolithophores , a type of marine algae that produces distinctive looking calcium carbonate plates as its outside boundary (Figure 6). Although not as common or extensive as calcium carbonate cliffs, there are similar deposits of 'diatomite' , a sedimentary rock formed from deposits of diatoms , another unicellular photosynthetic organism that produces an external skeleton, i.e., a cell wall, made of silica dioxide. Exactly how the material is precipitated in such a precise, and often ornate, manner is not known with certainty. 'Internal' cell walls A few organisms have an unusual structure where wall-like materials (i.e., structural components) occur just inside the membrane. One example is gram negative bacteria where there is a wall inside a membrane, but these bacteria also have a second membrane in its normal location, inside the cell wall. In contrast, dinoflagellates have plates of cellulose enclosed in membranes that occur inside of the plasma membrane. Cryptomonads have wall-like glycoprotein plates both inside and outside of the plasma membrane, forming a structure called the periplast that is unique to this group of organisms. Dermal tissues of multicellular organisms Most multicellular organisms have tissues, called dermal tissues, that form a 'skin' to an organism. These cells and tissues will be considered anatomically in a later chapter but they generally are tightly bound cells (no spaces between them) so that they collectively form a boundary to the organism. Often these cells have different components in their cell wall (e.g., cutin, suberin, lignin) and/or produce a secretion on the outside (cuticle, see below) that is important to their functioning. Additionally, many multicellular organisms produce structures, organs, that have specialized boundaries that are significant to their role. Most common of these are organs associated with reproduction, e.g., spore cases (sporangia), fruits and seeds. The 'skin' of these structures may be important in protecting the structures inside, e.g., the sporangium of mosses, the outside of an acorn (a fruit wall), the seed coat of apple seeds (in the latter two cases it is lignin depositions in the cell walls of dermal cells that are particularly important). The 'skin' of reproductive structures must eventually open up and allow the dispersal/release of its contents and sometimes features of the 'skin' actively participates in dispersing its contents (see discussion below on 'explosive' movements). In other situations, the permeability of the coating, in particular how much water/oxygen enters, can significantly influence the behavior of the enclosed structures. Specialized coatings Some organisms /colonies of organisms cover themselves or part of themselves with some sort of coating. A number of algae and bacteria coat themselves in a polysaccharide gel outside of the cell wall. A striking example of this is with some species of Nostoc , a colonial, filamentous cyanobacterium that sometimes forms gelatinous sheets or spheres that are sometimes several centimeters across (Figure 7). The bulk of the sphere is a polysaccharide secretion deposited outside the cell walls of individual cells. C oating s may be significant to the organism for a variety of reasons including: retention of water, protection, adhesion to substrates, keeping a colony of cells together, buoyancy. Similar coatings are sometimes important in producing biofilms, communities of one to several organisms including bacteria, archaea, fungi and others, that coat surfaces (e.g., dental plaque) and are sometimes important ecologically and to human disease). Figure 7 Nostoc, a cyanobacterium, can form spherical structures up to several centimeters in extent (left photo), the result of polysaccharide secretions. This photo on the right shows the filaments of the algae, the spaces in between the filament are filled with polysaccharide hydrogel secretions. Cuticle Most plants , who are terrestrial organisms exposed to a drying atmosphere, have a coating on the outside called a cuticle (Figure 8) that lessens water loss. The cuticle is a complex mix of chemicals including cutin (mentioned above as a component of some cell walls) and other similar (hydrophobic) constituents. The cuticle is much more impermeable to water (it has a high resistance to water movement ) than the membrane because it is substantially thicker and also because proteins do not span across it. The cuticle's high resistance to water movement is significant because it lessens water loss from plants to the atmosphere. However, the cuticle is also impermeable to gases, in particular carbon dioxide, and this feature has important consequences for photosynthesizing plants. The cuticle is produced by the cells on the outside of the plant, and the outer part of the cell walls of these cells have extensive deposits of cutin. In addition, hydrophobic materials are deposited completely outs ide of the cell wall (outside the area where cellulose microfibrils are present). The mechanism whereby materials can be deposited outside of the cell walls is not completely understood. In addition to reducing water loss, the cuticle is a physical barrier to the entrance of organisms into plants, and it also serves to absorb and reflect UV radiation, thereby protecting tissues within. Also, the dryness of the cuticle, along with other specific chemical features, makes it a very inhospitable place for the growth of other organisms, adding to its protective function. The cuticle of many plants may be ruptured by growth from within (discussed later). In these cases, the protection of the cuticle is replaced by a new layer or layers of cells that are produced with suberin in their cell walls, forming the outside portion of what we know as bark. Spropollenin Pollen grains (of seed plants) and the spores of a variety of organisms are coated with a sporopollenin, a chemical that is particularly resistant to degradation and thought to be significant in protecting against desiccation, oxidation and enzymatic degradation. It is the resistance of sporopollenin to breakdown that allows pollen buried in sediments several hundred million years ago to be preserved and recognized. Its exact chemical nature has not been determined (partly because it is so hard to breakdown!) but it has some similarities to cutin in having hydrocarbon components as well as phenolic components. Boundary diversity The following table summarizes boundary materials for organisms that we cover (plus a few others) grouped based on features related to their boundaries. Table 1 Boundary and organism type Organisms Features Unicellular organisms with no walls Some bacterial groups Mostly parasites Cellular slime molds For parts of their life cycle they do have walls Plasmodial slime molds Like a giant amoeba Euglenoids No wall, but the membrane is reinforced with protein filaments forming a structure called a pellicle, often exhibiting parallel striations on the outside Cryptomonads Wall-like materials (glycoproteins) both inside and outside of the plasma membrane, forming a periplast. Dinoflagellates Often possess multiple 'plates' of cellulose that lie interior to the cell membrane Multicellular organisms with cells with no walls Animals Many do have coatings ( 'skin' ) that are groups of cells Unicellular organisms with cell walls of some sort Bacteria (most), including all Cyanobacteria Wall contains a peptidoglycan polymer with polysacharide and amino acid components. Some bacteria have a second, 'outer membrane' outside the peptidoglycan layer Archaea Wall contains a polymer similar to peptidoglycan with polysacharide and amino acid components Diatoms Wall is made of silica, (SiO2) — Silicon (Si) is an element that most organisms do not accumulate. The wall is also distinctive because it is not organic (i.e. carbon based), does not absorb water and is very rigid (some) Green algae (Chlorophyta) A variety of wall materials (and sometimes none at all) many green algae have walls containing cellulose, a polymer of glucose Haptophytes (Coccolithophores) Round plates of calcium carbonate outside the cell membrane Bread molds (Zygomycota) Cell walls are composed of chitin, a polymer of acetyl glucosamine units (essentially sugar units with a nitrogen attached) Water molds (Oomycota) Cell walls are contains cellulose, a polymer of glucose units. Multicellular organisms with cell walls Club fungi (Basidiomycota) As is the case in all fungi, the cell wall is composed of chitin, a polymer of acetyl glucosamine units (essentially sugar units with a nitrogen attached) Sac fungi (Ascomycota) Same as Club fungi Red algae (Rhodophyta) Wall contains cellulose and sulfated polysaccharides Brown algae (Phaeophyta) Wall has small amounts of cellulose with large amounts of alginate, a polysaccharide polymer composed of uronic (sugar-acid) units Green algae (Chlorophyta) Variable but some with cellulose as the main constituent, other green algae have mannans (polymers of mannose), xylans (polymers of xylose), glycoprotein polymers or no wall at all Plants (mosses, conifers, flowering plants) Cell wall contains filaments of crystalline cellulose connected by hemicellulose polymers and imbedded in pectin polymers. Many plant cells develop an inner secondary cell wall containing cellulose and lignin, a complex, phenolic polymer. Cell walls, cell membranes and structural integrity One reason that an organism's boundary is significant is because the boundary resists physical forces that are acting on the organism. These forces can come from the outside (e.g., wind, gravity) or from the inside (internal pressure). For unicellular organisms it is the strength of the boundary that prevents (or allows) deformation that would come about as a result of these forces. For multicellular organisms it is the boundaries of individual cells and also their linkages to each other that determine how the organism will respond to external forces. Osmotic forces A common factor that might cause a cell to change shape is 'osmotic disruption' , brought about by osmosis, the diffusion of water. All other things being equal ( more in chapter 22 ) water moves by diffusion from areas where it is purer (i.e. has less solutes) to areas where it is less pure (has more solutes). Since living things acquire and manufacture solutes and the impermeability of the cell membrane allows these solutes to be concentrated inside cells, cells are often are in situations where water is going to spontaneously move into them. The cell membrane offers little resistance to expansion and is not able to be stretched. Consequently cells/organisms with only a membrane will burst if exposed to pure water, or any water that is purer than that inside the organism, unless they have mechanisms to eliminate the water. The presence of a cell wall outside the membrane solves this problem because it resists expansion. This allows the cell to pressurize, and this pressure prevents the entry of more water (note that diffusion is NOT just dependent upon differences in purity, as it is often described. It is also dependent upon pressure, more in chapter 24). It is important to note that the strength required to resist expansion is 'tensile' strength. The cell 'resists' water absorption because components of the wall (e.g., cellulose or chitin microfibrils) are resistant to being stretched. If the cell with a cell wall were in an environment causing it to lose water, e.g., an aquatic habitat high in solutes or in a terrestrial habitat where organisms are generally losing water to a drying atmosphere, water would diffuse outward and the presence of a wall would not prevent the cytosol from collapsing unless the membrane were somehow glued to the cell wall to prevent it. This is not thought to be the case. Moreover, for plant cells with only primary cell walls (no lignin reinforcement) or fungal cells, the wall is not strongly resistant to compression; if water leaves the cell the cell will shrink in size (collapse). Although cellulose fibers have a high tensile strength, they are not very resistant to compression, i.e., have little compressive strength. Consider a string (which often times is actually a collection of cellulose microfibrils): you can pull on the string and it resists stretching but it is very easy to collapse the string, it has very little compressive strength. Walls and 'structural integrity' Cells and organisms do need compressive strength to: (1) provide protection from certain predators who would like to crack them open to get to the goodies inside, and (2) allow the organism/cell to resist various forces in the environment, e.g., gravity. Resisting forces becomes more significant if organisms are bigger , especially for organisms in terrestrial environments where the surrounding medium (air) provides little support. In terrestrial environments, organisms will be collapsed by gravity if they are more than a few centimeters in height unless they have structural strength to resist it. Three-dimensional wall materials (e.g., peptidoglycan, calcium carbonate, silica dioxide), can resist compression but these wall materials are only present in very small organisms. Plants are 'big' and terrestrial, how do they resist gravity? Walls with lignin, another 3-dimensional material, will resist compression, but not all plant cells have lignin. Plant cells lacking lignin have structural integrity against gravity because of the combination of water, a membrane that 'holds' solutes but allows water movement and a cell wall that has tensile strength. Water is very difficult to compress as long as it is contained in something that doesn 't allow water to escape. It might seem that water should be able to be ' squeezed out ' of cells by the force of gravity but this doesn' t happen because water movement out, as a cell is squeezed and pressurized by gravity, is balanced by water movement in due to purity (low water purity inside because of solutes, Chapter 24). Plants cells without lignin can withstand the force of gravity because of water's compressive strength when it is inside a cell membrane surrounded by a cell wall with tensile strength. This structural feature is demonstrated in wilting plants. Deprived of a supply of water many plants are unable to resist the force of gravity and to maintain their structure. The walls in and of themselves cannot resist compression, they need water, if re-watered a wilted plant will once again stand up against gravity Figure 9). Woody plants, at least the woody parts of woody plants, do not wilt because they have cells with secondary walls containing lignin that provides the compressive strength to resist the forces of gravity. And some non-woody plants have structural elements that prevent them from wilting. Although most cell walls resist expansion, the resistance is not absolute and c ells can yield (i.e., expand) to some extent when pressures increase inside them. The yielding of cell wall is both elastic (the wall yields , but returns to its original form when the force, internal pressure, is eliminated) and also plastic (the wall yields but does not return to its original shape if the internal pressure is reduced). Because cell walls are present even in newly created cells, plastic deformation is essential for cellular growth. Considering a tree trunk being pushed by the wind, the windward side needs tensile strength, the lee side needs compressive strength. Woody stems are almost entirely composed of lignified cells that have both tensile strength from the cellulose and compressive strength from the lignin. Such a composite material is comparable to 'reinforced' concrete (concrete poured around wire/steel rods) or fiberglass (resin poured around glass fibers), where the concrete/resin provides compressive strength and the wire/glass fibers provides the tensile strength. Moreover, the lignin in plant cells was deposited while the cellulose was under tension, because the cell was pressurized when the lignin was deposited in the secondary cell wall. This produces a composite material like pre-stressed concrete, a concrete produced by pouring concrete around steel cables that are under tension. Pre-stressed concrete has superior strength when compared to regular reinforced concrete. Finally, a tree trunk blown by the wind not only has to have structurally strong cells, the cells need also to stick to each other because separations between cells will cause structural failure, and indeed when stems break or lumber fails it is both because of separations between individual cells and also failures within individual cells. Boundaries and organism movement Organisms move by manipulating their boundaries relative to the environment. For familiar organisms (lions and tigers and bears) this is done with appendages whose positions are manipulated internally. But there are other means of movement and the diversity of organisms that we cover illustrate a diversity of movement mechanisms , all of which are related to manipulation of boundaries. Some examples are given below: Flagellar motility Most similar to the motion of animals is the motion of flagellated organisms, who also have appendages whose position is changed, resulting in movement. Flagellar movement is found in some B acteria , a variety of protist groups ( Green, Red and Brown algae, Dinoflagellates, Cryptophytes, Euglenoids (some), Water molds) and in the sperm of most plant groups including mosses, liverworts, horsetails an d ferns , but NOT the two most familiar plant groups, flowering plants and conifers . The structure of the flagellum, its location(s), and the resultant manner of motion is often distinctive for these different groups. For example, the Dinoflagellate s ha ve two flagella located at right angles to each other; their motion produces a distinctive type of spinning motion. Cytoplasmic streaming Like amoebae, t he amoeboid cells of Cellular slime molds move by pushing and pulling on their boundary by means of microtubules, keeping the volume of the beast constant while changing its form. This allows them to move through their environment or to flow around a particular food item. Plasmodial slime molds , though much bigger and multi nucleate , are able to move in a similar manner. Their cytosol is seen to stream back and forth but more so in one direction , carrying the organism in the direction of greater flow. Euglena motion Organisms in the Euglena group can move by both flagellar movement and by a movement that involves reshaping their form, comparable to an amoeba or slime mold. Growth Fungi and plants move by growing, which requires the extension of boundaries into new territory. This process will be covered later but it requires the extension of individual cells, accomplished by the pressure inside these cells exceeding the tensile strength of the cell wall and also exceeding the resistance to movement provided by the medium that they are moving through (e.g., soil). Stomatal movement Vascular plants and a few non-vascular plants have the ability to change the shape of pairs of cells (guard cells) in the skin tissue of (generally) leaves, thereby opening pores (stomata) in the leaf surface. This is accomplished by means of changing hydration levels of cells, thereby changing their pressure and shape and in turn opening a hole in between them. Stomatal movement ties into two topics of this chapter: (1) the change in shape in guard cells is a consequence of asymmetric deposition cellulose microfibrils in the cell walls, (2) the opening of stomates dramatically changes the dermal permeability to carbon dioxide and water, allowing water to escape the leaf and carbon dioxide to enter. Leaflet/organ movement In addition to moving by growing , a number of plants are able to move appendages, usually leaves. This is accomplished in a manner similar to the operation of stomates: by changing hydration levels of specific cells and groups of cells , thereby changing their pressure and volume and in turn changing their shape. In flowering plants, the changes in cellular shape happen in special cells at pivot points that allow leaves to move. In mosses , changes in cellular shape happen in all the cells of the 'leaves' (microphylls) , sometimes causing them to twist and curl up next to the main axis of the moss. Most mosses also possess appendages called peristome teeth at the end of the spore-producing capsule. Changes in the hydration of the cells in these teeth change their shape, which allows the capsule to close in times of high humidity, when spores are less likely to be dispersed, and open in times of low humidity, when spores are more likely to be dispersed. Although not a boundary movement, a similar mechanism and motion happens with groups of cells called elaters that are present in the sporangia (containers where spores are produced) of horsetails and liverworts and whose movement aids in the dispersal of spores. 'Explosive' movements Mentioned earlier was the fact that as cells absorb water and expand, the change in size may be elastic, in which case energy is being stored in the wall; this energy can be utilized to cause movement. Such an energy storage and a resultant movement is significant in spore and seed dispersal. A container, which may be a cell (the basidium of club fungi (Basidiomycota ) or may be a container with a wall of dermal cells (the fruit of dwarf mistletoe or squirting cucumber, both flowering plants) becomes pressurized and stores energy in the wall(s). Then a part of the wall(s) breaks open and the pressure is rapidly released, expelling the contents (spores or seeds). A similar phenomenon occurs in Pilobolus , a bread mold (Zygomycota) except that what is expelled is the whole spore container (sporangium), occasionally with other organisms hitching a ride. D ehydration can also result in movement. C ells in the fruit wall of some fruits (e.g., witch-hazel) and also in the spore containers (sporangia) of many ferns dehydrate as the fruits/sporangia mature. Dehydration results in shrinkage that is resisted by the cohesive strength of water bound to cell wall materials. More and more force builds up as more and more water is lost. Eventually the force exceeds the cohesive strength of the water in the walls of the cells, again causing the structure to rupture. This is often accompanied with an extremely rapid change in the form of the fruit/ spore capsule that can result in the forceful release of seeds/ spores, like a catapult. Further Reading • “Exploding myths about seed dispersal” by Stuart Gillespie Boundaries and communication/sensation A final point about boundaries is that they play a role in the sensation of the environment and communication between organisms. Organisms need to sense their environment, which means that either signals need to get through the boundary or alternatively that there exists a sensor molecule that extends through the boundary and allows a molecular interaction outside to cause a response inside. Both of these things happen. It is also the case that important signals are actively transported out of organisms and that some signals are components of the boundaries (e.g. cell wall compounds, or derivatives of enzymatic action on cell wall compounds). A great example of this is the communication between Rhizobium , a nitrogen fixing bacteria and the plants they associate with.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.03%3A_Boundaries.txt
In the famous Star Wars bar scene, an attempt was made to illustrate diverse organisms. It was a remarkably unimaginative effort: all of the life-forms illustrated had a striking resemblance to humans, all about the same size and with the same basic components (e.g., head, legs, arms). Without going outside this planet one can come up with a much more diverse set of organisms, as I hope this chapter demonstrates. Organisms vary from each other in multiple ways but in this chapter, I will focus on three aspects, two of which, size and form, are very straightforward, but the third aspect, composition, is less familiar. These characteristics have been shaped by evolution, and e vidence of convergence (unrelated groups converging on a common form) and divergence (related groups showing a variety of forms) abound. Consequently, although form, size and composition are extremely important to an organism 's biology, they are remarkably poor indicators of phylogeny. This makes attempting to characterize the form of larger taxonomic entities (class, order, phylum) challenging, if not impossible. Composition, size, and shape are interrelated and significant to other aspects of an organism' s biology. Moreover, they are also often dynamic, changing during the existence of an organism. TOPICS • Composition • Unicellular • Multicellular • Colonial • Coenocytic • Size • Size and shape considerations • Organism shape: spheres, flattened, cylinders Composition What are organisms composed of, i.e., what are they constructed of? A later chapter will consider composition in chemical and molecular terms. In this chapter 'composition' refers to an organism 's cellular nature. Most would agree that all organisms are made of cells, but is it one cell or many? And are the cells all the same or do they differ? And are the cells ' typical' in their organization? Here are four composition types, two of which are very familiar, and two of which are less so: • unicellular organisms — the organism is a single uninucleate cell • multicellular organisms ( ' complex multicellularity ' ) — the organism is made of multiple (usually many) cells but the cells are different shapes and have a specific organized arrangement that involves tissues and organs • colonial composition ( ' simple multicellularity ' ) the organism is made of multiple cells but the cells are generally similar in size and shape with no obvious tissues and organs • coenocytic composition — the organism is made of 'atypical' cells, atypical in that they have multiple nuclei, sometimes thousands of them. The entire organism is sometimes just a single cell that has many nuclei, or it may be composed of multiple units, that might be called cells, except that they are generally larger than normal and have multiple nuclei. Unicellular Organisms In spite of the fact that plants and animals, the two groups of organisms that most people are familiar with, are multicellular, unicellular composition is by far the most common type of organism. Clearly it is a successful way for an organism to be constructed and most of the 'living' that happens on earth is a consequence of unicellular life. As will be demonstrated by the examples of unicells that are covered here, there is a tremendous diversity in unicellular organisms. Unicellular organisms are NOT always simple in form and function. They may be very elaborate in form e.g., diatoms (e.g., Thalassiosira ) and dinoflagellates (Figure 2). While any cell is a complex entity, there are many unicellular organisms with components functionally analogous to the (multicellular) organs of more familiar organisms. For instance, Euglena cells possess a remarkable amount of internal organization, including organelles (eye spot, contractile vacuole) that perform functions covered by whole organs (eye, kidney) in multicellular organisms. Also, Euglena (Figure 3) (along with many bacteria and unicellular algae) can move as a result of coordinated re-positioning of extensions that are not multicellular legs, wings or fins but rather an extension of the individual cell called a flagellum ; additionally, Euglena and other unicellular organisms can also move by altering the form of the cellular body, comparable to what earthworms do, but without the aid of muscles and other tissues. Most organisms go through a stage or stages that is/are unicellular (e.g., spore, gamete, zygote) and these unicells, many of which can be considered organisms because they are often distinct spatially and temporally, are often very elaborate in structure and function. Examples th at will be discussed later are the sperm of multiple groups of plants (e.g., ferns, mosses), often referred to as a spermatozoids (Figure 4). Although being unicellular is rightfully considered a primitive condition, yeasts are unicellular fungi and demonstrate that the unicellular condition can sometimes 'reappear' in a lineage that previously had some other type of composition, i.e., that unicellularity is sometimes a 'derived' condition. The vast majority of fungi are colonial/multicellular but yeasts have appeared independently multiple times in several different fungal groups and they do NOT represent the primitive condition. In many yeasts the unicellular growth habit is tied to environmental conditions and the organism can be induced to grow in a colonial matter by adjusting conditions. Colonial Organisms Colonies of cells (colonial organisms) can form two ways. The less common way is for individual cells to come together to form a colony. This behavior has evolved multiple times, several times in the bacteria (in groups described as 'social bacteria' ) and also in the cellular slime molds like Dictyostelium. (Figure 5) Colonies produced this way will contain cells that are not necessarily all the same genetically. The second and far more common way to form a colony is a result of repeated cell divisions where the daughter cells adhere to their parent. For a cell with a cell wall, the adhesion between daughter cells is accomplished with an adhesive layer deposited between the new cell walls that are produced during cytokinesis. In colonial organisms, repeated cell divisions produce an organism with many cells attached to each other but the cells are all (or almost all) identical. This type of composition is sometimes described as 'simple multicellularity' or 'plurocellularity' that is distinguished from 'true multicellularity' or 'complex multicellurity' , or sometimes just 'multicellularity' by a variable set of criteria that usually include cellular differentiation and the production of tissues (more on this in the next chapter). A wide variety of colonial forms are possible and result from the patterns in the planes of cell division, e.g., filaments (Figure 6) are formed if the plane of cell division is always the same, producing a chain of cells connected top to bottom. Filaments can grow from the basal end ( if the original cell continues to divide but the daughter cells do NOT divide) or it can grow from the tip ( if the original cell does NOT divide and the daughter cell repeatedly does divide) or it can grow throughout the filament. F ilament s may branch if some cells in a filament divide in a direction parallel to the direction of the filament; flattened sheets (Figure 7) are produced if cells repeatedly divide in two perpendicular planes; globular cluster s of cells are produced if the original cell and its derivatives divide repeatedly in multiple planes. Filamentous growth is found in archaea, bacteria, (Figure 8) and fungi and many of the groups that used to be put in the Protist Kingdom, in particular the green, red and brown algal groups and some diatoms. It is also found as a brief stage in most mosses and ferns (Fig 10). Most fungi exhibit a distinct type of filamentous growth where the filaments, called hyphae, grow from the tip but commonly branch, both at the tip and below it, and with the branches capable of fusing with other hyphae to form what is called a mycelium, an interconnected, anastomosing mass of hypha l filaments (Figure 10). Two dimensional colonial growth, forming sheets one-to several cells in thickness, is most commonly found in photosynthetic forms, primarily in the algal groups. It also is present in some of the non-vascular plants: all of the hornworts and some of the liverworts (Figure 11), where it presents in the haploid (gamete-forming) form but not the diploid, (spore producing) form (see Chapter 13). Spherical colonies are occasionally found, particularly in the green algae. The advantages of colonial growth, i.e., of having cells aggregate or having daughter cells remain attached to parental cells, may be different in different situations. One advantage is size; it allows for much larger organisms than a single cell and larger size is sometimes, but not always, advantageous. As discussed below, size affects interaction between organisms and their environment. Colonial growth may be successful because it allows for exploration of the habitat: an organism in a marginal habitat may be sustained as it explores for greener pastures. The larger size of colonies makes possible the exploitation of different habitats/regions. For example, algae are able to exploit both a substrate (for attachment) and the water column (for light and nutrients). Most workers feel that colonial growth (simple multicellularity) is a step on the way to complex multicellularity, but the abundance of highly successful (i.e., diverse and plentiful) colonial forms indicate that colonial growth is itself an advantageous composition type. Coenocytic Organisms Probably the least familiar composition type is coenocytic, where the organism's cells, or sometimes its single cell, is multinucleate. This results from mitotic divisions that are unaccompanied by cytokinesis, often repeatedly so. Part of the significance of the coenocytic condition has to do with size. Cell size may be limited because a single nucleus can only control a limited volume of cytosol and for the cell to get bigger there needs to be additional nuclei. Coenocytic cells are usually large and sometimes extraordinarily so. An extreme case is found in the plasmodial slime molds (e.g., Physarum), an amoeba-like organism that consists of a single wall-less cell that may be as much as a meter in length with hundreds of thousands of nuclei (Figure 12). The form of slime molds is dynamic, owing to the ability of the cytoplasm to flow in channels inside the single cell, thereby allowing the organism to explore its environment, engulf food, and even climb up over obstacles. Unlike wall-less plasmodial slime molds, coenocytic organisms with walls can produce specific, permanent forms, but not the way that form is typically created in multicellular organisms (adding cells to create a form), but instead as a result of the creation of shape in individual large cell(s). The bread molds (Rhizopus). produce rhizoids, stolons and stalked reproductive structures, all formed out of a single cell with multiple nuclei (Figure 13). Similarly, t he notorious invasive green algae Caulerpa , can appear very plant-like, i.e., with 'stem and leaves' , but it's remarkable size and complexity occurs without recourse to cells and tissues. Many coenocytic organisms are very similar in form to colonial organisms, most commonly filaments but also sheets and spheres. The 'fungal' structure of hyphae/mycelium that is cellular (i.e., colonial) in the sac fungi (Ascomycota ) and club fungi (Basidiomycota) is coenocytic in the bread molds (Zygomycota ) and the mycorrhizal forming Glomeromycota . And this same fungal-like coenocytic form is found in a non-fungus group, the water molds, e.g., the plant pathogen Phytophthora. The structure of water molds explains why the group used to be placed in fungal phylum and also why grouping things by 'looks' , i.e., form, is dangerous! Water molds are now placed in a group that includes brown algae and coccolithophores , two groups that are not at all fungal like nor coenocytic. Many would not consider these coenocytic organisms to be unicellular, even though technically many are. They are closer to a colonial organism. If one defines organ as a component of an organism that provides a particular function (e.g., anchorage, elevation) then it is apparent that organs can be formed in both colonial and coenocytic organisms (Figure 14), in both cases without the presence of specialized cells and tissues. Multicellular Organisms Most workers would not unify all organisms composed of two or more cells as 'multicellular' but developing criteria for useful definitions (e.g., 'simple vs. complex' multicellularity) is challenging and there is no universal agreement as to where to draw lines. For most researchers 'true' multicellularity involves specialization of cell types, a topic that will considered in the next chapter. Organism Size Organisms vary tremendously both in volume and their extent in three dimensions. The smallest organisms (Table 1) are prokaryotes (bacteria and archaea), unicellular organisms that lack nuclei or other cellular organelles, with longest dimensions typically of a few um (= 10 -6 mm) and volumes of less than 1 um 3 (= 1 femolitre, where a billion (10 9 ) femolitres equals 1 ul; a quadrillion (10 15 ) femolitres equals 1 litre). These tiny organisms are usually shaped as spheres, rods or spirals. Although most prokaryotic cells range from 0.5 to 10 um, there are a few giant prokaryotes whose cells might be up to 500 um in length, meaning that they can be seen with the naked eye, albeit as a speck. Unicellular eukaryotes possess cells with nuclei and other cellular organelles. They are generally bigger (10-100 um) than prokaryotes although there are a number of unicellular eukaryotes with small cells, in particular the yeasts (unicellular fungi generally with cells less than 10 um). The fact that unicellular organisms are almost always small in size is generally thought to be a consequence of the need for nuclear control of cellular activity; larger size is difficult because in large cells messages (mRNA, proteins) moving by diffusion take too long to get from the 'control center' (the nucleus, the ribosome) to all parts of the cell. This idea is supported by the following observations: • coenocytic cells, which have multiple nuclei, are often much larger than cells with a single nucleus • larger unicells often exhibit cytoplasmic streaming which provides for more rapid movement of signals throughout the cell • larger unicells (found in plants, fungi and algae) possess a large central vacuole that takes up much of the cell 's volume and that is in some ways a metabolic ' dead space ' that is relatively inactive (or at least not as dynamic as the cytosol); consequently, the amount of cytosol that the nucleus must ' control' is actually much smaller than appears based on cell size There are a few extremely large unicellular organisms, Acetabularia, (Figure 16) standing up to 5 cm tall, being one of them. Acetabularia is unique not just for its size but also because it demonstrates that 'organs' ( 'rhizoids' , 'stems' , 'leaves' ) are possible even in organisms that are unicellular. Acetabularia cells are over 1000 times larger than typical eukaryotic cells, with maximum dimensions of over 50, 000 um (= 50 mm = 5 cm). Other large unicells e.g., bread mold ( Rhizopus) , Physarum (plasmodial slime mold) are coenocytic and the case could be made that they really should not be considered unicellular. Most organisms over 100 um in size are colonial, coenocytic or multicellular. While the cells of coenocytic organism vary greatly in size, the cells of colonial and multicellular organisms are commonly 10 – 100 um in their maximum dimension and the organism 's overall size is determined by how many cells are produced/accumulate. Some of the particularly large organisms that we will consider are: redwoods , up to 85 m in height and weighing an estimated 2100 metric tons (= 2100 * 10 3 kg = 4620 * 10 3 pounds = 2310 tons); giant kelp (brown algae) up to 50 m in length; ' Pando', a clone of trembling aspen that weigh s over 6 million kg, extend s over 43 hectares and may have an age of 80, 000 years (more in the discussion of Populus ); and a honey mushroom (Armillaria) that extends over 4 square miles (1000 hectares), weighs an estimated 55, 000 kg and is considered to be 2400 years old. Size and shape—influence on surface area & interactions with the environment Size and shape are particularly significant because they dictate the degree of interaction between the organism and the outside environment. Appreciate that the conditions inside organisms are different from the outside; this is part of what defines life. The second law of thermodynamics (which we will consider in Chapter 24) dictates that differences between the inside and the outside diminish with time: if some chemical is concentrated inside an organism it will tend to leak out; if something is excluded from an organism it will tend to leak in; if an organism is warmer than its environment it will cool; if an organism is cooler than its environment it will warm. Whatever conditions an organism develops to promote its life functions will tend to disappear because the second law dictates that systems change to develop uniformity, i.e., there is a tendency for the inside to become more like the outside. Given this, one might think that having little interaction with the external environment is 'best' . However, interaction with the environment is essential: (1) to obtain materials—food, oxygen, minerals—that are needed to maintain life, and (2) to rid the organism of 'materials' that it produces, e.g. heat and carbon dioxide, that will bring it harm if allowed to accumulate. The size and form of an organism control how it interacts with the environment that it is in. Significantly, size and form affect two important parameters that are related but not exactly the same thing, the surface area of contact with the environment and the volume of the environment in proximitywith the organism. Both of these parameters are important in controlling the interaction between the organism and its environment. The significance of surface area is familiaridea.More surface area allows for more interaction with the environment, which may or may not be beneficial.For any shape, smaller objects always have a greater surface area per unit volume than large objects(Table 1). Table 1. Influence of size on surface area : volume ratios for spheres, cubes and cylinders with heights ten times longer than the radius. shape dimension (in arbitrary units) r = radius, s = side volume (units3) surface area (units2) surface area : volume (units-1) sphere r = 0.1 units 0.004 0.126 31.5 sphere r = 1.0 units 4.19 12.6 3.01 sphere r = 10 units 4190 1257 0.3 cube s = 0.1 units 0.001 0.06 60 cube s =1.0 units 1 6 6 cube s = 10 units 1000 600 0.6 cylinder r = 0.1, height = 10 x r 0.314 0.691 22 cylinder r= 1.0, height = 10 x r 3.14 69.1 2.20 cylinder r= 10, height = 10 x r 31.4 6911 0.22 formulae sphere: volume = 4/3 (pi) (r)3; surface area = 4 (pi) (r)2 cube: volume = (s)3; surface area = 6 (s)2 cylinder: volume = height (pi) (r)2; surface area = 2 (pi) (r) (height) + 2 (pi) (r)2 Keeping volume constant, a sphere has the minimum surface area of any shape, and departures from an isodiametric shape increases the surface area and thus the surface area: volume ratio (Table 2). If one compares the surface area of two common shapes, 'filaments' (elongated in one dimension) and 'sheets' (elongated in two dimensions) while keeping the volume constant, the degree of elongation increases the surface area and elongation in two dimensions has a greater effect than elongation in one dimension (Table 3). Table 2. Surface areas of different symmetric shapes (sphere, cube, cylinder with diameter = height), all with the same volume, arbitrarily set at 1 unit cubed. shape dimensions surface area = surface area / volume sphere radius = 0.62 4.83 cube side = 1 6.0 cylinder diameter = length = 1.08 5.49 Table 3. Surface areas of different shapes elongated 10-fold and 100-fold in one dimension cylindrical threads and cuboidal threads (i.e. a filament made of cubes), or two dimensions (disks and cuboidal sheets (i.e. a sheet made of cubes), with all shapes having the same volume, arbitrarily set at 1 unit cubed. shape dimensions surface area = surface area / volume thread length = 10 x diameter 8.34 thread length = 100 x diameter 17.28 disk diameter = 10 x length 10.32 disk diameter = 100 x length 40.69 cuboidal thread 0.464 x 0.464 x 4.64 9.04 cuboidal thread 0.215 x 0.251 x 21.54 21.73 cuboidal sheet 0.215 x 2.15 x 2.15 11.09 cuboidal sheet 0.0464 x 4.64 x 4.64 43.92 Consequences of form and size To see how surface area and form are significantwe will use the example ofthe flow of heat from a warmer environment to a cooler cell, but the same principle would apply to the heat flow from the cell to the environment or the movement of materials, e.g., nutrients into the cell or waste products out ofthe cell. Because smaller objects have relatively more surface area than larger ones, smaller organisms heat up more quickly than larger ones. In fact, because of effective heat exchange between them and their environment, small organisms are always very close to the same temperature as their environment. Only large organisms, with a small surface area to volume ratio, can develop temperatures substantially different from their environment. Considering shape, spherical bodies, withthe least surface area per unit volume, heatmore slowly than any other shape when put in an environment that is hotterthan it; the more deviation from a spherical shapethe faster it will gain heat. If you had three pieces of ice, one spherical, one filamentous and one disc-shaped, all of the same volume, the disk would melt first, then the filament and last the sphere. Assuming equal volumes for ice cubes, the best ice cubes, if you want them to last (not melt), are spherical ones, the best ice cubes if you want them to cool the drink that they are in, are shapes that deviate the most from spheres A second influence of form: the extent of environment that is explored An often-overlooked fact is that organisms change their environment around them. In the example just given, the transfer of heat to the cell results in a cooling of theenvironment adjacent to cell. Thecoolingof the environment next to the cell will reduce the gainof heat bythe organismand diminish the significance of surface area to heat transfer. Because of this, a second characteristic related to formbecomes important:the volume of the environment that is within somedistance (the distance depends characteristics of transfer) of the organism. To see why, consider two spherical organisms with a cylindrical 'distortions' of their otherwise spherical boundary: one has an 'outie' (a projection that extends outward), the other has an 'innie' (an invagination that penetrates into the organism) (Figure 18). As long as the dimensions of the projection / invagination are the same, both the cells will have the same surface area, yet the heat exchange between the 'outie' cell will be faster than that from an 'innie' cell. This is because the conditions of the environment inside the 'innie' projection will become more similar to those of the organism than to the conditions of the bulk environment outside of the cell. The volume of 'the environment' that is in the 'innie' is small and the surface area between the innie and the cell is relatively large, consequently as the 'innie' part of the environment loses its heat to the cell it would become less and less significant a source of heat. Thus, the additional surface area resulting from the 'innie' would become of little consequence in terms of interacting with the environment. In contrast, the additional surface area of the 'outie' can remain more effective in facilitating heat transfer because this area is surrounded by the environment, not the cell. Hence surface area by itself is not always the best measure of how much interaction an organism (or object) might have with its environment. A consequence of this is that form is important in influenc ing the transfer of materials between the organism and the environment in two ways: (1) by determining surface area of a given volume of organism, and (2) by influencing the volume of the environment that is in close contact with the cell. Although an 'innie' does increase surface area, this does little to influence the volume of environment close to a cell; an 'outie' does much more. The significance of how much of an environmental volume is explored depends on several factors including the rate at which heat or material is conducted through the environment and the rate at which heat or material can be transferred from the environment to the organism. If the environment transfers heat or material readily, or if the rate of transfer into the cell is slow, the importance of how much environment is explored is of less importance. Consider another example of two cells with the same number of multiple outies, extensions outward, and the same surface areas. One has the outies close together, the other has them spaced out (Figure 19). The cell with spaced out extensions explores more of the environment than the other and will be able to acquire more heat or material from its environment (or lose more heat or material to its environment), especially if the rate at which heat or materials move through the environment is relatively slow, or the rate at which they are absorbed/lost is relatively fast. A parameter can be calculated that is the volume of environment within some distance of the cell surface; outies that are close to each other are less effective in increasing the amount of environment being 'accessible' than are more separated outies. Some (perhaps) familiar situations demonstrate the importance of form and some of the complications related to it. The microvillae, small projections of small intestine that extend out into the gut track, are often cited as being important in the absorption of materials from the gut because they provide increased surface area. This is certainly the case but it should also be pointed out that the movement of material through the gut track, a result of peristalsis, is what allows the additional surface area to be significant. If not for peristalsis continually bringing 'fresh' material to the dense stand of microvillae, the increased surface area would be of little utility. Peristalsis changes the environment next to the microvillae. Root hairs, cylindrical extensions from the cells on the outside of roots, are another situation where increased surface area is cited as being significant to the water absorption function of roots. This may not always be the case, especially when the root hairs are extremely dense and if water is abundant, which allows it to move more readily through the soil. However, roots and root hairs don't just absorb water, they also acquire nutrients and the impact of root hairs may be different for different nutrients compared to the impact for water. Moreover, the conductivity of the soil to water and minerals is very strongly affected by how much water is present, a very dynamic property for most soils. Root hairs probably do multiple things that are significant for absorption of water and minerals: (1) increase surface area, (2) increase the volume of soil in close proximity to the root, (3) improve contact between the root and the soil by preventing gaps (air spaces) which would drastically reduce absorption of water and nutrients, (4) perform metabolic functions that facilitate nutrient absorption, e.g., active transport. Shapes of Organisms While there are a wide variet y of shapes of organisms, three common forms are cylinders, sheets and spheres. Many organisms are composites of different shapes, i.e., they have some pieces that are one shape and other pieces that are another shape, e.g., m any animals have cylindrical appendages attached to a spherical core. M ost above-ground plants are composed of flattened sheets ( leaves ) attached to cylindrical stems. Both the above-ground and below-ground form of plants typically are filaments that branch repeatedly, a form that is also found in fungi. Common forms for the organisms covered in this text are outlined in the Table 4. Table 4. shape examples notes spheres many unicellular organisms, some colonial and multicellular ones low surface area to volume ratio and small amount of environmental volume explored per unit of organism flattened many colonial and multicellular algae including sea lettuce (Ulva) and kelp (Laminaria); the haploid form of all hornworts and many liverworts high surface area to volume ratio, often significant for photosynthetic organisms to absorb more light cylinders (branched or unbranched) most fungi, many green and red algae, some bacteria, the roots of vascular plants both a high surface area to volume ratio and potentially a large amount of environmental volume explored per unit of organism cylinder with (non-cylindric) appendages some macroalgae (red, brown and green); most plants–including most mosses, many liverworts and almost all vascular plants the appendages typically are flattened and photosynthetic and their shape increases the amount of surface area exposed to light Spheres As mentioned above, spheres have a minimum surface area per unit volume. Assuming that there is a specialized boundary on the outside of the object, be it unicellular or multicellular, a sphere would require the minimum amount of boundary, which often is composed of relatively expensive materials. Spherical shapes are also more mobile in many situations owing to their reduced drag, which in general increases with surface area. While there are a number of roughly spherical animals, spherical multicellular organisms from other groups, in particular, the groups we are covering, are uncommon. However, the form is commonly found organisms that are unicellular: many bacteria, many unicellular green algae, dinoflagellates, cryptophytes and coccolithophore are roughly spherical in shape and the shape occasionally occurs in colonial organisms (some green algae). Spheres are also common in dispersal units: pollen, seeds, spores, all of which are entities that might be considered organisms. And spherical shapes are also a common shape for the structures (organs) that contain elements to be dispersed: sporangia (spore containers), fruits (seed containers), anthers (pollen containers). The advantage(s) of spherical shapes no doubt varies on circumstances and may also reflect other constraints on development. In rare occasions, round shaped seeds, fruits and even whole plants may aid in the dispersal of propagules by wind and gravity. A whole-plant example of the this is the tumbleweed, whose spherical shape promotes the dispersal by the wind of the seeds which are released from the rolling plant. Spherical forms are typical of the (usually underground) storage organs of flowering plants: corms, bulbs and tubers and this is probably a consequence of surface area to volume considerations. Flattened structures Flattened structures are especially common in photosynthetic organisms, undoubtably because of the importance of intercepting light. While it is often stated that flattened shapes 'intercept more sunlight' than other shapes (e.g., maple leaves vs. pine needles), this is misleading; similar amounts of light can be acquired given any particular shape. What is significant is how much volume is required to produce a given area of light absorbing surface, and also how much total surface area is required. Table 5 compares morphological characteristics for three different leaf shapes: cubes, sheets and filaments. In each situation the assumption is made that one 'face' of the shape is facing the light source and that light absorption only occurs on this surface. As can be seen the same amount of light could be intercepted by ten cuboidal leaves, each 10 x 10 x 10 cm in size, or ten filamentous leaves, each 100 x 1 x 1 cm or by ten planar leaves 10 x 10 x 1 cm. While both filaments and planar leaves can produce the same amount of absorbing surface per unit volume of leaf, cuboidal leaves 'cost' much more (illuminated area: total volume) (Table 5). The difference between filamentous leaves and planar leaves is that planar leaves reduce the total surface area required to produce a given amount of absorptive surface. It is probably these two factors that are significant in ensuring that light absorbing surfaces are generally planar: thick leaves require volume that cannot be used effectively for photosynthesis; filamentous leaves produce excess total surface area which may be costly in terms of other factors, e.g., water loss for terrestrial organisms. The flattened structure may be the entire organism (some green, red and brown algae, some liverworts (including Marchantia , hornworts ) or, most commonly, the flattened structures occur as leaves / leaf-like structures off of a cylindrical stem. Table 5. shape number of leaves dimensions total volume total surface area illuminated area / total area illuminated area / volume cuboidal 10 10 x 10 x 10 10000 6000 1 / 6 1: 100 filamentous 10 100 x 1 x 1 1000 4020 1 / 4.02 1 : 1 planar 10 10 x 10 x 1 1000 2400 1 : 2.4 1 : 1 Certainly, the above treatment is superficial and some complicating factors should be noted: light is usually not only absorbed by one surface of any structure as the sun 's position changes during the day and season; light penetrates through a surface to layers below; although most leaves move only minor amounts during the day or season, some leaves change position to ' track ' the sun; and some leaves change position to reduce solar exposure. And, in spite of the trend of generally planar light absorbing surfaces, there are multiple examples of filamentous ' leaves ' and also examples of spherical' leaves.' A planar shape is also sometimes found in propagules, the dispersal stages of organisms, where the flattened 'wing' aids in dispersal in the air. Interestingly, wings are primarily found in relatively large propagules, the seeds and fruits of seed plants, with dimensions greater than a few millimeters. 'Wings' are uncommon in aquatic organisms and in small propagules: e.g., spores and pollen. Although most conifer pollen has two 'wings' , they are not particularly flattened and, in spite of the fact that conifers are wind pollinated, the role of the wings may not be to aid in dispersal but rather to orient the pollen grain after it has been dispersed. Cylindrical structures Cylindrical structures are extremely common, both as parts of organism and as the whole organism. Cylindrical unicellular organisms are found in rod-shaped bacteria and archaea; filamentous colonial forms are represented by some bacteria, many cyanobacteria, colonial diatoms, many green algae and some red and brown algae. For most of these colonial organisms, the filaments are all one cell thick, but, especially in the red and brown algae, the filaments may be thicker, often several cells thick. There are many coenocytic green algae that are filamentous. A branched filamentous structure is particularly effective as a 'feeding' (for fungi) or 'mining' structure (for plant roots) that explores an environment for resources. Such a form is also effective in providing anchorage because it allows for extensive interaction between the organism and its substrate. In contrast to roots, which have dual functions of absorption and anchorage, the holdfasts of algae and rhizoids of mosses, liverworts and hornworts perform little absorption but primarily serve an anchorage role. Across the diversity of organisms, what it is that forms the branched structure and the size of the branched structure vary tremendously. Unicellular chytrids (fungi) form 'rhizoids' for absorption and anchorage that are extensions of a single cell. The 'arbuscules' (literally meaning 'little tree' ) of Glomeromycota fungi are also extensions of parts of the fungal cell that enters into plant root cells. Root hairs are also extensions of individual cells. The rhizoids of mosses, liverworts and hornworts are usually a filament made up of a string of individual cells. Holdfasts of macroalgae and the roots of plants (as opposed to root hairs), are multicellular and made up of multiple cells. Cylinders with non-cylindrical appendages Cylinders also function to position organs in favorable locations, e.g., the stem of plants or the stipe of the larger algae, distributing flattened leaves/leaf-like structures in order to obtain more light. The vast majority of plants, ranging from mosses, most liverworts and all vascular plants, have an above-ground structure that can be described as a 'stem with leaves' . Typically, the cylindrical stem branches and is erect but sometimes it is unbranched and sometimes it is prostrate, running along the ground surface. Phytopthora, a water mold, is a parasite that grows inside plant leaves and produces branched structures that emerge from the leaf through stomates, regulated pores in the leaf surface, and form cylindric, branched structures upon which are produced reproductive structures which are dispersed. Cylinders (stalks) also repeatedly serve to elevate structures that are producing propagules (mobile reproductive structures) and thereby facilitate dispersal of propagules. T he ubiquity of the structure reflects the structure 's significance in multiple situations over quite a range of size s: from stalks as short as 1 micron in myxobacteria, to 1 millimeter in slime molds, to 1 centimeter in mosses, to meters in height (flowering plants). The cylindrical stalks can be parts of a cell (bread molds, some slime molds), made of a single filament of cells (fungi), a collection of intertwining filaments (fungi) or truly multicellular (some fungi, mosses, vascular plants). Generally, such structures are found in terrestrial organisms with stalks that carry propagule-producing-structures upward into the air. Apparently even a very short upward extension can enhance dispersal by allowing the propagules to be released above the most sedentary part of the boundary layer, the layer of still air that blankets all objects, and in particular the ground. Apparently, such structures are not as advantageous in aquatic situations because they are much less common. In some situations, a stalk is significant not by moving the propagule-producing-structure up (relative to gravity) but because it moves the structure outside of the organism' s own body or outside the body that it is growing inside of (e.g., fungi, some parasites). As the last example demonstrates, cylinders are significant to a number of organisms as a means of mobility, to arrive at new places. Although most of the organisms that we study are considered immobile, they are capable of movement that is due to growth, and a cylinder is an effective structure to cover territory. Examples include: horizontally running above ground stems (stolons) and below ground stems (rhizomes) of plants, the 'stolons' of bread molds, rhizomorphs of fungi, horizontal 'runners' in Caulerpa , a green alga.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.04%3A_Organism_form-_composition_size_and_shape.txt
The discovery of the first cell is often attributed to Robert Hooke in the middle of the 1 7 th century. But people had observed cells before (fish eggs, frogs 'eggs, birds' eggs). What was significant about Hooke's observation was that he noted that organisms , at least some of them, were composed of smaller entities that he called cells. H e was able to see them in part because he was using the recently developed microscope. But what also made the cells visible were that they were plant cells, cells that not only are larger than most animals cells but also have cell walls that outline each cell and are rigid and do not collapse when the material is cut into thin sections. The material he was looking at was cork, the outer bark of a tree, and what he was obser ving was the remnants of cells that were no longer alive; their existence was preserved because of their thick and persistent cell walls (Figure 1). While Hooke 's observations illustrated that at least some parts of some organisms were composed of smaller units, the generalizat ion that all organisms were composed of one to many ' fundamental units ', cells, was not to be fully realized for another 200 years when ' cell theory' was proposed and championed. Although people were very aware of fish eggs and frog eggs, they had not appreciated that when the eggs turned into tadpoles the material was first divided up into many, many small units , each with the same basic construction. With time, these units diversified from each other and transformed into groups to serve specific roles. T hese are arranged in a particular way to produce a complex whole , a frog embryo. Think of making castles out of legos. A similar transformation occurs as the fertilized egg of plants transforms into a plant embryo, although the egg cell of plants (about 20 um) is 100 times smaller than those of frogs and about five times smaller than those of humans. One of the great themes of biology is the unity and diversity of life: how organisms can simultaneously be so similar and so different. The same concept also applies to cells and is fundamental to 'cell theory' : living things are made up of cells, whose basic organization, chemical composition and organization is similar; but these cells are also diverse in terms of shape and function and the diversity is seen both between different organisms (plant cells are different from animal cells) but also within (multicellular) organisms. Diversity of cells within an organism is one, and for some people the only, criterion for a multicellular organism, not simply that they are made of multiple cells but that at least some of the cells differ from one another. Before describing the diversity of cell types found in some of the organisms that we cover, we will consider additional criteria that might be used to define multicellularity. TOPICS • Multicellularity • Cell Structure of Fungi • Chytrids • Coenocytic, filamentous fungi — bread molds and Glomeromycota • Septate fungi — Club and sac fungi • Cell Structure in water molds • Cell structure in algae • Brown algae • Red Algae • Green algae Multicellularity Can a unicellular organism be multicellular? One might think that this is absurd, yet it can be true, depending on definitions. An illustrative case is the Apicomplexa, a group that includes is the causal organism for malaria, Plasmodium. Members of this group are always unicellular but have multiple cell types (Figure 2), cells that look different, behave differently and live in different places. Most biologists would not consider the Apicomplexa to be multicellular and would rather consider it as a biological entity with multiple forms, but in a developmental sense it raises the same question that multicellularity poses: if one cell is identical genetically to another cell, how can they end up looking and behaving differently? If you study the life cycle of Plasmodium carefully you will note that some of the cellular diversity is associated with reproduction and the sexual process, a topic that will be dealt with in more detail later but for now simply note that most organisms produce different cells that are associated with reproduction and/or sex. Chlamydomonas , a unicellular green algae (Figure 3) , produces bi-flagellate cells that all look and behave alike except for: (1) some cells look different because they lose their flagellae and divide twice to produce four cells while still within the parental cell. Eventually the parental cell wall is digested and the four typical-looking cells are released, (2) some cells look normal but are 'special' , functionally different, because they are able to fuse with other 'special cells' . Cells become 'special' because of changing conditions, e.g., nutrients become less available. (3) the cell formed by the fusion of two special cells develops into a very different looking cell, one with no flagellae and a thick cell wall. It also functions differently, being metabolically inactive. Eventually it becomes active and divides to produce four typical looking (bi-flagellate) daughter cells that are released after the cell wall is digested and weakened. The three atypical cell types are associated with sex and the process of meiosis (right-hand side of the above diagram) will discussed in more detail later , along with a consideration of reproduction (left-hand side of diagram). Obviously very few would consider unicellular organisms like Plasmodium or Chlamydomonas to be multicellular in spite of the fact that they may exhibit multiple cell types. The point is that the possession of different-looking or different-behaving cells (e.g., egg, sperm, zygote, spore) that are associated with the reproductive or sexual process are not sufficient to label an organism as multicellular. This is trivially true for unicellular organisms but is also true for colonial organisms that are made up of multiple cells that are almost all the same and is the reason for the distinction between 'simple multicellularity' and 'complex multicellularity' . Consider the filamentous green algae Ulothrix , (Figure 4) which exists as strings of cells, most of which all look alike (see the center part of the drawing above, labelled 'a' ), but sometimes some of the cells transform (i.e., develop) to produce mobile cells that have four flagellae ( 'c' in the diagram) and are released from the filament. These cells can establish new filaments by attaching to a substrate and dividing to produce new filament ( 'd' ). Other cells transform and produce and later release cells with only two flagella ( 'f' ). These cells must find another bi-flagellated cell, fuse with it ( 'g' ), then undergo meiosis to form four quadriflagellate cells ( 'h' ) that can attach to a substrate and form new filaments. Another example of simple multicellularity with diverse cell types associated with reproduction and sex is found in Oedogonium , (Figure 5) another filamentous green alga. Most cells are cylindric with lengths about five times longer than their width. But there are also egg cells, that are shorter and bulge in the middle and much shorter sperm producing cells, with lengths the same or shorter than their width. Both these cell types develop holes in their walls that allows the short cells to release mobile sperm and allows the sperm to enter into the egg cells resulting in the production of cell with genetic information from two parents. This develops into a dormant spore that is eventually released from the filament. An additional cell type can develop from the normal cells as they develop flagellae and eventually are released from the filament as cells capable of forming new individuals. These examples demonstrate common cell types associated sex and reproduction and found in organisms with colonial growth (showing 'simple multicellularity' ): (1) cells that are capable of fusing with each other, called gametes that are sometimes differentiated into egg and sperm, (2) zygote, a cell formed by the fusion of gametes, ( 3) zoospores, flagellated cells specialized for mobility (dispersal in space) (e.g. the cell labelled 'c' in the Ulothrix diagram), (4) inactive, dormant cells that allow for dispersal in time. In general, these are called spores (but note that zoospores are NOT inactive). These inactive cells are called endospores in bacteria and akinetes in cyanobacteria. In a number of organisms (e.g., Chlamydomonas, Oedogonium, bread mold ) spores develop from zygotes and are called zygospores. We will see a number of different spores in the fungi. To repeat, none of the examples considered so far would be considered multicellular even though they produce multiple cells, some of which are different structurally and functionally from others. What additional features contribute to the case for 'true multicellularity' ? One feature is mutual dependency. Most of the cells of Anabena , a cyanobacteria, have chlorophyll and photosynthesize to feed themselves. Anabena also produces cells called heterocysts that lack chlorophyll and are unable to photosynthesize. They are 'fed' by adjacent, 'regular' cells. Heterocysts are significant because they can take dinitrogen gas, a form of nitrogen that 'regular' cells cannot utilize, and convert it into a form that the regular cells can utilize (more details in chapter 22). Hence, the heterocysts and the regular cells depend on each other. At least some workers would consider the dependency of one cell type on another to be a criterion that makes Anabena multicellular. Another feature that Anabena demonstrates and that is significant to the concept of multicellularity is material movement (food, nitrogen compounds) between the cells of the organism. This really is a form of intercellular communication, and many workers consider intercellular communication to be a key requirement defining multicellularity. Features that enhance communication include trans-cellular connections, plasmodesmata in the case of plants. Another criterion that has been applied to define 'true multicellularity' is a three-dimensional cellular organization, i.e., not just cells added in one dimension (a filament) or added in two dimensions (a sheet), or added in three dimensions without a determinate developmental program. True multicellularity to some workers requires a developmental program that produces a distinct three-dimensional form that requires that the size, shape and activities of cells be influenced by a combination of location (where they are in the organism) and where they came from (cellular heritage). Such a structure requires extensive communication and coordination between cells. Note, h owever, it does not necessarily require tissues made up of different cell types. Workers who study the evolution of life believe that simple multicellularity (colonies) has appeared at least twenty-five times. Complex multicellularity (or what some would call 'true' multicellularity), but defined without the requirement of multiple cell types and tissues, has evolved at least ten times: once in the group that led to animals, once in the green algal group that led to plants, once in another green algal group that did not lead to plants, twice in the red algae, twice in the brown algae, three times in the fungi, and several times in the prokaryotes. If the definition of multicellularity requires tissues with multiple cell types (not associated with sex and reproduction) then the number of multicellular groups is much reduced: just animals, plants and a very few fungi. The cellular structure of select groups of inanimate organisms, organisms that might be considered multicellular, is described below. Excluded are the vascular plants; these are considered in the next chapter. Cellular Structure in Fungi While many biologists characterize the fungal group as being 'multicellular' , many clearly are not. Three fungal groups are coenocytic and none of these are easily characterized as being multicellular. And unicellular fungi, which exist in several fungal groups, would certainly not be considered multicellular. The fungi that might be considered as possessing complex multicellularity do so for only a small portion of their existence and only in a small portion of their structure. Almost all fungi produce a filamentous structure, a hypha (plural hyphae), that is hardly multicellular and is better described as being colonial, a filamentous organism with no specialization of cells whatsoever. In three of the fungal groups the hyphae lack cross walls and are coenocytic. Hyphae grow from the tip and can branch in two. Branching can also occasionally occur away from the tip. Hyphae may also fuse with one another, thereby producing an anastomosing structure. The network of hyphae thus formed is termed a mycelium. The typical mycelium is a feeding structure with a dynamic (growing and dying simultaneously), diffuse , form that is well suited to obtain nutrients: it possesses both a great deal of surface area for absorption and it also penetrates a large environmental volume , allowing it to 'mine' a substrate for nutrients. The feeding mycelium is the digestive system of fungi and simultaneously serves as: (1) a structure to digest food, (2) a small intestine to absorb nutrients (3) a circulatory system to move nutrients to other parts of the fungus and ultimately to reproductive structures. Note that none of these functions are associated with specific cell types, tissues or organs. Two fungal groups are considered cellular because they do have cross-walls of sorts. These are called septa (singular septum) and they only partially seal off cells because they are perforated by pores that are large enough to allow many materials (ribosomes, mitochondria and sometimes nuclei) to move from one cell to another. Thus, the composition of these fungi is in between coenocytic and cellular. The cellular structure of specific groups of fungi are described below. Chytrids The fungal group considered most primitive (probably better described as the group that diverged at the earliest time from the rest of fungi) are the Chytridiomycota (chytrids). Chytrids are small aquatic organisms, both marine and freshwater, with some existing in the film of water surrounding soil particles. Most are microscopic, usually the size of a typical unicellular organism (less than 100 um). They may be truly unicellular (one nucleus) or coenocytic (multiple nuclei). Many produce forms that are roughly spherical. Several chytrids form what are called rhizoids, root-like extensions off of the main body that attach them to a source of nutrition, often pollen, the spores of other organisms, or a single cell of a living or dead multicellular organism. Besides attachment, the rhizoids also serve to increase surface area and allow for more effective digestion and absorption. A few chytrids form filaments (hyphae) that occasionally branch to form a very small mycelium. The group is distinguished from all other fungi by having flagellated, mobile, spores. Coenocytic, filamentous fungi Two additional fungal groups, the bread molds (Zygomycota) and the Glomeromycota , are substantially bigger than chytrids and produce a coenocytic hyphae and form mycelia. While both these groups lack specific cell types, some do form specific structures which one might term organs, except that they are parts of cells, not composed of cells. For the bread molds these structures, stolons, rhizoids and sporangiophores , are relatively large and can be seen with the naked eye. In the Glomeromycota the 'organs' are much smaller structures, but again are parts of cells, not cells. The Glomeromycota are the fungi that, together with plants, form endomycorrhizae , associations between plant roots and fungi. In endomycorrhizae, the fungus penetrates individual root cells ( 'endo' means inside) and inside these cells the fungus form two structures, tree-like arbuscules and spherical vesicles (endomycorrhizal fungi are sometimes called vesicular-arbuscular mycorrhizae or simply VA mycorrhizae). These structures are extensions off of the coenocytic hyphae. Arbuscules are structures with some similarities to the the rhizoids of chytrids. They serve no anchorage role but are significant in increasing the area of contact between the fungus and the plant, thereby allowing for greater material movement between them. Vesicles are spherical bodies that are thought to store materials for the fungus and which may develop into spores. Septate fungi—Club and Sac Fungi The two largest groups of fungi, club fungi (Basidiomycota) and sac fungi (Ascomycota) are not coenocytic. They produce hyphae that are septate, with cross walls to delineate individual cells. As the growing tip of a hypha extends, nuclear divisions (mitosis) are coordinated with the cellular divisions (cytokinesis) that produce new cross walls with a substantial pore. These cross walls are oriented perpendicular to the long axis of the hypha. As a result, new cells, each with a nucleus, are sequentially produced at the tip as it grows. The tip cell is also capable of occasionally dividing in a manner to cause the tip to bifurcate, to split in two, forming a branch. Branching sometimes also occurs away from the tip, the result of an outgrowth from a previously formed cell. Under certain conditions the hyphae of Ascomycota and Basidiomycota may also form much more compact mycelia, usually associated with reproduction, and some of which approach in form structures that are more typical of multicellular organisms. These structures may range in organization from an amorphous mass of compact hyphae (aka a dense mycelium), termed a stroma, in which 'fruiting bodies' (spore producing structures) are formed (see tar-spot disease ), to much more defined and determinate structure such as a typical mushroom with a stalk and cap. Usually, spores are produced from a structure that is somehow elevated, allowing for enhanced spore dispersal by the wind. Most of these spore producing structures are called mushrooms if they are visible with the naked eye; and most are club fungi (Basidiomycota) but a few are cup fungi (Ascomycota). Within the two groups there are a wide variety of fruiting body forms, all developing as a result of pattern of growth of multiple hyphae. Although these structures are clearly organized and produce a consistent (determinate) three-dimensional final form, they generally show little evidence of tissues or specialized cell types, except those directly associated to sexual reproduction. Another dense, compact hyphal structure produced by septate fungi is called a fungal cord or a rhizomorph. It consists of a multiple hyphae running parallel and glued to each other, forming a thread that may be several millimeters in diameter (cf. to a fungal hypha which typically is ten-times smaller in diameter than a human hair). Rhizomorphs are the result of repeated hyphal branching at very low angles to the orientation of the parent hyphae, consequently allowing the branch to stay closely associated and fused with the hypha that produced it. The result is a structure with little capacity to feed (or lose water) when compared to a diffuse mycelium because of its reduced surface area and reduced penetration of its environment. But the rhizomorph is specialized for mobility and allows the fungus to traverse low-nutrient space or environmentally hostile (e.g., dry) space and potentially arrive in a more favorable location. When and if the rhizomorph arrives in a nutrient rich zone the growth form reverts to a diffuse mycelium, again suited for nutrient absorption. The extension of rhizomorphs requires transport of nutrients in order to feed the tips of hyphae (where growth is occurring) using nutrients that are being acquired at some distance from the tip. This transport function is served by specialized, large diameter hyphae, analogous to tubes found in brown algae and vascular plants. Another specialized cell type found in rhizomorphs, and located toward the outside of them, are thick walled 'sheathing hyphae' that have a structure again similar to some cells (fibers) found in vascular plants. These give the rhizomorph structural integrity and make it is less likely to be severed, something that is of much more consequence to a rhizomorph than to an individual hypha. A few fungi produce structures called sclerotia, again a dense mass of hyphae, but sclerotia often develop into distinct forms and sometimes show specialization between a hard outer 'rind' and inner cells. The cells on the interior often have substantial food reserves and sclerotia are typically overwintering structures, structures that can become dormant. The stored food allows the sclerotium, which is sometimes dispersed, to survive the winter and resume growth when favorable conditions return. Cellular Structure of Water Molds The water molds, or Oomycota are similar in form to the bread molds (Zygomycota) with both groups being composed of coenocytic filaments, hyphae, that collectively form a mycelium but show no cellular specialization other than cells associated with reproduction. The group includes some important plant pathogens, including late blight of potato, sudden oak death syndrome and 'damping off' diseases. In spite of the name, they aren't molds (fungi) and many are terrestrial not aquatic (although the representative probably most commonly seen, at least if you have an aquarium, is a white fuzz occurring on dead fish). Water molds were once grouped with the fungi because of morphology but they are now considered to be in the heterokont grouping that also includes brown algae and diatoms. Cellular Structure of Cellular Slime Molds During the unicellular part of cellular slime mold 's existence there obviously is no cellular differentiation, but when aggregation occurs the cells acquire different fates and one might consider this to be reflective of complex multicellularity. In particular, and of evolutionary significance, only some cells of the aggregate ultimately end up producing reproductive cells. Other cells, e.g., the cells in the stalk of the spore producing structure, contribute to reproductive success by elevating the spore producing structure but gain no evolutionary advantage for ' doing a good job ' since they are not necessarily represented in the next generation. This is in contrast to the more normal production of multicellularity where all the cells of a multicellular organism are derivatives (and hence share a genetic composition) with the original ' starter cell ', typically a zygote or a spore. Because of their relatively unusual path to multicellularity, the determinators of cell fate in cellular slime molds is an area of active study. There are no obvious visual/structural differences between the cells of the slug or the fruiting structure but their positions are different, some are on the outside, some inside; some are near the front, some are behind. And position appears to be important in determining cell fate, including the position at the time of aggregation. Moreover, there is strong evidence that cell fate and ' knowledge' of position, is a result of communication via chemical signals, one of the criteria that workers consider to be a defining aspect of complex multicellularity. Cellular Structure of Algae Algae are an artificial grouping of aquatic photosynthetic eukaryotic organisms whose classification remains in some flux. Many algae are unicellular or are colonial ( 'simple multicellularity' ) and do not show any cellular specialization except for cells associated with sex and reproduction. Most of these organisms are small, microscopic, or barely visible to the naked eye. But there are three groups of algae, colorfully named the red algae, brown algae and green algae, that include forms that are described as 'macroalgae' . They are large (i.e., not microscopic, generally at least 0.1 m in extent) and with an organized structure , often consisting of organs: cylindric stems and branches, flattened blades, air sacs, root-like holdfasts and other features. Almost all of the brown algae and most of the red algae could be described this way. This form is proportionately less common in the green algae where many members are smaller and where a considerable number of forms are unicellular. Using the more lenient definitions of multicellularity, most macroalgae would be considered multicellular. Using more restrictive definitions, in particular requiring intercellular connections and communication that allows for cooperation between cells, substantially reduces the number of macroalgae that are considered 'truly multicellular' . Nonetheless, it appears that rigidly defined complex multicellularity has evolved independently at least two times in each of the three macroalgae groups (along with three times in the fungi, one time in animals and twice in bacteria). Brown algae This group used to be considered a phylum but now is considered as an entity further down the taxonomic scale (a class, or a family, or a level in between). While almost all brown algae are macroalgae, many lack cellular differentiation and an obvious tissue organization. The structure is basically filamentous, with the filaments branching and interacting with each other to form a distinct structure, similar to the way that certain fungi produce mushrooms out of hyphae. It appears that 'true' multicellularity, with the presence of cellular differentiation and tissues, has evolved twice in this group, once in a line that includes rockweed ( Fucus) and once in a line that includes giant kelp ( Laminaria ) . In both these groups there are distinct organs (holdfast, stipe, blade, air bladders) along with some cellular and tissue differentiation; in particular, there are cells specialized to allow for the long-distance movement of carbohydrates throughout the organism. These cells are analogous (not homologous!) with transport cells of vascular plants and have similar features: they are elongate cells with large diameters and with multiple trans-cellular connections between adjacent cells. Another distinct cell type, also analogous with what is found in vascular plants, are cells with thickened cell walls that provide for structural integrity, allowing a large organism to hold together in spite of being pushed and pulled by ocean currents and/or waves. Red Algae The red algae group has roughly four times the number of species as the brown algae and is more diverse in terms of morphology. A substantial number are macroalgae with a definite organized structure. As was the case in fungi and some brown algae, their three-dimensional complexity is a consequence of the growth and interactions of multiple filaments. Tissues can be described in some forms, with the cylindrical portions ( 'stems' ) having distinct outer and inner layers and possessing cells distinguished by their size and pigmentation. Some red algae are crust forming ( 'crustose' ) and exist as a coating on the surface of various substrates. In many crustose forms there is a layered organization, with the filaments next to the substrate having different cells from those above. Some of the crustose red algae develop a layer of dividing cells near the top surface whose action allows the crust to thicken and also allows for the development of reproductive structures. Green Algae Of the three algal groups that include macroalgae, the green algae group is by far the largest (15, 000 species), with many unicellular, simple filamentous, and colonial forms. Consequently, the macroalgae are a much smaller portion of the total species. Some of the macroalgae are siphonaceous, often composed of multinucleate filaments that interact to form a three-dimensional form. Most modern (cladistic) phylogenies divide the green algae into two groups, one of which, in addition to including (some) green algae, contains all of the organisms considered plants. Both groups exhibit a variety of forms, including some macroalgae with 'complex' multicellularity, showing three-dimensional growth, cellular connections and distinct cell types.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.05%3A_Cellular_Structure_in_Inanimate_Life.txt
Most workers consider plants to be a monophyletic group derived from green algae. All plants are considered 'truly multicellular' although there are some members with very little cellular specialization and only very rudimentary tissue and organ structure (Figure 1). The majority of plants, and the ones that most people observe, are 'vascular plants' , a monophyletic group whose name refers to particular cell types and tissues that they possess. The remaining plants, non-vascular plants (mosses, liverworts and hornworts), are often put together in a group. However, grouping organisms on the basis of what they lack is generally not useful in a phylogenetic sense and it certainly is not in this case: non-vascular plants do not form a 'natural grouping' . Moreover, none of the three groups appears to be more closely affiliated with vascular plants than the others. Thus, the plant group is best separated into four units (generally put at the phylum level): mosses, liverworts, hornworts and vascular plants. M osses, liverworts and hornworts are all small, often less than a centimeter in height, but they can extend over a considerable area. They do vary in form and exhibit three basic body plans, that do not follow the phylogenetic groupings. These are delineated below. Non-vascular plants, and all plants, alternate between two stages: a haploid, gamete producing form (gametophyte) and a diploid, spore producing form (sporophyte) (Chapter 11). In all of the non-vascular plants the g ametophytes are much more likely to be encountered because of their greater size and longevity. When present, sporophytes often appear to be an appendage of the gametophyte which, in a structural sense, they are. For vascular plants it is the sporophyte plant that is dominant (much larger on longer lived) and the gametophyte stage will only be considered briefly here but will be described when considering sex and reproduction. TOPICS • Non-vascular plant gametophyte structure • Simple thalloid forms • Complex thalloid forms • 'Stem and leaf' forms • Non-vascular plant sporophytes • Vascular plant sporophyte structure • Organs • Tissues • Cell types Simple thalloid forms A thallus refers to a body form that lacks organs and tissues and is relatively amorphous, often occurring as a flattened sheet. In all of the hornworts (Figure 1) and some of the liverworts the form of the gametophyte is a simple sheet of cells, a few cells thick, often thin enough so that the thallus is translucent. There is no cellular specialization within the thallus, although the lower surface produces unicellular rhizoids that attach the thallus to the substrate. These cells lack chlorophyll and therefore must acquire nutrition from the photosynthetic cells above. Complex thalloid forms This form is present solely in the liverwort group. Like the previous form there are no obvious organs except those associated with sexual or asexual reproduction. The thallus consists of flattened sheets that spread over the substrate (soil, rocks or tree trunks and branches, leaves) and commonly bifurcates, splitting in two. The thallus is often over 20 cells thick and has discernible layers. There is an upper 'skin' (epidermis) that is coated with a cuticle and often is regularly perforated by pores. The pores are formed by barrel shaped clusters of cells that span the epidermis and, at least in some forms , are capable of closing the pore under dry conditions. Below the epidermis is a porous layer of cells, i.e., cells are not tightly packed and have air spaces in between them. Cells of this layer have abundant chloroplasts. Generally, the largest air spaces are below the por es. The porous nature of the upper thallus is a feature that is also be present in most vascular plant leaves. Lower layers of the thallus are less porous and have cells that lack chlorophyll. The lower epidermis often produces rhizoids, i.e., some of the cells have thread-like extensions that anchor the organism to the substrate. Structures associated with asexual reproduction (gemmae cups), and structures associated with sexual reproduction ( antheridiophores and archegoniophores ) are sometimes observed extending from the upper surface, their structure and function will be discussed in a later chapter. Stem and leaf form This is the form found in most mosses and many liverworts. The organism has a cylindrical 'stem' to which are attached small planar appendages, 'leaves' , that are typically two mm or less in length and increase the light absorbing area. The 'leaves' generally do not have a cuticle and are only one-cell thick, although moss leaves commonly are thickened with more cells along their center-line, forming a nerve (costa). The stem is often less than 2 mm in diameter and generally shows little cellular specialization. In a few moss species there are cells (hydroids) that are specialized for water transport by being elongate and hollow (i.e., the cell has died and the cytosol is absent), with openings in their slanted end-walls that allow water movement between cells. Similarly, a few mosses possess cells (leptoids) that have features that facilitate carbohydrate transport. Although hydroids and leptoids function in ways similar to cell types in vascular plants, they lack lignin and are not considered vascular tissue. They represent convergent evolution, not a close relationship between vascular plants and the few mosses that possess them. Sporophytes of non-vascular plants The diploid, spore producing form (sporophyte) of all the non-vascular plants grows out of the gamete producing form (gametophyte) and is generally short-lived and carries out little photosynthesis. Although they are sometimes green and photosynthetic, they have no flattened parts to increase photosynthetic light absorption and must depend on the gametophyte for carbohydrates during some or all of their existence. In hornworts, the sporophyte is a thin cylinder that splits open longitudinally, from the tip, to release spores. In liverworts and mosses, the most common sporophyte form is a 'ball on a stick' , with a roughly spherical spore producing structure (sporangium) at the end of a stalk that in almost all cases serves to elevate the sporangium to a higher position, presumably to aid in spore dispersal. The sporangium opens to release spores by splitting apart (liverworts) or through an opening (mosses) whose size is regulated by teeth that move in response to humidity, closing the opening under humid conditions. In some liverworts the sporophyte is extremely small and although it is not elevated, its stalk is produced in an umbrella shaped organ (the archegoniophore) that is elevated. Organs, tissues and cells of vascular plants Although non-vascular plants are clearly successful existing and thriving in most terrestrial habitats, their size and activity is severely limited in ways that were overcome with the appearance in vascular plants of vascular tissues possessing cell types that make possible long-distance transport of water and carbohydrates. Vascular tissue allowed terrestrial autotrophs to exist as two connected entities, both essential to the other: a water and nutrient absorbing structure and a photosynthetic structure. The three organs of vascular plants, roots, stems and leaves, reflect thebasic biology of terrestrial autotrophs: leaves acquire sunlight and carry out photosynthesis to 'feed' the organism, roots explore the soil and acquire the water and nutrients that is required for photosynthesisand growth, and stems connect the photosynthetic part with the water-and-nutrient acquiring part and also serve to distribute leaves effectively in their aerialenvironment. Each of thesethree organs possess three fundamental tissues: a 'skin' (dermal tissue), transport tissue (vascular tissue), and ground tissue (everything else, the tissue that fills the spaces between dermal tissue and vascular tissue). Cells of vascular plants show substantially more specialization than is found in non-vascular plants and multiple cell types have been defined, primarily on the basis of the following features, summarized in Table 1. 1. Whether the cell is alive or dead at maturity. A number of plant cell types are significant to organism function only after they have died. In particular, cells important for water transport, for structural integrity (keeping the plant from falling over when the wind blows), and for mechanical protection are often dead when they are performing thesefunctions. Obviously, the cell is functioning before it dies, but its most significant contributions to the organism as a whole arewhen it is dead. These cells 'die young' as a result of a programmed cell death, i.e., a genetic program is triggered in these cells that causes it to die 'on its own' . Although the cells are only alive for a short period of time relative to the life of the organism, they contribute to the longevity of the plant for a prolonged period after their death and by so doing contribute to its evolutionary success. 2. Cell wall characteristics. All plant cells have what is called a primary cell wall described in chapter 3. It is composed of cellulose microfibrils imbedded in a matrix of hemicellulose and pectins, molecules that bind cellulose microfibrils to each other and also absorb water, forming a gel. The primary cell wall is present as the cell is growing and when the cell expands the wall is yield ing to the pressures that are present inside the cell. The cell stops growing when the cell wall stiffens and no longer yields to the pressures generated inside it. At this point some cells deposit a distinct type of cell wall material , called a secondary cell wall , inside the primary cell wall. Since the cell is not growing , the more secondary cell wall that is deposited, the smaller the space inside the cell wall becomes. When the cell dies , this space , where the cytosol (usually with a large vacuole ) used to be, is termed the lumen. Like the primary cell wall , the secondary cell wall contains cellulose microfibrils, but they are imbedded in a matrix of lignin, not hemicellulose and pectin. Lignin is a complex polymer composed of phenolic subunits. Unlike the primary cell wall, the secondary cell wall has substantial compressive strength and does not need a cell membrane and the pressurization of water inside the cell in order for the cell to resist compression (details on this process are discussed in chapter 22 ). Killing plant cells with only primary cell walls drastically affects their structural integrity (cooking spinach dramatically demonstrates the effects of killing plant cells on plant form ). A cell with a secondary cell wall is rigid even after the cell has died and the membrane is gone ; corn stems stand erect even after the plant is dead because of cells with secondary cell walls. Lignin is the material that makes plants woody , tough and rigid , but non-woody plants (e.g., corn) may possess lignified cells that are important structurally ; plants or plant parts (e.g., spinach and many other leaves) with cells possessing only a primary cell wall are herbaceous and much less resistant to forces produced by gravity or the wind. Such plants/plant parts lose all structural integrity if the cell membrane is destroyed or if lost water is not replaced 3. Cell shape . Plant cells come in a variety of shapes. Many cells are round or nearly so or rectangular with their long dimension being two to ten times that of the short dimensions. Other cells are very elongate with their long dimension being up to 1000 times that of the ir diameter. Generally, the long axis of cells runs the same direction as the long axis of the plant, i.e., up and down the stem /root. These features are summarized below. Specific cell types will be considered in more detail when considering the functioning of these tissues. Table 1. Vascular plant cell types. Note that some workers would classify fibers, tracheids, and vessel tube elements as types of sclerenchyma cells. Similarly, some workers consider sieve cells and sieve tube elements as types of parenchyma cells. Cell type Cell wall Shape Live at maturity? Parenchyma Generally, only primary, but may have secondary walls Round, rectangular, generally not elongate Yes Collenchyma Primary only but it is usually substantially thickened, often in the corners of the cell Elongate Yes Sclerenchyma Thick secondary wall, leaving a very small lumen Variable No Fibers (sometimes considered a type of sclerenchyma) Thick secondary wall, leaving a very small lumen Elongate No Tracheids Secondary wall deposited in a variety of patterns or sometimes uniformly Elongate, with a substantial lumen, cells are not stacked end to end but overlap No Vessel tube elements (vessel tube members) Secondary wall deposited in a variety of patterns or sometimes uniformly Elongate with large lumen; multiple cells are stacked on top of each other to form vessels no Sieve tube elements Primary only Elongate with large lumen; multiple cells are stacked on top of each other to form sieve tubes Yes Sieve cells Primary only Elongate, with relatively large lumen, overlapping cells, not stacked yes On the left: Tracheids are elongate cells with a secondary wall and large lumen. The cells overlap each other along the long axis of the plant. Individual cells are not lined up in stacks On the right: Vessels tube members are also an elongate cell with a secondary wall but they stacked on top of each other, the top of one cell directly underneath the bottom of the next cell and the junction between cells has holes, forming a 'perforation plate' The name for the stack of cells is a vessel. The individual cells of a vessel are called vessel tube members or vessel tube elements. By and large, vessel tube members are shorter and have a bigger diameter than tracheid cells. Both vessel tube members and trachieds have thick cell walls but differ in diameter (vessel tube members are larger). It is difficult to distinguish the two cell types in cross-section. However, in a longitudinal section, vessel tube members are recognizable because of their stacking, . Additional distinctions will be considered when discussing water transport. A Few Other Types of Cells Guard cells Guard cells are special cells found in pairs in the epidermis of leaves. Guard cells operate to open pores called stomata in the leaf that allow carbon dioxide to enter. Guard cells change shape as they take up (or lose) water and pressurize or depressurize. The changes in shape cause an opening to appear or disappear in the space between the pair of guard cells (discussed in Chapter 22) Fungal haustoria Fungal haustoria are specialized cells found in biotrophic fungi , fungi that that eat living things, usually plants, occasionally other fungi, animals, or protists. These fungi acquire nutrients from host cells and the haustoria penetrate into host cells and bring about the transfer of materials from the host to the fungus. Biotrophic fungi sometimes also have specialized cells (appressoria) that are able to penetrate the cuticle of their host. Spores, sperm and egg These cells are associated with sex and reproduction. Sometimes they have special structural features, but most significant are their abilities and potentials. They are found in most of the groups considered here and will be considered the in later chapters. Additional Images Websites with excellent pictures of plant cells and tissues:	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.06%3A_Organ_Tissue_and_Cellular_Structure_of_Plants.txt
A feature of living things, and not just organisms, is that they are dynamic, they change, and they do so in a predictable way that can be described and observed over and over again in a variety of biological entities. This pattern of change through time is termed development and while the term is mostly associated with organisms, it is significant to realize that organized (i.e., controlled in some manner) change through time is seen in cells (e.g., the cell cycle, apoptosis), populations (e.g., logistic and exponential population growth) and communities (e.g., succession). TOPICS • Organism development • Development in unicellular organisms • Development of cell shape • Development in colonial organisms • Development in coenocytic/siphonaceous organisms • Development in multicellular organisms • Development in plants Organism development While development may include changes in a variety of aspects of an organism, from structure to physiology to behavior, we will focus here on how development produces and changes the structure and form of an organism throughout its lifetime. We have defined organisms as being distinct in time and space with a starting point and an ending point; thus , aspect s of development are the alterations in size, form and structure occurring during the organism 's lifespan. For most familiar organisms the starting point is a special cell that has the ability to proliferate, develop a complex structure, and grow to produce an ' end point ', a specific form that characterizes that particular creature. Many might think that this is the end of development, but for many organisms there are changes in the adult with time and sometimes the changes are dramatic and end the life of the organism. Some organisms ' self-destruct'as part of its developmental process , just as some cells do. Salmon die after spawning, as do wheat plants. In both cases the endpoint of the development al process is death. A corollary to this is that development does not just include growth and increases in complexity, it may also include, and in fact it often ends with, decreases in size and complexity and ultimately the end of the organism.Figure 6 The field of development has exploded in recent years and is being examined from molecular and evolutionary perspectives in great detail. We are focused at a very different level, considering the very basic developmental features that bring about the form and structure of the biological entities we describe as organisms. We have described several different forms of organisms: unicellular, simple multicellular ( filamentous, sheets), coenocytic, complex multicellular. We will briefly consider how each of these forms develops. An important aspect of d evelopment for many organisms is the process of sex, involving the combining the genetic information of two organisms and subsequently halving it. Sex and reproduction are considered later in chapter 11. Development in organisms that are unicellular A number of organisms under consideration here (e.g., many bacteria , archaea, diatoms, dinoflagellates, and many green algae) are unicellular and, while their devel opment is quite different than for multicellular organisms, they do change over time and show definite patterns of development. Universally, development in unicellular organisms has two visible manifestations (there are many more developmental events that are not visible): cell division (Figure 7) and cell growth. These processes are components of the 'cell cycle' , a repeating series where cells acquire materials, synthesize molecules from them , and partition these materials into two daughter cells in the process of mitosis. While the most obvious molecule that needs to be made is DNA, there are a host of others: molecules for membranes, ribosomes and (for eukaryotic cells) for mitochondria and plastids. The construction of these materials requires that the cell obtain the elements that they are made of: carbon, nitrogen, phosphorus, etc., and part of the cell cycle involves the acquisition of these materials and the construction of the requisite molecules. The relationship between cell division and cell growth is not the same in all organisms. Cells may divide repeatedly without any growth (e.g., in the early development of many animals). In this situation the original cell has plenty of 'materials' and the cell ular divisions simply partition these materials into daughter cells resulting in a multicellular organism that is basically the same size as the original fertilized egg. But this cannot go on forever, eventually there has to be material acquisition, reflected in an increase in mass and size (i.e., growth), to allow for continued cell division. The main component of all cells is water and its acquisition is generally what drives cellular growth (i.e., expansion in size). For organisms with cell walls, water entry into the cell is affected one of two ways: by weakening the cell wall strength or by increasing the concentration of solutes, leading to an increase in internal pressure. This is discussed more in chapter 22, but for now one should appreciate that both these processes can be controlled by cellular activity. Consequently w ater absorption and cellular growth may occur as a distinct phase that occurs before or after other materials are obtained, or it can occur gradually. That is, the cell can: (1) grow steadily as both water and other materials are obtained; (2) divide, acquire materials other than water while remaining about the same size, and once enough materials other than water have been obtained then rapidly acquire water and grow or (3) divide, grow quickly by absorbing water and show little growth as it acquires materials other than water, and then divide again. In the first case there are a range of cell sizes and the age of a cell is correlated with its size.. In the second case, cells that are about to divide are recognizable because of their large size. In the third, case a population of cells would all be the same size except for some small cells that have just been produced by cell division. The pattern shown by certain unicellular diatoms illustrates additional divers e possibilities. All d iatoms are enclosed in a silica shell with two halves; some are structured like a petri dish with a circular top half having a diameter slightly larger than that of the bottom half , allowing it to be a cover the bottom. When the cytosol divides (cytokinesis) the top half produces one daughter cell by grow ing a new bottom half and th is newly produced cell is 'fully grown' at its inception, i.e., it shows no growth. This cell, like all cells, goes through the G1 and G2 stages and during these stages 'materials are acquired and put together into biomolecules that can subsequently be partitioned between two daughter cells , but these phases , although often described as ' growth 1 ' and ' growth 2 ' do not involve an increase in cell size. Now consider the second daughter cell, the one that is associated with the old bottom dish, the smaller dish. This bottom dish becomes a ' top dish' as the cell generates a new bottom half. Like its sister cell it does not grow; it actually ends up slightly smaller than the parent cell because the bottom half of the original cell has become the top half of the daughter cell; consequently, this cell is slightly smaller than its parent (remember the bottom shell has to fit inside the top shell and hence must be smaller). Thus, after cell division, two cells are produced; one is the same size as the original cell and one is slightly smaller. Growth of individual cells is not occurring. Through time, the mean cell size of the diatom population becomes smaller and smaller until some critical minimum size is reached when sexual reproduction is triggered and results, among other things, in cells that are the same size as the original. Exactly what triggers a cell to divide is a tightly controlled process that has been extensively studied because of its connection to cancer. But the phenomenon is important in other situations as well. F or example , in 'algal blooms' , whe re a population of alga e starts reproducing rapidly, producing very large populations whose existence often has very significant consequences. In both cancer and algal blooms, the importance of control mechanisms , other than nutrients, is indicated by the fact that nutrients alone may not trigger population/cancer growth : nutrients are necessary but not sufficient for growth. T he control of the process is not simply that cells divide when they acquire enough materials to form a second cell. Development of cell shape Part of the development process, for both unicellular organisms and the cells of multicellular organisms, involves the acquisition of a characteristic shape. For some cells, growth proceeds equally in all dimensions and small cells have a very similar shape to large ones, but for many cells growth is decidedly different in different directions and this produces 'adult' cells with characteristic shapes, distinct from the typically spherical/cuboidal shape of the newly produced cells. The attainment of this shape is an important feature of their development. For organisms with cell walls the shape of cells is determined by the relative strength of the cell wall in different directions. The cells grow by having an internal pressure that exceeds the cohesive strength of the cell wall. The wall yields and cellular growth occurs. If the strength of the cell wall is uniform then the cell expands uniformly (think of a typical balloon). But if the wall has less strength in a particular direction, then the expansion will occur in that direction, think of the specialty balloons that become long and skinny, this is a result of the balloon being much more resistant (higher cohesive strength) to radial expansion than to extension. The strength of cell walls is determined by the orientation of the cellulose microfibrils and this orientation is determined as they are deposited. Development in organisms that are colonial An essential aspect to unicellular development is that the daughter cells separate, a result of the fact that the junction between the 'new' cell and the 'old' one is weak and can be broken by forces in the environment or by forces that accompany the expansion of one or both of the daughter cells. If this does not happen cell division brings about an accumulation of cells that can drastically affect the functioning of each by changing the environment that they are exposed to and by changing form. Clusters of cells are considered colonies exhibiting 'simple multicellularity' . They are biological structures that do not nicely fit into the organism category, being somewhere between an organism and a population. Often colonies have characteristic shapes that develop as a consequence of patterns of cell division. Three basic patterns were described earlier that result from the control of the plane of cell division: filaments , sheets and spherical colonies . Each of these patterns has consequences for individual cells and their interaction with the environment. Spherical colonies result in some cells (those in the interior) that have very little contact with their environment, sheets and filaments represent situations where the colony of cells has more interaction with their environment although never as much as would be the case if the cell s had separated from their parent. While most colonial organisms are indeterminate, with no specific endpoint, growing to sizes that are dictated by biotic and abiotic conditions, there are some colonies that are determinate, producing a colony with a set number of cells and usually with a specific form. Development in organisms that are coenocytic /siphonaceous The vast majority of organisms that are large (a mm or more in length) are made of cells that are organized in a particular, repeatable way to produce form, i.e., they are multicellular and their development from a single cell involves the creation of cells in particular places to create a form. But there are a few of 'large' organisms whose form is not a consequence of an accumulation of cells but rather they are a single large cell that has developed to considerable size. A remarkable example of this type of growth is Acetabularia , a green algae that ranges up to several cm in size and is shaped like a parasol. Acetabularia , and most organisms that are coenocytic/siphonaceous, possess a cell wall and have internal pressures that develop as a result of osmotic forces. The shape that such cells produce are a result of the pattern of cellular expansion, which , as discussed above, is a consequence of relative strength of the wall in different directions. Bread mold produces parts (stolons, rhizoids, sporangiophores) that are all outgrowths of a single cell and there must be developmental controls that direct where and when outgrowths are produced and what structure is to be formed. Similarly, some siphonaceous green algae (e.g. Caulerpa ) are capable of producing complex and large forms by controlling the form and direction of extensions off of a single cell (Figure 8). Some siphonaceous colonial forms are partly cellular in their construction: in Hydrodictyon individual cells are large (up to a centimeter) and multinucleate but are joined together into rings, commonly five or six-membered, to form a polygonal network. Development in the coenocytic plasmodial slime molds are particularly dramatic. Within a period of 20 hours a giant, multinucleate cell flowing in a network of channels and moving at rates of up to 1 cm per hour can transform into a rigid structure bounded with a cell wall and in the form of a miniature forest (~ 1-2 mm tall) of stalked structures that bear sporangia at their summit (Figure 10). Development in multicellular organisms Development in multicellular organisms is a much more complicated process. Multicellularity requires that an organism produce more than one type of cell. Except in the unusual case of cellular slime molds ( Dictyostelium ), all the cells of multicellular organisms have the same genetic makeup. T his means that there must control processes that dictate that some cells follow one set of instructions while other cells follow different instructions. Unicellular and colonial organisms may have the ability to do this to a limited extent. A lthough the majority of cells of these organisms are all the same, they may produce specialized cells to affect the sexual process, to carry specialized metabolic functions (e.g., the akinetes of cyanobacteria), or to accomplish dispersal. Complex multicellularity requires an additional significant feature besides the ability to produce different types of cells: the ability to organize multiple cell types in a three-dimensional pattern to form tissues and with tissues organized to form organs and with the organs organized to form organisms. This organization requires a developmental process that dictates what types of cells are produced, where they are produced, and to what extent and in what direction each cell expands. A significant developmental distinction between animals and most of the organisms covered here results from the presence of the cell wall. Animal development includes the possibility of cell migration, with the movement of cells allowing for particular arrangements and forms to be produced. Outside of the animal kingdom cell migration occasionally occurs but only in organisms that lack cell walls. C ells of cellular slime mold s must migrate in order to aggregate and subsequently move relative to each other, and cellular slime mold development involves a physical rearrangement of cells. When a 'final' form of a cellular slime mold is produced the individual cells are no longer capable of moving because they have developed cell walls and are stuck to neighboring cells. Almost all of the multicellular organisms dealt with in this book possess cell walls and a newly produced cell is 'stuck' to the cell that produced it. Moreover, for all plants, cell division occurs in a region called a meristem, a region that produces new cells with a three-dimensional organization. The new cells that are produced are not only attached to their parental cell, but are also attached to multiple cells that are being simultaneously produced around them. In contrast, as discussed previously, fungi and some red, green and brown algae produce three-dimensional multicellular structures in ways that do not involve a meristem, generally by having individual filaments (one-dimensional structures) glued together in ways to form a three-dimensional form. Development in plants Plants (here used to include mosses, liverworts, hornworts and vascular plants) have several developmental features that are not found in familiar animals: 1. Plant growth is generally indeterminate, i.e., without a defined endpoint 2. Plants possess meristems, embryonic regions, throughout their life. 3. Plants exhibit modular growth, a pattern also found in some less-familiar animals (e.g., hydroids, corals, sponges), but not in familiar animals. 4. Plants show alternation of generations, meaning that there are two forms of the organism, one haploid and one diploid. Alternation of generations (Chapter 11) is also present in some green algae, brown algae, red algae and a few chytrids (fungi). The first three points are considered below with the final point considered in a later section of the book. Determinate and indeterminate growth and the growth of plants By far the most familiar pattern of organismal development is that shown by mammals who grow for a short period of time (relative to the entire life of the organism) and then spend most of their life as an adult form. This type of development can be termed 'determinate' because the final form is 'determined' , there is an endpoint (an adult) to the development process. While some of the organisms covered in this course, in particular many of the unicellular forms, show this type of development, most 'non-animals' , and in particular plants and fungi, show a very different patterns of development, one that is described as indeterminate, where there is no endpoint and the organism is, in essence, everlasting. The key to its everlasting nature comes from the fact that that plants retain portions of their body that are permanently embryonic . In the familiar mammalian pattern of development an organism is an embryo for a portion of its life and then transforms into a juvenile and eventually an adult. An embryo is often defined as a 'young organism' but what makes it special is not its age but the fact that it cells are capable of cell division, cell differentiation and cellular growth. In animals these cellular abilities are only found for a short period of time. The whole animal is basically the same age and through time it transforms from an embryo into an adult. In order to observe development in animals one observes an embryo through time. While the adult does replace cells, in terms of development it is not changing in form. In contrast, plants always have regions that are embryonic and capable of dividing, differentiating and growing; and at any one point in time one can see the developmental process by moving from the embryonic parts of the plant to the older parts of the plant, i.e., the entire plant is NOT all the same age. If you planted an acorn ten years ago you might consider the structure that you now see is 'ten-years old' , but most of it is considerably younger and one can even find parts in the embryonic regions that were 'born yesterday' . At any point in time one can observe the entire development al process, from embryo to 'adult' , by moving distally, from the embryonic regions, located at the tips of roots and shoots , to progressively older tissues further from the tips. The embryonic regions of plants are called meristems. There are two basic features that distinguish embryonic regions : (1) cells are dividing and thereby producing more cells, (2) cells are small, undifferentiated and not yet committed to a final cell type. The activity of meristems may vary seasonally , it often has periods of quiescence or dormancy, but its ability to produce more cells that develop into a variety of cells is intrinsic to the meristem region. Very early in the life of the plant the entire plant is embryonic but soon some of the cells become developmentally programmed to mature into particular types of cells and , along with this, lose their ability to divide. In seed plants this transformation takes place within the seed and a mature seed has within it a small plant with two embryonic regions on opposite ends of a very short root/shoot axis. Throughout the life of the plant this axis will extend because of the expansion of the cells produced at the two ends. The meristem s produce more and more cells and the expansion of these cells pushes the two meristem s further away from each other and elongates the root and shoot. The se embryonic regions are called primary meristems (they are the first ones formed) and also apical meristems (they are located at the tips, apices, of roots and shoots). Root apical meristems divide to produce cells that extend the root axis. Shoot apical meristems serve a similar function for shoots but while producing new shoot material they are also producing leaves. Growth from apical meristems is called primary growth . In general, the oldest part of the plant is at the soil surface and one encounters younger and younger tissues as one moves towards the tips of shoots or tips of roots. The actual region of growth is generally restricted to a small portion, typically a centimeter or less, just below the meristematic regions. Plant growth is modular In addition to being indeterminate, plant growth is modular, producing structures that are fundamentally self-similar and recursive. There are two basic modules to a vascular plant: roots and shoots, and both can produce new modules, branch roots and branch shoots, that are replicas of the original shoot axis and root axis. With time, a seemingly complex entity is produced, yet the rules governing its construction are very simple: the shoot can generate branches and these can generate more branches and these can generate even more branches. The same thing is true for roots. The growth of all the modules results from the activities of apical meristems and all such growth is considered primary growth. Figure 11 Modular plant growth: Plants grow in a modular fashion with two basic modules: shoots (which bear leaves) and roots. Both of these modules have at their tip a meristematic zone (shoot apical meristem and root apical meristem). These modules are capable of producing additional modules, branch roots and branch shoots and these in turn can produce more branches, i.e., the branches have branches. It is a recursive structure. The original root and shoot meristems are created in the seed. Branch shoots originate in specific places, adjacent to where the leaf was or is attached to the stem. A group of meristematic cells, called a bud (branch) primordium is left behind by the apical meristem each time that it produces a leaf. These generally do not develop immediately and although a potential branch is produced at every leaf junction, many of them never develop. The production of branch roots is not as rigidly determined. The growth produced by apical meristems is considered 'primary growth' whether it occurs on the original root or shoot or occurs on branch roots or shoots. Leaf development: In contrast to the roots and shoots, whose growth is indeterminate, leaves are determinate, producing a defined form, the product of a structure with a defined (determined) development process. The shoot apical meristem produces mounds of embryonic tissue, called leaf primordia, that divide for a period of time, grow for a period of time and then exist in a static form until the process of senescence is triggered that culminates with the leaf becoming detached from the rest of the plant. Origin of new modules. To create a new module, one needs to create a new apical meristem. These originate differently in roots and shoots. In roots, new apical meristems form as the result of the activity of certain cells in the outermost layer of the central core of root vascular tissue (more details in the next chapter). Some of these cells are stimulated to start dividing and become organized to form a root apical meristem. Growth of cells produced by this meristem pushes the branch root apical meristem out of the original root and into the soil, where it continues to grow in a fashion similar to the original root. Branch shoots are created in a differently and originate from a shoot apical meristem. In addition to extending the shoot and producing embryonic leaves, the shoot apical meristem also produces a new shoot apical meristems in the 'axil' of each leaf. These are new shoot apical meristems and are called bud primordia. They are produced in a dormant state and need to be stimulated to start dividing and produce new cells that will allow the branch to elongate. Most bud primordia are never stimulated to grow; if they all were stimulated a very 'branchy' structure would result, with a branch being produced at every position where there was or is a leaf. Often, but certainly not always, branch shoots are only stimulated to grow after the leaf they are adjacent to has fallen off the plant. Plants are also capable of producing new modules in non-standard ways. Roots and shoots thus produced are termed 'adventitious' . Sometimes roots are produced from stem tissues and these would be described as adventitious roots because all 'standard' roots are formed off existing roots. Similarly, sometimes root tissues can develop shoots; obviously these are not originating in the axil of a leaf, thus these would be termed adventitious shoots. The ability of some plants to produce adventitious roots or shoots allows for the vegetative propagation of plants: if detached stems can be stimulated to produce roots then one can propagate plants from 'cuttings' ; similarly, roots can be used to propagate plants. And for some plants leaf tissue can be stimulated to produce adventitious roots and shoots; thus, propagation is sometimes possible from leaves. In all of these situations, certain cells, called parenchyma cells, are stimulated to start dividing and organize to form an apical meristem. Once one module (a root or a shoot) is started, new modules can be formed from it. A unique feature of parenchyma cells is their ability to 'de-differentiate' and resume an embryonic condition, capable of dividing and producing a variety of cell types, even after they have differentiated to become parenchyma cells. Cell types of vascular plants, along with the anatomy of roots, stems and leaves will be discussed in greater detail in the next chapter.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.07%3A_Producing_Form-_Development.txt
As described in Chapter 6 the three organs of vascular plants (roots, stems and leaves) have the same basic structure: a boundary of dermal tissue enclosing ground tissue that has one too many strands of vascular tissue running through it. The three organs differ in the distribution of vascular tissue: in roots it occurs as a single central strand; in stems, the vascular tissue occurs as multiple bundles imbedded in ground tissue; and in leaves the vascular tissue often occurs as a reticulate network of veins or as parallel strands of vascular tissue. In both cases there is ground tissue filling the space between vascular strands and dermal tissue. This basic anatomy is easily seen in asparagus if one trims the base and looks at the cut end, the dermal tissue is the tougher outside, the vascular bundles are seen as small circles scattered in the outer portion of the stem, and ground tissue makes up the rest. Roots and shoots show two polarities, a radial polarity, meaning that tissues and cells differ as one moves outward from the center (along a radius), and a proximate/distal polarity, meaning that cells at the tips of organs, where they are produced, differ from cells away from the tip, cells which are older. Leaves have a tip to base polarity and often have a top/bottom polarity. In this chapter, we describe in more detail the plant anatomy of flowering plants resulting from primary growth (growth derived from root or shoot apical meristems), and consider the developmental changes and consequently the patterns shown with age (distance from the apex). TOPICS • Root development • Mature root anatomy • Shoot development • Mature shoot anatomy • Leaf development • Leaf anatomy Root Development If a root is sectioned along the long axis (i.e., a longitudinal section) its developmental pattern is readily apparent. Near the tip is the meristem, recognized by the small size of cells and by mitotic activity , often evidenced by the appearance of chromosomes. Moving back from the tip (proximally, towards the plant body) one encounters older and more mature cells, recognizable because they are larger, no longer dividing , and possess features that distinguish different cell types, e.g., secondary cell walls of tracheids and vessel tube members. Because there is no more cell division or expansion after one moves a short distance from the root apex , the diameter of the root showing only primary growth is generally constant along its length , except for the terminal few millimeters. (Roots exhibiting secondary growth do increase in diameter and are discussed in the next chapter). Cells that are produced by the root apical meristem expand the most in a distal/proximal direction (up/down, assuming the root is vertical) and produce cells that are elongate in this direction. There is much less expansion radially, hence roots primarily grow longer, not wider and this growth occurs near the root tip. Even more significant than the expansion of individual cells is the fact that most cell divisions in the meristematic zone divide cells in cross-section, so most of the additional cells that the meristem produces are in the longitudinal (distal/proximal) plane. This is similar to how a unicellular filament divides to extend itself, with cell divisions that are perpendicular to the long axis of the filament. Cell divisions in the root apical meristem adds cells in the distal direction and only to a limited extent do roots add cells radially. M ost roots are roughly 20 to 100 cells wide ( a ssuming only primary growth) but roots are often millions or trillions of cells long. Assuming a cell division that adds to the number of cells in the distal/proximal plane, a second key consideration following cell division is whether the cell that remains meristematic (and does not grow) is distal (towards the tip) or proximal (towards the rest of the plant). In the vast majority of cell divisions of root meristematic cells, the cell that remains meristematic is distal, and the expansion of the other cell pushes the meristematic region into the soil. However, in a small portion of cells it is the proximal cell that remains meristematic and the distal cell matures and becomes part of the protective root cap, located at the extreme distal end of the root. The cells of this root cap are continually sloughed off as the root extends through the soil, and the root cap ensures that meristematic cells themselves are not sloughed off. Developmental changes in primary root growth Proceeding proximally from the root tip one encounters the following regions which transition gradually and overlap: • zone of cell division, the embryonic region, often less than one millimeter • zone of cell expansion, generally only a few millimeters in extent, a region where cells are elongating, and to a much lesser extent, getting bigger in diameter;. • zone of cell maturation, a region where cells develop characteristic features. This zone extends from less than a cm to several cm in length. In the youngest part of this zone root hairs are produced but they soon senesce and are lost from the plant Significant aspects of cell maturation zone include (in order from the tip as one moves proximally): • conducting elements of the phloem become functional • the waterproof compound suberin is deposited as a casparian strip • conducting elements of the xylem become functional • root hair appearance and disappearance. Root hairs are extensions off of dermal cells. They are produced after these cells have stopped elongating but are present for only a short time before senescing. Hence, root hairs are only present in a relatively small section of the root. The significance of the casparian strip These hydrophobic deposits initially occur as a band that blocks water movement through the wall from the outside to the inside. Eventually the entire endodermal cell wall is coated. The casparian strip forces water and any minerals dissolved in water to enter the cytosol at some point in their journey between the soil and the xylem tissue. Before the casparian strip is deposited, i.e., in the youngest part of the root, water can move from the soil to the center of the root through the ' apoplast ' , a term that describes the collective space of cell walls and any water filled spaces between cells, which typically includes at least 10% of the tissue volume. Because the endodermal cells are tightly bound to each other, once the casparian strip is deposited water is forced to move through the symplast in order to cross the endodermis and get to the interior of the root. The symplast is a term that describes the collective volume of the cytosols of all cells, collective because all cells are interconnected by plasmodesmata, membrane bordered cytoplasmic threads that run between cells. The casparian strip of the endodermis, once deposited: 1. allows the plant to regulate what minerals do and do not enter the xylem tissue, the conduit to the top of the plant 2. allows the plant to, under certain conditions, concentrate solute concentrations in the root xylem because the apoplast solution inside the endodermis and connected to the xylem tissue is separated by a two membranes (one providing entry into the symplast, one providing exit from the symplast) from the apoplast solution outside the endodermis that is continuous with the soil 3. decreases the ease with which water can move from the soil to the root xylem. Role of root hairs Root hairs appear when of the epidermal cells produce a thin outgrowth, called a root hair, that extends perpendicularly from the root into the soil. The root hair is thin (~ 10 um) but may extend several mm into the soil. As discussed earlier , although root hairs greatly increas e the area available for water and nutrient absorption , their more significant effect might be in increasing the volume of soil within certain distance to the root. Considering root hairs, w ater/nutrients may : • enter the cytosol of the root hair and then proceed inwards through the symplast • enter the cell wall of the root hair and move through the apoplast to the interior of the roo t (note that once the casparian strip is deposited in the endodermal cell walls, this root is blocked • move through the soil to the root proper, by-passing the root hair For moist soils water may move most quickly through the soil rather than using the routes involving the root hairs and it is possible that root hairs may be most significant in nutrient absorption rather than water absorption Mature root anatomy A typical root cross section shows dermal tissue on the outside, surrounding a region of ground tissue (the cortex) which surrounds the endodermis, recognizable because the suberized layer of the cell wall picks up stain. Just inside the endodermis is the pericycle, a ring of parenchyma cells which can be stimulated to form root apical meristems that grow out of the root to form lateral roots. Inside the pericycle is the vascular tissue which is arranged differently in different roots. Some roots have a central pith of parenchyma cells while most roots have a central, solid core of vascular tissue. Shoot Development The basic pattern of development for shoots is the same as that for roots: a terminal region of cell division above a region of cell growth above a region of cell maturation. But shoot growth is more complicated than root growth in several ways, one is the fact that shoot apical meristem not only extends the stem but it also produces embryonic leaves (leaf primordia) and branch shoots (bud primordia) positioned just above the leaves. The presence of these structures divides the stem into nodes, the places where leaves connect with the stem, and internodes, the spaces between nodes. Both of leaf and bud primordia develop vascular tissue that needs to be connected with the vascular tissue of the main stem. If one were to follow the vascular tissue in a leaf or a branch back to the main stem, one would observe one or more bundles of vascular tissue extending from the leaf/branch to the stem. This accounts for the presence of 'vascular bundles' in the stems of flowering plants: fundamentally they represent the traces of vascular tissue running to the leaves and branches. At the nodes one can see vascular traces diverging from the stem to enter leaf and branch primordia. Ferns, horsetails, clubmosses and a number of fossil plant groups have different patterns of vascular tissue distribution within the stem (described as 'stelar structure' ) and, because vascular tissue is often represented in fossils, its distribution has been useful in classifying fossilized vascular plants. Leaf primordia are produced in a characteristic pattern that depends upon the species of plants. The most easily described pattern is one where leaves are produced in pairs on opposite sides of the stem. S equentially, leaves are produced in pair s occur ring with a 90 o rotation from the previous pair of leaves, i.e., if you were viewing a stem from the top and the first pair of leaves were north and south the next set of leaves would be east and west. The next set of leaves produced would be back to the original north-south orientation. Most plants have a more complicated phyllotaxy , i.e., arrangement of leaves, that can be described by counting the number of new leaves and the number of rotations around the stem before you end up with a leaf directly under another leaf. While the elongation of roots, brought about the expansion of newly produced cells, is generally consistent in time and space, occurring soon after cells are produced and very close to the root apical meristem, elongation of stems is not as consistent. Elongation of shoots results from extension of the internodes. In some plants, internode growth occurs close to the shoot tip, resulting in a stem with leaves that separate from each near the tip of the shoot and at a pace consistent with the production of new leaf primordia. In other plants internodal growth is delayed or absent, producing very short stems with multiple leaves very close together (rosettes). Such a structure may be permanent or may be temporary until a particular cue is received and the stem 'bolts' , rapidly elongating by increasing the space between leaves, e.g., in spinach. Some monocots (see below), in particular grasses, have meristematic zones at the nodes of stems and at the base of the blade of the grass leaf. This meristems are activated if the stem or leaf above them is damaged (usually from grazing). In contrast to roots, there is no maturation of cells on the distal side of the shoot apical meristem, i.e., there is no 'shoot cap' (cf. the root cap) derived from the apical meristem. Generally, the shoot apical meristem is not being pushed through the soil so the function that the root cap provides is not generally required. However, the shoot apical meristem is covered by young leaves which grow very close to the tip of the shoot and are able to cover it. Some stems, called rhizomes, do grow through the soil and they are protected by modified leaves called cataphylls that protect the shoot apical meristem and form a pointed structure that can more easily be pushed by growth through the soil. Similar modified leaves, called bud scales, cover the shoot apical meristem of woody plants during the extended periods when they are not growing. While roots often are actively growing much of the year and certainly all of the growing season, shoot growth for plants in seasonal habitats is often much less extensive. Many plants, especially trees, exhibit growth (extension of stems) for only a short period, often less than 30 days. Often cell division occurs much earlier than cell growth, often as much as eight months earlier. Mature shoot anatomy Traditionally, flowering plants were separated into two groups, monocots and dicots, based on a number of features, one of which was stem anatomy. While the monocot group is still considered to be a valid phylogenetic entity, most workers consider 'dicots' to be an artificial grouping, and have separated dicots into 'eudicots' and several other groups. The vast majority of the former dicot group are eudicots and in the discussion below we will use the term dicots. Dicot stems have vascular bundles arranged in a ring close to the margin of the stem. The tissues running from the outside to the inside are: epidermis, cortex, vascular bundles (in a ring), with variable amounts of ground tissue in between the bundles), pith. Monocot stems differ from dicot stems in having vascular bundles scattered throughout the stem. Leaf development Unlike roots and shoots, leaves are determinate structures whose developmental pattern is comparable to humans and frogs. They start as an embryo called a leaf primordium whose cells both divide and subsequently grow for a defined period of time to produce a three-dimensional form that is often substantially more complex than the cylindrical structure of roots and stems. Moreover, the diversity in leaf form found in vascular plants, especially for flowering plants, far exceeds that found in roots or stems. After cellular division and growth cease, the leaf remains in an 'adult' form for a (generally) defined period of time before it undergoes its final developmental process of senescence that ultimately results in the leaf's separation from the plant (abscission). Leaf senescence and abscission will be discussed later but it is important to emphasize here that these developmental processes are highly significant to the life of the plant. Intercalary meristems are present in some leaves, in particular grass leaves, and allow a leaf whose tip (distal portion) has been grazed to resume growth and replace lost photosynthetic area. The ability to grow in this manner has been particularly important to the success of grasses. Leaf structure Many leaves show a polarity between the upper surface and the lower, with the lower epidermis having stomata while the upper surface does not. Additionally, the ground tissue of the upper part of the leaf is layered with cells that are oriented parallel to ea ch other (this region is called the palisade mesophyll) while the mesophyll cells of the lower part of the leaf (called the spongy mesophyll) has cells that are not oriented in a consistent way relative to each other and have much larger air spaces between individual cells. Many monocot leaves have veins that run parallel to each other and this means that if you cross section the leaf you are likely to see cross sections of all the vascular bundles. In most dicot leaves the veins run at various angles and a cross section through the leaf is unlikely to show cross sections through any other bundle except the main central vein.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.08%3A_Vascular_plant_anatomy-_primary_growth.txt
Pr imary growth extends the root/shoot axis and produces branch roots and shoots. Recall that the width of a root or shoot produced by primary growth is limited because most cells do not expand very much in the radial direction. And for most plants cell division in the apical meristem is almost exclusively in a direction that causes more cells in the long axis, with very few divisions that would increase the number of cells across the diameter of the root or shoot. Primary growth allows the plant to get longer and 'bushier' (because of the added branches) but in general it does not allow the roots and shoots to get very wide. This lack of radial growth limits the height of the plant—without thicker stems to resist the combined efforts of wind and gravity, it is hard for a plant to become tall. At the same time, competition for light gives a clear advantage to taller plants. Another problem with only having primary growth is that the source of water (the youngest parts of roots) keeps getting further from the place that needs water, the shoot tips where the leaves are and where new growth occurs. While branch roots, or adventitious roots may be created to shorten the route, the fact still remains that primary growth separates water sources from parts that need water. Additionally, both the conducting cells of the xylem and those of the phloem can fail for a variety of reasons. Because repair of existing cells is often not possible and because primary growth does not allow for the production of replacement conducting cells, the ability to make stems wider, and in particular make them wider with the addition of transport cells and structural support cells, provides some clear advantages, including but not limited to longevity. Radial growth is possible in plants that produce what are known as lateral meristems. These meristems are capable of increasing the girth of roots and shoots beyond what is produced by primary growth. Lateral meristems are cylinders of embryonic cells running the entire length of the root/shoot axis. Cell division in these embryonic regions, followed by expansion of the new cells, allows stems and roots to increase in girth in a type of growth defined as secondary growth. Because any radial expansion will rupture the tissues outside of where the growth occurs, the dermal tissue produced in primary growth is going to be split open and a new 'skin' needs to be produced. Consequently, radial growth in roots and stems requires two lateral meristems, one, the vascular cambium, responsible for most of the increase in girth, and one, the cork cambium, responsible for making a new skin. In contrast to the new cells produced by the apical meristems, the cell divisions of the lateral meristems are generally parallel to the surface of the root or shoot and the new cells expand in a radial (inside/outside) direction, thereby increasing the diameter of the stem or root but not changing its length. TOPICS • Vascular cambium • Secondary xylem and secondary phloem • Rays • Cork cambium • Evolutionary origins of secondary growth • Wide and woody monocots Vascular cambium The vascular cambium produces new vascular tissue and is responsible for most radial expansion of it. In a cross section of a stem or root the vascular cambium exists as a circle of cells, only a few cells in width. In three dimensions the vascular cambium is a cylinder. Developmentally the vascular cambium originates from undifferentiated cells located between the xylem and phloem that were produced by the apical meristem. Recall that the primary growth of stems produces xylem and phloem in bundles that, for all groups other than monocots (which do not exhibit secondary growth), occur in a ring within the stem. To make the vascular cambium a continuous ring requires that cells between the vascular bundles be stimulated to start dividing. The vascular cambium may also develop in roots, again originating from cells located between the xylem and phloem and additional cells to form a continuous ring. Secondary xylem and secondary phloem Cell divisions of the vascular cambium produce xylem and phloem that is called 'secondary' to distinguish it from the primary xylem and phloem produced by the apical meristems. Whether any particular cell produced by the action of the vascular cambium differentiates into secondary phloem or secondary xylem depends on its position, a common factor controlling cellular differentiation. In the simplest case, when a vascular cambium cell divides it produces one cell that remains embryonic (does not expand or differentiate) and one cell that is destined to expand radially and differentiate. If the maturing cell is to the outside of the cell that remains meristematic it is destined to become a phloem cell: a sieve tube member, a parenchyma cell, or a fiber. If the maturing cell is produced to the inside of the cell that remains meristematic it is destined to become a xylem cell: a vessel tube element or a tracheid or a fiber or a parenchyma cell. Most of the new cells produced by the vascular cambium are on the inside thus more secondary xylem is produced than secondary phloem. The vast majority of the cells produced by the vascular cambium are elongate along the long axis of the stem (fibers, sieve tube elements, sieve cells in the phloem; fibers, tracheids, vessel tube members in the xylem). This shape is not the result of the growth of these cells; any elongation of these cells in the up/down direction is impossible: a woody stem cannot elongate in the middle, only from the tip. The elongate shape of these cells is the result of shape of the cell that divided to produced them. The vascular cambium consists primarily of cells, called fusiform initials, that are elongate and which, after dividing, produce daughter cells that are also elongate. These cells only expand in a radial direction, i.e., they get fatter, not longer, producing a stem that is wider, not taller. Rays There are, however, a few cells of the vascular cambium, called ray initials, that are not elongate but are roughly cubical and they produce parenchyma cells that are not elongate in up/down direction but are slightly elongate in a radial direction. The rectangular parenchyma cells produced by ray initials are found in clusters (i.e., a ray initial is likely to have a ray initial above and/or below it in the vascular cambium), and they form structures called rays that run radially from the inside to the outside of the stem. Rays range from one cell in thickness and less than 10 cells in height (i.e., along the longitudinal axis of the root/stem) and invisible with the naked eye, to rays that are hundreds of cells in height and tens of cells in thickness and easily visible with the unaided eye. Rays are produced in both the secondary xylem and secondary phloem and are particularly significant for carbohydrate storage. Carbohydrates transported by the phloem are stored in rays and then can be mobilized when needed. In secondary xylem rays are also significant as being the only living cells present because the other secondary xylem cells (fibers, trachieds and vessel tube elements) all die very shortly after being produced. While the ray cells do not live forever they do live for multiple years, and in addition to carbohydrate storage can respond to pathogens. Finally, when they do die, they produce anti-bacterial/anti-fungal compounds that permeate the surrounding tissues, usually darkening it and producing what is described as heartwood in the central part of a woody stem. The cylinder of secondary xylem still with living parenchyma cells is termed sapwood and it generally is lighter in color. Wood In almost all plants, the xylem cells that are produced by the vascular cambium, termed secondary xylem, have a substantial secondary cell wall containing lignin and are strongly attached to adjacent cells. Thus, this secondary growth is a tissue that is structurally strong and rigid and we know it as wood, a material that is of much utility because of its m echanical characteristics and also its beauty. In many regions of the globe the action of the vascular cambium is seasonal, e.g., only occurring in the spring and early summer. Often the nature of the xylem cells produced by the vascular cambium varies seasonally in a characteristic way. For instance, it is quite common that the cells produced late in the season have smaller lumens and proportionately thicker cell walls than cells produced in the early spring. Another common pattern results from vessel tube elements only being produced in the early spring, so that each spring 's growth is easily identified by the presence of large vessel tube elements. Consequently, there is generally a substantial contrast between the last cells formed at the end of the summer and the first cells formed the following spring. This results in a pattern known as' annual rings 'when wood is viewed in cross section. In a longitudinal section the growth' rings'are present as parallel lines. Periderm As the new cells produced from the vascular cambium expand, the strength of the secondary xylem is enough to prevent it being crushed. Instead, the expansion of new xylem cells pushes outward and crushes most of the cells to the outside of the vascular cambium. Newly produced secondary phloem cells, as long as they are alive, can resist being crushed, as can highly lignified fiber cells which often are present, but most other cells are crushed by the outward expansion caused by growth of the cells produced by the vascular cambium. Additionally, this outward growth, ruptures the epidermis, the original 'skin' of the stem that was produced by the apical meristem. Plants with secondary growth produce an additional lateral meristem, the cork cambium, that produces cells that form a new skin called the periderm. Unlike the vascular cambium, the cork cambium usually is not a continuous cylinder. Instead, it generally exists as a series of arcs that collectively form a ring. Like the vascular cambium, the cork cambium produces different cells to the inside and outside; the cells produced to the outside are short-lived and have cells walls that are impregnated with suberin, a waterproof compound. The cells that are produced to the inside are parenchyma cells and live for a longer time, usually several years. This is significant because the cells of the cork cambium, unlike those of the vascular cambium and apical meristems, are not long-lived; they die within a few years, and a new cork cambium forms to the interior, originating in the parenchyma cells that were formed to the inside of the older cork cambium. In shoots, the initial cork cambium originates within the cortex and subsequent cork cambia originate from derivatives of earlier ones. In roots the cork cambium originates from activity of the pericycle and again reforms inward from parenchyma cells produced by earlier cork cambia. Thus, through time the cork cambium moves inward while the whole stem is growing outward because of the action of the vascular cambium. The cells that the cork cambium produces, as well as the secondary phloem cells, are continually being compressed by expansion from within; these tissues are also being split apart as the trunk's girth increases. In general, the cells produced to the outside by the cork cambium are closely packed and have no cracks or air spaces, as was the case for the original epidermis. But the cork cambium regularly produces areas called lenticels where there are cracks and fissures. It is thought that lenticels are significant in allowing oxygen penetration into the stem. At the same time lenticels provide a space to allow water to escape and pathogens to enter. This again highlights the fact that while some aspects of life are favored by isolation from the outside environment, other aspects of life require connection with the outside environment. In woody stems the material to the inside of the vascular cambium (all of it secondary xylem, ignoring the tiny bit of primary xylem and pith that may remain in the center of the stem) is called wood. All the material outside of the vascular cambium–secondary phloem, the cork cambium and the products of the activity of one-to-many cork cambia, plus tiny bits of primary phloem, cortex and epidermis, are collectively called bark. The look of bark varies tremendously due to differences in behavior of the cork cambium. Evolutionary origins of secondary growth Secondary growth and along with it, woody, tree-like plants has apparently originated multiple times: once in a group containing present day clubmosses, once in a group containing present day horsetails; at least once and probably several times in extinct groups of plants ( 'seed ferns' ) that are not grouped with any of the existing plants with seeds, and once in the group that produced all extant seed plants (flowering plants, conifers, cycads, ginkgo and gnetophytes). Although secondary growth appeared several times, it has also disappeared multiple times: no extant clubmosses or horsetails show secondary growth and many seed plants, in particular many flowering plants, show no secondary growth. The extinct woody forms were highly significant in the past, in particular in the late Paleozoic (350-250 million years ago) when they formed extensive forests whose productivity is utilized still through coal and gas deposits. Wide and woody monocots! If wood is defined as secondary xylem and monocots have no secondary growth then monocots have no wood—but this does not prevent some monocots from being woody, that is possessing lignified tissues. Primary growth often does produce lignified cells, but usually not extensive tissues that are lignified. In most primary growth there are relatively few woody cells, but in some monocots (e.g., bamboo, which is a grass) primary tissues can be quite woody. Also, because monocots lack secondary growth and because primary growth is generally limited in a radial direction, monocots are generally narrow. However, some monocots show prolonged radial expansion in primary growth and consequently can produce stems of substantial girth (e.g., palms, joshua tree).	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.09%3A_Secondary_growth.txt
One of the striking features of plants is their diversity in form. This is nicely demonstrated with a visit to a greenhouse but can also be seen by looking at outdoor plants, both in native habitats and in gardens. At the same time, all seed plants are fundamentally the same in form and follow a pattern depicted in the Figure 1 and described as being 'modular' and 'recursive' . What accounts for the apparent diversity in plant form when they are basically put together the same way? There are six key areas of variation that influence the above-ground form of flowering plants and these are listed below and are main sections of this chapter. While the bulk of the chapter deals with flowering plants the form of non-flowering seed plants and vascular plants without seeds is also discussed. TOPICS • Flowering plants • Factors affecting above ground form • Internode length • Branching frequency • Variation in the size, shape and orientation of leaves • Direction of growth of stems and branches • Presence or lack of secondary growth • Loss of parts (leaves and branches) • Below-ground form • Form of non-flowering seed plants • Form of vascular plants without seeds Factors affecting flowering plant form I: Internode length Do dandelions have stems (Figure 2a)? They must, because they have leaves and leaves are always attached to stems, but dandelion stems certainly are not very evident because they are so very short. You could say that dandelions are 'vertically challenged' and as a result, their leaves are very closely clustered, forming what is known as a rosette. Rosettes are a common plant life form and result from the fact that the distance between individual leaves is extremely short, making it appear that there is no stem. While the leaves of dandelion typically run horizontally, parallel to the ground, some plants, like Amaryllis (Figure 2b) also have very short stems but with leaves that are oriented more vertically. Dandelions live for a number of years and never produce a recognizable stem, although they do produce branches that are flowering stalks. Other plants, including both agricultural crops (e.g., carrots, beets, cabbage, turnip) and common weeds (e.g., mullen, burdock, 'wild' carrot, garlic mustard) are biennials. They form a rosette in their first growth season (Figure 3) and in their second year of growth they 'bolt' as the stem produces much longer internodes to produces a more 'normal-looking' , elongate stem, upon which are born flowers (Figure 4) . A small number of plants, including the one used to make tequila, are a rosette for multiple years, maybe 7-10, before the stem 'bolts.' What determines internode length? Recall that leaves and stem material are produced in the embryonic region called the apical meristem at the very tip of stems. In this region new cells are produced by mitosis and the cells are organized as new stem material and as leaf primordia, outgrowths from the stem that grow and produce the structures that we know of as leaves. In dandelions and other rosette plants, the distance between leaves is very short. As mentioned above, internode length may vary with age, or more specifically vary with environmental factors that coordinate with age, in which case plant form may drastically change with age (see images of mullen, above). Internodes produced in the first season of growth are very short, those in the second season of growth, after the plant has been exposed to a cold period, are a great deal longer. What are the consequences of producing rosettes as opposed to stems with leaves more widely spaced (Figure 5, 6)? One factor is microclimate, rosette leaves, if they are close to the ground, may be in a very different environment that leaves that are elevated. A second factor is self-shading of leaves, although this is influenced by several other factors including the size of the leaves and their distribution. Additionally, plants with short stems and clustered leaves are also more likely to be shaded from above because the stem is not carrying leaves upwards and potentially above the neighboring plants. At the same time, growing upward exposes the plant to a number of problems that are not present if it stays low to the ground. One is mechanical. Growing upward requires stems to be able to resist the combined effects of gravity and wind. Another problem is that an elevated shoot apical meristem becomes more apparent and vulnerable, at least to some herbivores. How significant this is depends on the herbivore—something big, and especially something big with a big nose (think deer!) might have a hard time nipping the tip of a dandelion, but have no difficulty nipping the tip of a tomato plant. However, this is not an issue for smaller herbivores like Japanese beetles. The loss of the terminal apical meristem is particularly damaging because it eliminates the source of growth, although growth may continue by the activation/stimulation of lateral buds. Factors affecting flowering plant form II: Branching frequency Note the images of Diffenbachia and cabbage. Like dandelion, they have no branches. 'Typical' plants with modular growth and a dendritic form have branches and the branches have branches. This repetitive pattern is one of the familiar aspects of plant form that makes them so appealing as an artistic model. However, some plants, like dandelion, have no branches, there is just one axis to the plant, and this gives them, and other plants, a distinct look. Recall that branches result from the fact that as the shoot apical meristem elongates and produces embryonic leaves it also produces a potential branch, called a branch primordium or bud primordium in the 'axil' of each leaf, placed just above where the leaf attaches to the stem. A branch primordium is a replica of the shoot apex, an embryonic shoot capable of elongating and producing a shoot with leaves upon it. All that needs to happen to produce a branch is that the branch primordium be stimulated to start growing. Branch upon branch upon branch can be produced as each shoot in turn produces leaves that have branch shoots appear from their base. This does not happen in dandelion and in many other plants, both rosette and non-rosette. In such plants, growth occurs solely from the original shoot, although many of them will form branches if the original shoot apical meristem is removed. In dandelion, although branch primordia are produced, they are only activated to grow after being transformed into flower primodia (technically inflorescence primordia). Thus, when activated, they produce not a branch but a leafless dandelion 'flower' (technically it is an inflorescence, a cluster of flowers, not a single flower). This type of growth pattern is also seen in Aloe and a number of other rosette plants. Frequently one may see a cluster of dandelion plants together, which might appear like a group of branches. However, these are usually formed when the stem of a dandelion is broken off (usually as the result of someone trying to pull it up). The root that remains is stimulated to form new (adventitious) shoots. Often what happens is that multiple shoots are produced by a single root, forming in a cluster of stems. Each of them originated separately from the root tissue, so what you see is not a cluster of branches but instead a cluster of adventitious shoots. Often branches don't look like branches In grasses, the branches often aren 't recognized as such. They appear at the base of the plant when branch (bud) primordia of the lowest leaves (more details on grass leaves are given below) are stimulated to grow in one of three ways (Figure 7): (1) extending vertically, producing a leafy stem called a tiller (on non-grasses this sometimes called a' sucker 'or a' pup') that is basically the same in structure and function as the original stem; (2) extending horizontally and above-ground, producing only rudimentary leaves with very reduced blades and elongate sheaths. These horizontal stems (branches) are called stolons; (3) extending horizontally but below ground, again producing only rudimentary leaves. These horizontal underground stems (branches) are called rhizomes. Stolons and rhizomes are sometimes considered a means of reproduction; they can also be thought of as providing mobility. Eventually both produce vertical, photosynthetic stems that originate from the bud primordia associated with the rudimentary leaves. A number of plants (e.g., goldenrods, asters) that appear to exist as vertical stems are actually a group of vertical branches all connected to a below-ground stem (rhizome). Factors affecting flowering plant form III: Variation in the size, shape and orientation of leaves In contrast to dandelions, which look like they don 't have a stem when they actually do, grasses (and a number of other plants, including bananas) possess something that looks like a stem but actually isn' t. The 'trunk' of a banana plant is actually a cluster of leaf bases tightly wound (Figure 8) around each other and called a 'pseudostem' because it has the appearance of a stem. Bananas and grasses are monocots, a group that includes orchids and a number of other flowering plants. One feature commonly found in monocots, and specifically in banana and grasses, is a leaf with two main parts (Figure 9) . One part is called the blade; this is typically flattened and extends outward from the plant and is often roughly horizontal to the ground. This is the part that most people recognize as a leaf. If you follow the blade back to the rest of the plant, it abruptly narrows (a great deal in banana, less so in grasses) to a section of the leaf that is vertically oriented and cylindric. This part of the leaf is called the sheath. Early in the growth of both grasses and bananas the structure that looks like a stem is actually just multiple leaf sheaths extending upward from a very short stem, like a dandelion stem. While dandelion leaves are generally horizontally displayed, in grasses the bases of the leaves (i.e., the sheaths) are vertical. The more recently produced leaf sheaths are located inside of older ones and they collectively form a structure that seems like a stem. In grasses and bananas, the stem eventually elongates, the result of very large increase internode length of the youngest leaves. If one were to measure the internode length for a grass for the first 10 leaves it might be (in mm and starting with the first leaf produced): 1, 1, 1, 1, 1, 10, 50, 100, 150, 200. After producing six leaves the stem is 6 mm in height, after producing four more leaves it is 506 mm in height. The stem 'telescopes' upward inside of the sheaths, and often exposes the uppermost nodes, the actual point attachment of leaves to the stem. When the stem of a grass or a banana elongates, it signals the end of the life of that stem and its associated leaves. An inflorescence is produced at the end of the stem, with flowers that develop into fruits. Nutrients are mobilized from the leaves to the developing seeds and fruits. As noted above, many grasses and bananas branch from the base and this may perpetuate the organism even if the original shoot flowers, senesces and dies. Dandelion, grass and banana leaves just scratch the surface of variation in leaf form. Palm leaves may be up to 25 m in length and duckweed leaves are about 3 mm. Most leaves are flat but some are thick (succulent) and may be round and bead like (Figure 11). Leaves can be lobed and toothed in a variety of ways. Many leaves are dissected into parts sometimes in ways that it isn't obvious whether one is looking at a leaf or a leaflet. Factors affecting flowering plant form IV: The direction of growth of stems and branches: vertical, horizontal or something in between Although most familiar plants have a main stem and branches that grow upwards, this is not always the case. Branches may be hidden below ground because they do not grow vertically but instead extend horizontally below the ground. As a result, multiple stems rising from the ground may not be separate plants but actually be branches that extend vertically from a main stem that is running horizontally below ground. While most familiar plants have stems that grow upwards, the exact angles vary and some run horizontally, producing what is known a 'prostrate' growth form seen in partridge berry and strawberry below (Figure 14-15) Some plants (pin oak) have branches that extend roughly 90 degrees from a vertically oriented stem, i.e., they extend horizontally. Other plants have branches that run more vertically, perhaps at an angle of 45 degrees from the main stem. It is also quite common that orientation changes, generally in a controlled manner. In the example of grasses or banana described above the original stem is vertical but 1st order branches may run horizontally (if they are rhizomes or stolons) and third order branches (i.e., branches off of the stolon/rhizome) again run vertically. Thus plants vary in the way that the original stem and its branches are oriented, both within a plant and between different species. Factors affecting flowering plant form V: whether or not the stems and branches exhibit secondary (generally woody) growth Secondary growth allows plants to become wider and taller. While most people associate woodiness with trees, two other plant forms are woody: 'Shrubs' have no rigid definition but are tree-like but show limited growth in height but abundant branching (Figure 16). Most vines (lianas) are woody and have an interesting cellular nature that lacks sclerenchyma fibers and consists almost entirely of water conducting cells with relatively thin secondary walls. This is possible because they utilize the structure of other plants to provide support. Consequently vine wood has a low density and rigidity when compared to tree wood. Factors affecting flowering plant form VI: shedding of plant parts A final factor that impacts the 'look' of plants is the shedding of plant parts. Most plants discard pieces as they grow. Generally, the discarded parts are leaves but branches may also be shed (Figure17-18). Moreover, the loss of parts may be synchronous, as it is with most deciduous trees, but other plants may shed parts continuously. Plant structure is dynamic and parts are not solely being added, they are generally also being removed. These changes are often not noticed, except by gardeners/landscapers, because the changes are relatively slow, the new growth looks just like the old growth and the pieces shed are matched by pieces added. For most plants both the growth and the shedding are usually sporadic, occurring in spurts with inactivity between them. Below-ground form Root systems also have a variety of forms but, obviously, it is harder to see the form of root systems. One distinction that is often cited is the distinction between a taproot system, where the embryonic root (the one formed in the seed) persists and becomes the main trunk of the root system that connects with the stem. Note that a carrot is perhaps not the best example of this, even though it is often used, because in carrot the root is performing a carbohydrate storage function, something that does not have to be the case for plants with taproots. In contrast to taproots, many plants have a root system that forms from adventitious roots that are produced off of stem/rhizome/stolon and do not have a dominant, primary root. Fibrous root systems may only have a few levels of branching whereas taproots typically have more, especially as they age. The primary function of roots is to acquire water and the pattern of water distribution is significant to root system form, specifically lateral spread vs. vertical spread. Alfalfa roots are known to penetrate 15 meters down in order to obtain water. On the other hand, most cactus roots spread extensively but do not penetrate deep in the soil. Cactus also commonly produce roots quickly after a rain and then rapidly loose them (i.e., they senesce and die) as the soil dries. Form of seed plants without flowers There are four groups of seed plants that lack flowers. Representatives of most of these groups are present in the 'Organisms to Know' section and are highly in red. The ginkgophyte group only has a single species, ginkgo , which in form is typical of a deciduous (angiosperm) tree (Figure 19) except that the leaves are unusual, being fan shaped with bifurcating parallel veins. Ginkgo also has 'spur shoots' ( 'short shoots' ), branches with a very short internode distance and consequently leaves clustered very close together. Spur shoots make identification of ginkgo easy during the winter months. A second group are the conifers, including pines, hemlock, redwoods and juniper . Conifer leaves are usually present on the plant for more than a year (i.e., they are evergreen). Many conifers have needle like leaves although some have small, scale-like leaves that overlap each other, producing what are essentially photosynthetic twigs which are shed as a unit after senescence. Most conifers have tree-like forms (Figure 20) with a fairly rigid branching pattern that produces the characteristic 'Christmas tree' shape. There are a few conifers that are shrubs, primarily in the yew-family and some in the cedar family. A third group of non-flowering seed plants are the cycads, most of whom have a distinct form, generally with an unbranched, short stem axis and relatively long pinnately compound leaves (Figure 21). These stem and leaf features are found in two other groups with which cycads may be confused: tree ferns (see below) and palms (a group of flowering plants). Distinguishing between the three groups is easy if reproductive structures are present: palms produce flowers and seeds; cycads have no flowers but produce seeds in a type of cone; and tree ferns produce no seeds but have clusters of spores visible on the leaves). The fourth group of seed plants lacking flowers, the Gnetum group, has only three genera, each with a very distinctive forms Welwitchia (there is only one species and it lives in southern Africa) is by far the most bizarre of the group (Figure 22). It produces only two leaves which grow from the base and grow long and strap-like, often shredding longitudinally so it appears that there are more than two leaves. The apical meristem dies after these two leaves are produced and hence there is no stem. Reproductive structures are produced by the 'crown' at the base of the leaves and plants are either male or female. A second genus in the Gnetophyta groups is Ephedra (roughly 70 species) are highly branched shrubs with photosynthetic stems and small leaves that are soon shed (Figure 23). The final Gnetophyte genus is Gnetum (roughly 40 species) which has species that look the most 'normal' (i.e., like many flowering plants) of the group, with 'normal' leaves (determinate structures with a petiole and a flattened blade) occurring on forms that could be described as small trees, shrubs or vines. Form of vascular plants without seeds We will consider three groups of plants that possess vascular tissue but do not produce seeds. Again, note that representatives of these groups are described in the 'organisms to know' section. The least diverse and easiest to identify are the horsetails ( Equisetum ). There are less than 20 species and all look similar and have a distinctive form (Figure 24-25). They have below-ground rhizomes that produce erect ribbed and 'jointed' stems with whorls of minute, scale-like leaves occurring at the joints. Some species vary from forms with and without whorls of branches, while other species are strictly unbranched or strictly branched. Although relatives in the Paleozoic era, 300 million years ago, had tree-like forms with secondary growth and stems up to 30 m high, all living species show no secondary growth. Most members of the clubmossgroup have a typical plant 'stem with leaves' structure. The stems and roots are vascularized and the leaves have a single vascular trace (vein). Probably because of this, leaves are small and often appressed to the stem, giving the plants a 'moss' look, although the plants and leaves are bigger than almost all mosses. Although representatives of the group used to possess secondary growth and tree-like forms, all forms present now are small, usually less than 20 cm tall, and non-woody (Figure 26-27). Most species have stolons or rhizomes from which vertical branches appear. These may or may not branch. One genus in the group (Isoetes, the quillworts) has a very different form. It is aquatic, unbranched plant with very short internodes, forming rosettes with awl-shaped leaves that may be 10 cm or more in length (Figure28). The fern group is by far the largest group of vascular plants without seeds and it is the group with the most diversity in form, although the majority of ferns seen in north temperate habits are generally uniform in structure with an underground, woody (i.e. showing secondary growth) rhizome from which leaves arise (see sensitive fern, wood fern ). Thus, when you see a fern you are generally seeing a group of leaves (fronds) that originate in a below-ground woody rhizome. Some species have rhizomes that are short and vertical and produce a circular cluster of leaves resulting in an urn-shaped display (Figure 29. Other species have rhizomes that run strictly horizontally and producing a more uniform 'patch' of ferns (Figure 30) the leaves can be more or less dense depending upon the pattern of leaf production along the rhizome. In the tropics there are some ferns that are tree-like with an above ground stem vertically oriented stem that may be 2 m in height and superficially resemble palms and cycads. There also are aquatic ferns that are small and float on the surface of water (Figure 31), comparable to growth of duckweed, which is a flowering plant. A final example of the diversity in fern form is Marsilea, a fern that resembles four-leaf clovers (Figure 32) and has a very interesting pattern of sex. Further reading	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.10%3A_Vascular_Plant_Form.txt
Reproduction is an essential component of organisms—organisms are 'living things' that can replicate themselves, i.e., reproduce. While some other 'living things' (e.g., cells, some organelles) can reproduce, many forms of life cannot (e.g., tissues, organs (usually) , many communities). We have defined organisms as biological entities that are discrete in time , i.e., they have a beginning and ending ; organisms originate as the result of a reproduction event carried out by some already existing organism(s). TOPICS • Reproduction — single celled organisms • Reproduction — multi-cellular organisms • Reproduction and dispersal in space • Sex • Examples from the green, red and brown algae • Chlamydomonas • Oedogonium • Fucus • Saprolegnia • Lamanaria • Ulva • Porphyra • Polysiphonia Reproduction by budding in brewer's yeast. The nucleus spans both parent cell and daughter as chromosomes are being delivered to the daughter cell. The daughter cell has already received a mitochondrion and other cellular organelles. Yeast reproduction can involve sex but rarely does. Reproduction —single celled organisms For single celled organisms, reproduction is a familiar and conceptually simple process (although the cellular details are far from simple!)–cell division. The original cell is partitioned by the synthesis and deposition ofa new boundary (Figure 1). For all cells, the boundary includes two plasma membranes (one for each cell) and for organisms with a cell wall the new boundary also has wall material between the two membranes. Note that for cell division to be a means of reproduction the daughter cell needs to detach from its parent celleither immediately following cell division or at some point in the future. Otherwise the new cell is simply increasing the size of the existing organism. The original cell need not be divided equally , but both cells must be provisioned with whatever is required for the cell to maintain itself , in particular it needs genetic information in the form of DNA. Consequently, before the cell divides it needs to replicate its DNA and give each daughter cell a copy. For eukaryotic organisms , the DNA is packaged in units, chromosomes, that replicate before division, with one copy going to each daughter cell , i.e. the process of mitosis. Also present in eukaryotic cells are organelles (e.g. mitochondria) that need to replicate before cell division with at least one ending up in each daughter cell. For photosynthetic organisms the same would be true for plastids that develop into chloroplasts. Remember that most biologists consider mitochondria and plastids to be remnants of unicellular organism s and their ability to divide is support for this idea. Reproduction has to involve growth at some point but, as discussed in Chapter 7, growthmight come after cell division (a cell is cut in half and then each half grows to full size) or before (a cell grows to twice its normal size and divides); ultimately reproduction requires that the organism acquire material, but this does notneed tobe a direct part of reproduction. Although basically simple in outline, cell division, and the reproduction that it brings about in unicellular organisms, involves a myriad of details, some of which are unique to particular groups and are used to unite (classify) organisms. Reproduction—multi-cellular organisms Reproduction in multicellular organisms involves another level of complexity because it requires the coordinated production of multiple cell types positioned in time and space in ways that achieve a functional organism(i.e., a developmental process). The information to direct this development is present in the DNA, and since all cells possess the same DNA, all cells of an organism potentially could develop into a multicellular organism.However, most cells are unable to express the required information and thus are NOT able to proliferate and grow into a new organism. The developmental potential that can transform a single cell into a multicellular organism generally only finds expression under very limited circumstances. For most familiar organisms (mammals) this potential is only revealed in a single cell, the zygote(defined and discussed below). In these organisms, in spite of the fact that all cells have the same genetic information, only the zygote uses it to develop into a new organismas it undergoes embryogenesis and transforms into an embryo. However, in many of the organisms studied in this coursethisdevelopmental potential is encounteredmore frequently, and cells that aren't zygotes can develop intonew multicellular organisms in a process described as somatic embryogenesis. This may occur spontaneously or may be induced to occur. Bryophyllum, or mother plant (Figure 2), nicely illustrates this. On the margins of its leaves new plants develop. This is possible because certain leaf cells behave like a zygote, using their potential to develop into a new organism (at least they will be new organisms when they detach from the parent plant). Another plant exhibiting the same ability is bulb-bearing fern (Figure 3) which also produces structures on its leaves that detach and grow into new plants. New multicellular organisms do not necessarily have to originate from the proliferation of a single cell. Reproduction can be achieved by the cleaving of an existing organism into two or more parts, as long as the resultant pieces of an organism are capable of regenerating the missing parts, or if the organism is so simple that it doesn 't have parts, e.g., a filamentous algae or a fungus. Such a pattern of reproduction is very common for many of the organisms covered in this book. Since a new organism can be produced by breaking a piece off an existing organism, a means of enhancing reproduction would be to have pieces that easily break off. This happens in Bryophyllum and in bulb-bearing ferns and in many other organisms as well. Both mosses and liverworts commonly produce' splash cups', cup shaped organs (Figure 4) that have at their bottom clusters of cells packaged intodisk-shapedgemmae (singular gemma) that are easily dislodged and can be thrown out of the cup by a water droplet whose force isfocused by the shape of the cup. Further Readings Reproduction and dispersal in space The phenomenon of splash cups points out that reproduction isn 't just about making new organisms, it is also about moving organisms around, i.e., dispersal. For many of the organisms dispersal may be the most significant aspect of reproduction, far more important than the making of a new individual. For familiar (determinate) organisms like mammals, reproduction is the only way to be perpetuated through time. In contrast, organisms that are indeterminate can potentially live forever, so continuation through time maynot be a significant consequence of reproduction, butdispersal often is. Environments are dynamic both in their physical conditions and their biotic conditions, thus the fact that an organism can survive at a particular time in a particular place does not ensure that it will be able to do so in the future. Particularly for the organisms covered in this class, most of whom are immobile, it is often the case that reproduction is less about making new individuals and more about getting to new areas.' Pando', the clone of aspengrowing in Utah, apparently has perpetuated itself for 80, 000 years just by growing. Although in the past 80, 000 years it has spread to new areas, it is not moving around very quickly. And, significantly, it is growing in an area where seedling establishment is impossible (i.e., conditions are less hospitable now than they used to be). Getting to new areas involves the production of propagules, a unit that not only makes new organisms (reproduction), it also can put them in a new place. A fungus that produces a million spores may seem impressive but the consequences in its immediate area may be trivial. Similarly, a pine tree that produces thousands of seeds may be doing nothing to its functional population size at that site and at that time; the more significant effect of producing propagules is enhancing the possibility of establishing a population at some distant site or this site at some time in the future. Common propagules are spores and seeds but certainly the 'bulbs' of bulb-bearing ferns and the gemmae of mosses and liverworts should be considered propagules as well. Probably the most significant feature that most propagules possess that enhances their dispersal ability is the fact that they are generally inactive, 'dormant' . A general feature of cells and organisms is that the less active they are the less sensitive they are to a variety of 'insults' , in particular desiccation and adverse temperatures. Cells and tissues that are in an inactive state, e.g., most spores, seeds, tree buds in the winter, can withstand conditions that active tissues cannot. The changes that accompany inactivity include changes in membrane and protein structure. An indicator of inactivity is a low metabolic (respiratory) rate associated with a general lack of any cellular activity such as protein synthesis or cytoplasmic streaming. Because of their inactivity, many spores can survive prolonged periods without the basic requirements that most organism require: moisture, matter and energy availability, temperatures within a particular range. This aids in dispersal simply because the propagule can travel longer distances while still being viable. Becoming dormant is a physiological process that may be triggered by specific environmental conditions or may simply be an aspect of a developmental pattern, e.g., a cell is programmed to become inactive soon after being created. What triggers the resumption of activity in a propagule varies from the return to 'favorable conditions' , e.g., warmth and moisture, to more specific environmental cues, e.g., photoperiod. Some of these are discussed in Chapter 16. The two common propagules found in the organisms covered here are spores and seeds. Seeds are only found in some plants and will be discussed in depth later. For now, simply appreciate that seeds function both in dispersal and reproduction. Spores are found in almost all of the organisms covered here (Bacteria, Archaea, Fungi, most protists, all plants (including those that have seeds). Their function varies considerably, from being a structure primarily associated with perpetuation in time (endospores of bacteria, akinites of cyanobacteria, zygospores of bread molds) to functioning primarily for reproduction (zoospores of water molds and Oedegonium) or primarily for sex (considered later in this chapter and in Chapter 14). Many organisms produce multiple types of spores which may differ in their structure and function, e.g., degree of dormancy, specific requirements required for resumption of growth (see bread molds, Oedogonium ). A common type of spore is called a zoospore, a flagellated spore found in many of the green algae, most of the water molds , many brown algae , and many of the chytrids (the only fungi that possess flagellated cells). Zoospores reflect the costs and benefits tied to mobility: their flagella provide them with the mobility that unflagellated cells lack, but flagella require metabolic activity and consequently zoospores have limited lifespans and this limits their mobility and dispersal ability. Another trade-off relates to size. Spores are single cells and generally very small. This enhances mobility by allowing for dispersal by wind. However, any spore benefits by storing material that will be utilized in establishing the new growth following spore germination. The more material saved the heavier the spore is and the more limited its dispersal. These same considerations are significant to seeds, which are multicellular propagules considered in a Chapter 14. Although r eproduction is obviously of significance to the organism(s) that are produced, o ne final general point about reproduction concerns its impact on the 'parent' organism. Because reproduction utilizes material and energy that might otherwise be used to perpetuate the life of the parent organism, r eproduction generally diminishes the likelihood that the parent will be perpetuated through time. The magnitude of this detrimental effect varies from highly significant, when reproduction insures the death of the parent (salmon, wheat plants) to extremely trivial, when reproduction has virtually no effect on the survival of the parent. Because of this impact on the reproducing organisms, reproductive effort is evolutionarily modified and often controlled by specific environmental cues (Chapter 16). Besides the impact at the individual level , reproduction also has potential consequences a t the population/species level , increasing the population size and perpetuating the species through time. Th is effect is strongly dependent upon on other conditions. Sex Most students equate sex and reproduction, but they really are two separate processes that happen to be combined in the organisms that we are most familiar with. Reproduction is about making new organisms; sex is about mixing the genetic information of two organisms. Bacteria and Archaea exchange genetic information by several different processes (conjugation, transformation, transduction) but none of these are considered to be sex. Sex is defined as a particular type of genetic exchange that can only happen in organisms with chromosomes (eukaryotic organisms). Sex requires the fusion of two cells (syngamy), producing a cell with twice the number of chromosomes as either of the parent cells. Generally, both of the fusing cells have one copy of each chromosome and are described as being haploid, while the fused cell has two copies of each chromosome and is described as being diploid. Sex also requires a mechanism that can produce haploid cells from diploid cells. This process is meiosis, unfortunately often described as a 'type of cell division, ' but is more aptly described as a process involving two cell divisions that produces haploid cells from diploid cells. Keep in mind that the haploid cells that are produced don 't simply separate the chromosomes of a diploid cell into two groups, the two groupst each have one copy of each ' type of chromosome '. Consider Arabidopsis (' Mouse-ear cress'), the most studied plant in the world. If one looks at the chromosomes of a diploid cell, one sees ten chromosomes. But closer examination of the chromosomes reveals that there are actually five distinct types of chromosomes present, and their are two chromosomes of each type. (A chromosome can be recognized by its size and shape. And genetic analysis reveals that they are also distinct in the genes that they possess.) In Arabidopsis, meiosis produces cells with five chromosomes not ten, moreover, it produces cells that have one of each type of chromosome, i.e., a complete set. Sex is a process that allows genetic material (genes) from two different organisms to be mixed. It almost always involves producing new individuals (reproduction). However, the unicellular organism Paramecium demonstrates that sex can happen with no reproduction: two cells, each with a diploid nucleus join temporarily. The diploid nucleus of each cell undergoes meiosis to form four haploid nuclei, three of these disintegrate and the remaining one divides mitotically to produce two haploid nuclei in each of the joined cells. Each cell sends one of these two nuclei to the other cell so that both cells have two nuclei, its 'original' one and one that came from its partner. Finally, in each cell, the two nuclei fuse to form a diploid nucleus, the original condition. Thus, the cells have undergone the sexual cycle but have not reproduced: there were two cells at the beginning and there are two cells at the end. Although sex and reproduction are different process, they often (especially in familiar organisms) occur simultaneously. Specifically, sex requires: • Fusion of two cells and the subsequent fusion of the two nuclei in a process called syngamy, combining the genetic information of each. A ssuming that the original cells had one copy of each gene (i.e., the cells were haploid), the product of fusion will have two copies of each gene, i.e., will be diploid. Only special cells have the ability to fuse with one another and these cells are called gametes . • A process (meiosis) that starts with a diploid cell and produces haploid cells, each with one copy of each chromosome. This process is feasible in eukaryotes because they have genes that are packaged into structures (chromosomes) that can be sorted and moved. Describing a cell as 'having two copies of each gene' is the same as saying that the cell has 'two copies of each chromosome' ( in fact it is more accurate since it is commonly the case that genes often get replicated, i.e. a haploid cell commonly has multiple copies of a gene, sometimes all copies are on one chromosom e, other times it has copies of a gene on several chromosomes.) Most students consider sex to be related to the fusion process, but it is important to appreciate that meiosis is also an essential part. The essential components of s ex (syngamy and meiosis) are sometimes distantly separated in time and may be separated between organisms. We will study a number of situations where two types of organisms are produced, both associated with the same species; one organism develops from a diploid cell (zygote) produced by syngamy and is diploid; the other results from a haploid cell (spore) and is haploid. However, there are other organisms where the cell created by syngamy immediately undergoes meiosis , i.e., both steps of sex, syngamy and meiosis, occur in the same cell. As we will see there are lots of variations on the basic sexual cycle. Sex is not universal. Many organisms, including some very successful groups ( Archaea and Bacteria , the endomycorhizal forming Glomeromycota, most dinoflagellates, many fungi) have no sexual process. While sex is generally considered to be significant to the process of evolution because it promotes the variation that natural selection can act upon, it is important to realize that variation and evolution can occur without sex and that the success of a group of organisms at one point in time , and through time , is possible even if that group has no sex. For multicellular or colonial organisms, reproduction, unless occurring by fragmentation of an already existing colony/organism, requires a cell that will proliferate and form the colony/organism. In the familiar case of humans, that cell is the zygote. But in many organisms it is a haploid product of meiosis, generally called a spore, that has the developmental potential to proliferate and form a multicellular organism. And for all plants and many of the macroalgae, multicellular/colony development can proceed both from a zygote and from a haploid spore produced by meiosis. Such organisms will alternate between a haploid stage derived from the spore and a diploid stage derived from the zygote. The rest of this chapter will illustrate several examples of sex and reproduction, showing a diversity of patterns from several different groups. It is important to realize that for many of the larger groups (generally phyla) that we study, in particular for the macroalgae (green, red and brown algae), sex and reproduction are NOT consistent across the group, i.e. there is no single, standard pattern of sex and reproduction. In separate chapters we will consider groups that do show some consistency: with several of the fungal phyla (Chapter 12), with non-seed plants (Chapter 13), with seed plants (Chapters 14 and 15). Chlamydomonas Chlamydomonas is a unicellular green alga that primarily reproduces asexually (left side of diagram below), i.e, . most new cells are not the product of a sexual process. On the right side of the diagram is shown the sexual process which is trivial in terms of reproductive effort but significant for the variation that it creates and also because the thick-walled 'zygospore' (so named because it develops from a zygote) is able to withstand hostile conditions (dispersal in time). The sexual process is 'triggered' by conditions that make normally asexual cells behave like gametes, with the ability to fuse with other cells. The only diploid cell is the zygospore. Oedogonium Oedogonium, a filamentous green algae, shows the same basic patter as Chlamydomonas except that: (1) it is colonial, not unicellular, (2) in the sexual cycle the gametes do not look alike but are structurally very different with one (called the egg) being large and immobile and the other (called sperm) being much smaller and mobile. Sperm are released from the colonial filament to swim to and join with the egg (syngamy). Both the egg cell and cell producing sperm need to develop a hole in the cell wall in order for the sperm to escape and enter the egg cell. The zygote develops into a zygospore that is released from the filament and eventually undergoes meiosis and releases flagellated zoospores that, like the asexual zoospores, are capable of attaching to a substrate and developing into a filament, i.e., the cell that initiates a colonial organism is not a diploid zygote, rather it is haploid zoospore. Fucus Fucus is a multicellular brown algae with a life cycle comparable to humans (Figure 7-9). The organism is diploid and the only haploid cells are gametes, which come in two varieties: a large, unflagellated egg and a small, flagellated sperm. Unlike in humans, gametes are released to the environment and syngamy occurs there. The zygote is formed outside of a parental gamete-forming organism. The zygote develops into a new diploid organism, which, unlike humans, generally can produce both male and female gametes. Note that in contrast to the two previous examples the zygote divides mitotically and does not undergo meiosis, hence there is a diploid organism, not simply a single diploid cell.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.11%3A_Reproduction_and_sex.txt
The 'vegetative' (i.e., not associated with sex and reproduction) structure of most fungi are generally very consistent: they are composed of branched filaments that explore the volume of material that they feed on(be it living or dead) and this structure provides for acquisition of materials that they need to grow and survive. The consistency of vegetative form makes it difficult to classify fungibecause they mostly look alike, although some vary on the basis of whether or not the filaments on coenocytic or septate (with cross walls and therefore cellular). However, fungi do show variation, and can be grouped, based upon structures that are associated with sexual reproduction. The exceptions to this are the two groups where sex is either completely absent (Glomeromycota—the endomycorhizal forming fungi) or rare (Chytridomycota—the chytrids). The remaining three groups (bread molds = Zygomycota, cup fungi = Ascomycota, and club fungi = Basidiomycota usually exhibit specific features associated with sexual reproduction that are used define thesegroups (generally considered phyla). Fungi that show no sexual features used to be put into a group called the 'Fungi Imperfecti' (Deuteromycota), but molecular techniques now allow these fungi to be placed in one of the groups mentioned above. Fungi have the following features associated with sex and reproduction that are different from most familiar sexual organisms: • R eproduction often involves both sexual aspects and asexual aspects. Cells called spores — defined as cells with both dispersal capabilities (i.e., mobile cells) and reproductive capabilities (i.e., cells that can grow into new fungal organisms) are often important in both asexual and sexual reproduction. • Gametes(cells that can fuse with other gametes) are quite different from what most wouldconsider 'typical' ; they are usually hyphal cells (part of the fungal filaments) that have the ability to fuse with other hyphae. Depending upon the group, these special hyphae may or may not have structural features that would distinguish themfrom the normal hyphae. • Syngamyoften involves two steps separated in time and often in space. This is a consequence of the fact that the fusion of the hyphae serving as gametes is generally not followed immediately by the fusion of nuclei. Cellular fusion is called plasmogamy and nuclear fusion is called karyogamy. Plasmogamy followed by a delayed karyogamy allows fungi to have a novel condition, the dikaryon state, wherea cell hastwo nuclei ( 'dikaryon' means 'two nuclei' ), one from each parent. This condition is often perpetuated: the dikaryon cell divides while both nuclei divide, thereby forming a new cell that is also dikaryon. This process can continue, producing multiple dikaryon cells and dikaryon hyphae. Note that although a dikaryon cell has two copies of each chromosome, it is not considered diploid because each nucleus is haploid, with only one copy of each chromosome. • At some point, some of the dikaryon cells become diploid as a result of the fusion of the two nuclei(karyogamy).The diploid cells are NOTperpetuated; they undergo meiosis to form haploid nucleiwhich develop walls to become haploid cells. Thus, the diploid state is very brief in extent(i.e., size and number of cells) and often brief in time as well—the diploid cells neverdivide mitotically to form more diploid cells, they only divide meiotically to form haploid cells. These haploid cells are, or soon become, spores and aredispersed from the parent fungus to a new location where they germinate and form haploid hyphae. • 'Mating strains' are a common mechanism thatensures that fungi do not mate with themselves. Within a particular species there are two to many mating types. A particular mating type needs to find a different mating type in order to interact sexually (i.e., fuse hyphae). The simplest situation has two mating types: “+” and “-” and they need to find each other to mate, but there may bemore than just two types, e.g., types A, B, C, D, E, and A could mate with any of the othersbut not with another A. Generally, the interaction, or lack of it, involves chemical signals (pheromones)that are emitted by one mating type and sensed only by fungi of a different mating type. In response to the pheromone, hyphae grow and find each other, bringing about plasmogamy. TOPICS • Zygomycetes (bread molds) • Ascomycetes (cup fungi) • Basidiomycetes (club fungi) Zygomycetes , the bread molds In the zygomycetes (Figure 2-3), most reproduction is asexual and results from the production of a stalked structure (sporangiophore) terminated with spherical sporangium. Inside the sporangium is the only cellular tissue produced by the group, meaning it is a structure where individual nuclei are packaged one to a cell. These cells mature into spores that are dispersed when the sporangium disintegrates. Much less frequent is reproduction associated with a sexual process and a specific structure, the zygospore, from which the group gets its name. The process is initiated when two compatible hyphae sense each other's presence because of pheromones. This triggers hyphae grow towards each other and the production of specialized hyphal branches that are capable of fusing with each other. Since bread molds are coenocytic, the fusion of two hyphae (plasmogamy) allows multiple nuclei to come into proximity (Fig 4). Unusual for the group, two cross walls, one in each of the fusing hyphae, form near the point of fusion, creating a single coenocytic cell with nuclei derived from each of the two mating strains (Figure 5-6). This is the only dikaryon cell produced by the bread molds and it develops into a structure called a zygospore (Figure 7-8) by enlarging slightly and developing a thick wall. Inside the zygospore haploid nuclei of one type pair withnuclei of the other type and fuse (karyogamy) to form diploid nuclei, transforming the cell from being dikaryon to being diploid, but it is still multinucleate. The zygospore is generally dormant and generally has more specific germination requirements and a longer lifespan than the asexual spores. When the zygospore germinates it produces a sporangiophore comparable to those produced asexually with a sporangium at its tip. As this develops the diploidnuclei undergo meiosisand the haploid nucleiare individually packaged into spores as cell walls are produced. The spores are subsequently dispersed, and when they germinate they produce haploid, coenocytic hyphae. Note that the dikaryon state is limited to a single cell and has a very brief existence. Ascomycota — the cup fungi Unlike the bread molds, the cup fungi (Ascomycetes), are septate, i.e., they have cross walls and the 'feeding hyphae' , the ones that acquire nutrients, are constructed of cells that have a single haploid nucleus. Many members of the group, reproduction is primarily to exclusively asexual a consequence of the production of specialized hyphal branches that produce small cells (conidia) that are easily broken off to serve as propagules. Generally, these cells are dormant and have other cellular features, e.g., stored food, that promote their role in reproduction and dispersal. When and if sexual reproduction occurs, it is initiated when compatible mating strains are close to each other and communicate by pheromones. Inflated hyphal branches are produced, one on each strain, producing cells that are slightly different in form and are multinucleate. When they are close to each other one of the cells produces an extension that touches the expanded cell of the other mating type and fuses with it (plasmogamy occurs) and haploid nuclei move from one of the structures, termed the antheridium and considered male, to the other one, called an ascogoniumand considered female. As a result of the migration of nuclei, the archegonium cell becomes dikaryon, with two types of nuclei, one from each parent. The ascogonium develops extensions and two nuclei (one from each mating type) associate and migrate into them. A cross wall is formed, producing the first cell of what is described as an ascogenous hypha. These hyphae grow from the tip and remain dikaryon, with two haploid nuclei per cell, a result of a coordination of tip expansion, two nuclear divisions (one for each nucleus), nucleus migration, and septum formation. Growth of the ascogneous hyphae plus growth of both (haploid) parental hyphae produce a fruiting body of densely intertwined hyphae. The size of the fruiting body ranges tremendously in size, from roughly 100 um to 10 cm or more, with most at the smaller end. The size and shape vary and can be used to identify species. The common name for the group ( 'cup fungi' ) relates to a cup shaped fruiting body. Cup fungi are found both living independently and also as the fungal partner of a number of lichens; many lichens produce ascocarps (Figure 10) that are relatively large and visible to the naked eye. Other fruiting bodies are flask-shaped or completely closed and typically are less than a mm in extent. In a specific part of this fruiting body the sexual cycle is completed. The tips of the ascogenous hyphae form a hook, turning back on itself and the two nuclei fuse (karyogamy occurs) in the cell that has formed the hook (crozier), making it (briefly) a diploid cell. The only diploid cells found in the Ascomycota are these specific cells, eventually called asci (singular = ascus) situated at the ends of the ascogenous hyphae (these hyphae produce no additional cells after forming the hook). The diploid cell then elongates and undergoes meiosis to form an elongate cell with four haploid nuclei. Each of these then go through mitosis to produce an elongate cell called an ascus with eight haploid nuclei in a row. Each nucleus acquires a cell wall and develop into what is called an ascospore. Asci with eight ascospores are diagnostic for the Ascomycota. Hydrostatic pressure within the ascus causes ascospores to be forcibly dispersed when the tip of the ascus ruptures. Dispersed ascospores germinate to form haploid hyphae, which form haploid mycelia which may reproduce asexually via conidia or other spores. If a haploid mycelium comes in contact with hyphae of a different mating type, sexual reproduction may be triggered. Basidiomycetes —club fungi The club fungi are septate like the cup fungi (Ascomycota). Of all the fungal groupsthe club fungi have the most extensive dikaryon state. As is the case for almost all fungi, the dikaryon state is initiated when two compatible haploid, monokaryon hyphae find each other as a result of chemical attraction. Plasmogamy occurs, forming a dikaryon cell. This cell divides and grows extensively, forming a feeding mycelium that is dikaryon. Many of the basidiomycota produce 'clamp connections' (Figure 17) that may help to maintain the dikaryon state as the hyphae elongate. The nuclei undergo mitosis, and cross walls formed. As the terminal cell elongates an arch is formed between the terminal cell and itsparental cell. When the two nuclei divide the arch allows one of the two nuclei to move to the parental cell as septa form. This ensures that both the daughter cell andmother cell hasone of each type of nucleus. Recallthat that there is only a single dikaryon cell in the bread molds (Zygomycota)and the only dikaryon cellsof the the cup fungi (Ascomycota) are foundin the fruiting bodies. Thus, if one encounters a dikaryotic hyphae outsideof a fruiting body then it must belong toa club fungus (Basidiomycota). The dikaryotic hyphae of club fungi grow and feed extensively until appropriate conditions are encountered to trigger 'fruiting' . At this point the growth pattern of at least some of the hyphae changesfrom one where their substrate is explored for nutrition to onewhere hyphae intertwine with each other, forming the dense mass of hyphae that will becomefruiting body. Often the fruiting body emerges from the substrate that the fungus is feeding on, e.g., a mushroom emerging from the soil or from the trunk of a tree. Somewhere on or inthe dense mass of hyphae special cells are produced, termed basidia, that are 'club-shaped' (Figure 18). Inside these cells karyogamy occurs, transforming them intodiploid cells. The diploid nucleus undergoes meiosis to produce four haploid nuclei, but no cytokinesis occurs, making the basidium 'quadra-nucleate' . Four extensions grow out of the basidiumand the four nuclei migrate into these. This is followed by cell wall formation to produce a basidium with no nucleus but with four loosely attachedhaploid cells, called basidiospores, extending off from them. The spores are ballistically released and are dispersed by the wind. When they germinate they form new haploid hyphae. Unlike the cup fungi, whose fruiting bodies are generally small and not typically noticed, the fruiting bodies of many club fungi are often relatively large, 10-30 cm and have characteristic shapes that we describe as mushrooms (with a stalk and a cap) (Figure 19-20) or bracket fungi (roughly hoof shaped and attached without a stalk to the trunks of woody plants). Two very common patterns of basidia distributionare (1) extendingfromthin finsof tissue termed 'gills' , typical of the commercially available mushroom, or (2) basidia extending fromtubes (cylinders) of tissue which, when viewed at the surface, appear as numerous pores. Two large groups of Basidiomycetes, the smuts (Figure 22-23) (Class Ustomycetes) and the rusts (Figure 24-25) (class Teliomycetes) have slightly different and sometimes involved patterns of sex and reproduction associated with their obligate parasitic lifestyle. Many of these organisms are very important economically because they can drastically reduce yields of important crops. Neither form 'fruiting bodies' , made solely of fungal material, but rather cause abnormal growth (galls) on the plant that they are growing in. These galls are composed of infected plant cells, uninfected plants cells growing abnormally because of the parasite, and some fungal hyphae interconnecting infected cells. While the typical basidiomycete described above has a single type of spore, the haploid basidiospores formed in the fruiting body, both rusts and smuts commonly produce teliospores, one to several celled spores, that contain dikaryotic cells. When teliospores germinate karyogamy occurs, followed by meiosis, producing a basidium with haploid nucleithat producehaploidbasidiospores. While most smuts only produce these two types of spores, rusts may have two or three more types of spores and a complicated life cycle that sometimes involves two hosts. The life cycle of wheat rust is shown in Figure 26 and discussed in Chapter 30. Basidiospores infect host #1 (barberry) and form structure called pycnia on the upper surface of the leaf. Pycnia produce two structures that bring about syngamy. One of these are haploid spores called pyncospores (or spermatia) that might be considered gametes. Pycnospores are released as single cells into a sweet 'nectar' that attracts insects who can transport them to other compatible (i.e., different mating type) pycnia where they can fuse (plasmogamy) with the second structure produced by pycnia involved in syngamy: 'flexuous hyphae' that extend out of the pycnia. Fusion of the pyncospore with the haploid cells of these hyphae brings about syngamy and forms the initial cell of a dikaryon hyphae that grows to the bottom of the leaf, forms a ball and releases dikaryon spores (aeciospores) that infect host #2 (wheat), causing it to form another type of dikaryon spore, uridinospores, that can infect more wheat plants. Late in the season the final type of spore, the teliospore, forms on wheat. Karyogamy and meiosis occur in teliospores and from them promycelia (basically basidia) emerges and produce basidiospores.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.12%3A_Fungal_sex_and_fungal_groups.txt
Almost all plants are capable of reproduction without sex. Most commonly this happens as a consequence of the plant being severed into pieces and these pieces being able to regenerate the parts that were lost. Additionally, some species have developed pieces that are particularly prone to be broken off, e.g., the gemmae (singular of gemma) of some mosses and liverworts. It is relatively common for flowering plants to produce asexual propagules in the places where seeds normally develop, producing seed-like structures without the normal process of sex. Although reproduction without sex is common in plants and for some species it represents their sole means of reproduction, most plants rely on sexual reproduction, and two innovations, the seed and the flower, have been particularly significant to the evolution of plants. With respect to sex, the plant kingdom illustrates wonderful patterns of unity and diversification. On the one hand, all plant life shows a fundamentally similar pattern of sex, on the other hand, plants illustrate remarkable diversification of this common theme. TOPICS • Alternation of generations • Mosses, liverworts and hornworts • Ferns • Horsetails • Clubmosses All plants exhibit alternation of generation s , they produce two types of multicellular organisms: one diploid and derived from the development of a zygote, and one haploid and derived from the development of a haploid cell called a spore. 'Development' involves the proliferation of cells, the differentiation of cells and the formation specific structures with specific roles, i.e.. morphogenesis. All plants exhibit alternation of generations and alternate between haploid and diploid organisms. To complete the sexual cycle the haploid organism must produce gametes that unite to form the zygote. That is, among all the haploid cells that are produced as a result of cell divisions of a haploid spore, some of the cells are endowed with special capabilities that allow them to encounter and interact with another gamete to form a zygote. Similarly, of all the diploid cells derived from the zygote, some, called a 'spore mother cells' , are endowed with the ability to undergo meiosis to produce haploid cells, spores, that grow into haploid individuals.. Note thatmeiosisdoes NOT produce gametes, rather it produces spores that are dispersed and develop into haploid plants. The diploid plant that produces spore mother cells and spores is called a 'sporophyte' . The gamete-producing organism, which is haploid, is called a gametophyte. Thus, there is an 'alternation of generations' with a haploid form alternating with a diploid form (Figure 1). Often one of the two forms is challenging to appreciate, largely because they are often challenging to see— they are often small, short-lived, and may not live a separate existence from the previous generation. That is, the haploid and diploid forms maynot spatially distinct from each other; they may be temporarily, orpermanently, a part of their parent! Like those of familiar animals, the gametes of all plants are of two types, a larger, immobile egg and a smaller sperm that must in some way bemobile in order to encounter the egg. The gametophytes of plants may be bisexual (hermaphrodites), producing both egg and sperm, or unisexual, i.e., there are separate male and female gametophytes. In some plant groups, including all of those discussed in this chapter, the sperm is mobile because they possess flagella. Sperm swim away fromthe male gametophyte that produced it and are chemically attracted to the structure producing eggs. Because plants are terrestrial organisms, the water required for a flagellated sperm to swim to the egg is not always present. We will see in the next chapter that some plants have circumvented this problem by having male gametophytes become mobile, not the sperm they produce. As in animals, the female gamete, the egg, does not move. Itis retained in the organism that produces it. In the case of plants this is a haploid gametophyte(not a diploid individualas in mammals). And in some of the plants discussed in this chapter the zygote formed by the fertilization of an egg grows out of the archegonium (the structure in which an egg is produced) and after fertilization produces a sporophyte attached to the gametophyte. Alternatively, the entire (female) gametophyte of some plant groups is embedded inthediploid plant (the sporophyte) that produced the spore that developed into the female gametophyte. That is, in some plant groups, the spores produced by sporophytes are not dispersed, instead the spore germinates where it is produced and grows to produce a gametophyte plant on or inside a sporophyte plant. Mobile male gametophytes and sedentary female gametophytes are features of a few plants discussed in this chapter but are much more significantly developed in seed plants, discussed in the next chapter. In this chapter we consider the more readily observable and understandable alternation of generations that is found in plants without seeds. Mosses Liverworts and Hornworts In mosses, liverwortsand hornworts (the three groups of plants lacking vascular tissue)it is the gametophyte plant that lives the longest and is the most visible. It produces a form capable of gathering materials for growth, primarily through photosynthesis (Figure 2). The most common form, found in all mosses and many liverworts, isan elongate axis bearing flaps of tissue that increase the photosynthetic area. At some point, often once a year, the gametophyte produces gamete producing structures that are called archegonia (singular = archegonium) if they produce eggs and antheridia (singular = antheridium) if they produce sperm. These structures are typically produced in the midst of modified 'leaves' at ends of stems/branches in mosses or, in some liverworts, they occur on the underside of umbrella/mushroom-shaped structures that extend upwards from the main body of thalloid liverworts.. The antheridia (Figure 3) are roughly spherical containers in which cells differentiate into flagellated sperm and are released when the antheridia break open. The archegonia are flask shaped structures with a single egg near the base and an elongate neck that develops a canal through which sperm can swim in order to fertilize the egg. The resulting zygote develops inside the archegonium, producing a sporophyte that eventually extends typically one to six cm beyond the archegonium andexists as an appendage of the gametophyte, never livingan existence independent from it. Although the sporophyte sometimes is green and capable of photosynthesis for part of itslife, itsstructure, a simple stalk with no 'leaves' to increase surface area, is not particularly suited for photosynthesis. Rather the structure is suited for the dispersal of spores; the stalk usually elevates the capsule, which is the site where spore mother cells develop, undergo meiosis, and produce spores. If 'spatial separation' is used rigorously to define an organism then these sporophytes would not be considered a separate organism, they are simply a part of the gametophyte (Figure 5) . B ut , in light of the sexual cycle and pattern of alternation of generations, it is helpful to consider them to be separate organisms. This is supported by fact that they have a different number of chromosomes than the gametophyte that they grow out of. In all other plants besides mosses , liverworts and hornworts it is the spore producing plant that lives the longest and is the most visible ; it is the form that we see and recognize as a plant. T he sporophyte still begins its development growing out of the archegonium where the egg was produced and was fertilized, but the sporophyte's growth is such that it becomes completely independent of the gametophyte that it emerges from and eventually has a completely autonomous existence. Thus , when we see ferns, horsetails, club-mosses, and seed plants, what we are observing is a diploid plant that produces spores. In all these groups the gametophyte is small and elusive but the basic life cycle is the same as in all plants: an alternation of generations between a gametophyte and a sporophyte. Seeds and seed plants are discussed in the next chapter, below are considered aspects of the sexual cycle, in particular features of the less commonly seen gametophytes that are produced by seedless vascular plants. Ferns Most ferns have a small, photosynthetic gametophyte that usually is less than 1 cm acrossand one cell thick, i.e., a sheet. It lacks a stem axis and is often 'heart-shaped' (Figure 6-8 and 11). It is generally attached to a substrate via rhizoids (filaments of non-photosynthetic cells). As was the case in the mosses, the fern gametophytes produce structures where the egg and the sperm are produced as a result of cells dividing in a particular pattern to produce archegonia (Figure 7-9) and antheridia. It is important to note that gametes are not produced by meiosis because all the cells of the gametophyte are haploid already. Fern gametophytes are generally have flask shaped female structures (archegonia) located in the notch between the lobes and globular male structures (antheridia) located on the on the lobes. While most fern gametophytes are hermaphroditic, some are unisexual and for some their sexual expression depends on environmental conditions. All the cells of the gametophyte are haploid but it produces a cell, the egg, with special developmental abilities. The antheridia release sperm which have flagella that allow them to swim to the archegonia , where the eggs are located, swim down a narrow canal and fuse with the egg cell at the base. The zygote develops into a sporophyte, producing stems and roots. The stems produce leaves which shade the gametophyte and it soon dies (Figure 9) The sporophyte continues to grow to produce the fern that we recognize. It has the same structure as most plants: a root-shoot axis with leaves produced by the shoot. Most of the ferns in this area have stems (rhizomes) that are below ground and relatively short. What we see are the leaves emerging above ground from thisrhizome. At some point this diploid organism produces structures termed sporangia, inside of which are spore mother cells that undergo meiosis to produce a group of four (a tetrad) haploid spores that are released to the environment. When these germinate, they grow into haploid gametophytes and the process is repeated. Generally, the sporangia are produced in clusters called 'fruit dots' that are located on the underside of leaves (see wood fern). Other ferns have entire portions of their leaves that are obviously different and where spores are produced. A few ferns in this area are dimorphic (see sensitive fern), producing two types of leaves, some that are green and photosynthetic and which never produce sporesand other leaves that are non-photosynthetic and produce abundant spores, while being nourished by the photosynthetic part of plant. While this is the general pattern for ferns, there is some variation, one example of which is the water fern Marsilea, which has several interesting features (see the information sheet on Marsilea). As is the case in a number of ferns, spores are produced on a specialized leaf that is very different looking from normal photosynthetic leaves. Whereas the normal leaves are green and shaped like clover leaves, the spore bearing leaves are initially packaged into a seed-like structure, hard on the outside and capable of being dried out and revitalized (germinated) when re-wetted. At this time the 'fruiting' (i.e., spore bearing) leaf emerges into the water, looking very little like a leaf: it is without chlorophyll, very small and gelatinous. It produces spores in clusters and there are two types of spores, male spores called microspores and female spores called megaspores, each in separate sporangia. The technical name for plants that produce two types of spores is heterosporous. In contrast, most ferns are homosporous, producing only one type of spore that generallyproduces hermaphroditic (bisexual) gametophytes (described above);a few homosporous formsproduceunisexual gametophytes, both male and female, but bothcoming from identical looking spores. The two types of spores of Marsileaare readily distinguished by size. The megaspores are around 1 mm in length and germinate to produce egg-producing, female gametophytes. The microspores are only ~ 70 um in length and produce sperm-producing male gametophytes. Without any increase in size and without emerging from the microspore, the male spores germinate to produce a 'plant' with ~35cells, 32 of them are spermatazoids, multiflagellated corkscrew shaped sperm cells, roughly 10 um in size, that are released from the male gametophyte when the microspore wall is broken. The spermatazoids are chemically attracted to the female gametophyte. The female gametophyte is substantially larger than the male gametophyte but it still is small and, like the male gametophyte, exhibits endosporic development, its developmentoccurs within the spore case of the megaspore, with only the very short neck extending from it. It produces a single archegonium with a single egg which the sperm swims toand fertilizes, forming a zygote. While the new sporophyte plant seemingly sprouts from the female spore, it actually is coming from a female gametophyte that is growing inside the spore case. Further Reading “Marsilea: Habitat, External Features and Reproduction” on Biology Discussion.com Another interesting fern is the Appalachian bristle fern, which is only known from the gametophyte form. Apparently, it has been reproducing asexually for millions of years! There are several other species of ferns known only as gametophytes. Horsetails The basic pattern found in ferns, with a dominant sporophyte generation and a diminutive gametophyte generation, is found in the horsetails, a group of vascular plants that originated in the Paleozoic and produced a number of tree forms that were significant in producing extensive deposits that became coal and oil. There only remains one genus of horsetails and there are less than 20 species worldwide. All are herbaceous with perennial rhizomes that send up vertical branches which have a very distinctive pattern of growth with photosynthetic stems , very small scale-like leaves, and whorled branches or no branches. Spores are produced in a terminal cone-shaped structure, which is a cluster of sporangia. Spores are dispersed by the wind but their movement and release from the sporangium may be aided by structures called elators, strap-like appendages on the spore that move in response to the absorption and loss of water. Germination of the spore produces a small (~ 1-3 cm) photosynthetic gametophyte that looks like a pin cushion. Very short 'stems' are present with appendages that increase photosynthetic area. Antheridia and archegonia are usually both produced from the same gametophyte , although it may be unisexual for a period of time. Sperm are multi – flagellated and need to swim to reach the egg. Fertilization results in a zygote that develops into a diploid sporophyte that soon overgrows the gametophyte that it emerges from, producing roots and both horizontal stems (rhizomes) and vertical stems. Clubmosses, Spikemosses and Quillworts The se three groups are thought to be closely related and are grouped together as 'Lycopods' or 'Lycophytes' , a group that also includes a number of fossil forms, including tree-like forms that were very important at the end of the Paleozoic era. The group has 1200 species and is considerably more diverse than the horsetails but much less diverse than the ferns (12, 000 species). The sporophytes of extant clubmosses, spike mosses and quillworts are all herbaceous perennials. They generally spread extensively with above-ground and below-ground stems (tropical members are usually epiphytes). Although ancient members of the group exhibited woody growth, none of the species alive today do. Clubmosses (Figure 13) are unique in having gametophytes that are subterranean and non-photosynthetic, surviving as parasites by feeding off of fungi. These gametophytes live much longer than most gametophytes of vascular plants, some over 15 years. Spikemosses and quillworts are heterosporous and, like the aquatic fern Marsilea, the gametophytesdevelopendosporically;livingoff the material that was provisioned in the spore by the sporophyte plant. The male gametophyte is very short-lived and has little stored material (the microspore is small), but the female gametophyte is considerably bigger and lives for months on material present in the spore. Early growth of the sporophyte, out of the female gametophyte that is present in a megaspore, looks like a germinating seed (Figure 14) and we will see in the next chapter that these are analogies — it is notthought that seed plants developed from the lycopods. Another feature of some spikemossesis that the 'female' spores, the ones that develop into female gametophytes, sometimes develop ON the sporophyte plant, anotherfeature that is repeated in seed plants.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.13%3A_Sex_and_reproduction_in_non-seed_plants.txt
Superficially, the production of seeds (Figure 1-2) resembles the production of offspring in familiar animals: inside a diploid parent there develops a member of the 'next generation' , which is nurtured inside its parent during the critical early stages of development and then is deposited outside its parent to finish its life. But appreciate that all plants exhibit an alternation of generations, so if a diploid (sporophyte) plant produces a new diploid (sporophyte) plant in a seed, one must account for the haploid gametophyte generation that had to come in between the two sporophyte generations. And one must appreciate that s eeds are NOT a substitute for spores, in fact, spores are critical to the production of seeds. The appearance of seeds (both in the sense of evolution and in the sense of development) is a complex story, one that involves the pattern of 'alternation of generations' shown in all plants. In light of this pattern, seeds represent a 'babushka' (Russian doll) with multiple generations found inside each other. An appreciation of this 'generation within a generation' is essential in understanding 'how seeds came to be' both evolutionarily and developmentally. While itwas long assumed that a structure as complex as seeds evolved once, many now feelthatseeds evolved multiple times. Seeds therefore may represent an example of convergent evolution, where multiple lines have converged on a common feature. Whether or not this isactually the case, we can cite several features that allowed seeds to evolve and someof these features are exhibited in groupsthat do not produce seeds. Central to the appearance of seeds, in both a developmental and evolutionary sense, is the appearance of ovules, dynamic entities whose composition changes, ultimately ending up as a seed. In this chapter, we consider the transformations in the life cycle of plants that allowed for the development of seeds. In the next chapter, we consider the specific structures and patterns seen in conifers and flowering plants. Althoughwe are focused on the seed, we will also consider a companion entity that is essential for the development of seeds: the pollen grain, which we will see is a miniaturized mobile, male gametophyte. TOPICS • Seed Structure • Reduction • Retention • Arrested Development • Provisioning • Packaging Seed Structure A seed consists of three components: an embryonic sporophyte plant, a tissue that provides nutrition to that embryo, and a 'seed coat' , the containertissue in which the embryo and nutritive tissue develop. The embryonic plant is diploid and it develops from a zygote formed by the union of egg and sperm. The seed coat is also diploid and it also is derived from a sporophyte plant, but it is an earlier sporophyte generation than the embryo. In both a temporal and also in a physical sense, a seed is a generation 'babushka, a Russian doll' , with 'nested' generations. There are two sporophyte generations, the older one (seed coat) on the outside, and the new one(embryo)on the inside, with a gametophyte generation, or remnants of one, sandwiched between them. Seeds are the consequence of the megaspores not being dispersed but instead being retained in the sporophyte that produces them. The spores germinate and egg-producing female gametophytes are consequently present on/in the sporophyte. Later, embryos, resulting from the fertilization of eggs produced by the gametophytes, are also present on/in the sporophyte. The structure where the retained spore is located and where the seed ultimately develops iscalled an ovule. Ultimately ovules develop into seeds containing a new sporophyte 'packaged' in the seed coat which is a tissue derived from the original sporophyte. Prior to this, an ovule contains afemale gametophyte; prior to this, ovules contain a spore that produces a female gametophyte; earlier still they contain a megaspore mother cell that produces that spore. Finding gametophytes, both male and female, and understanding their development is key to the understanding of both the evolution and development of seeds. Seed plants and their ancestors are heterosporous, producing two types of spores that develop into two types of gametophytes, one male and one female. Both the evolution of seeds and the development of any individual seed involve modifications of both the male and the female gametophyte, modifications in the structures that produce them, and modifications of the timing and location of important developmental processes. We can describe the transformations that allowed for the evolution of seeds and also allow for the development of seeds with the acronym RRAPP: Reduction, Retention, Arrested development, Provisioning, Packaging. Reduction Both the male and female gametophyte of seed plants are greatly reduced in size when compared to the gametophytes of other plants. The gametophytes of most plant groups are less apparent than the sporophytes, but in the seed plants they are so reduced that the pattern of alternation of generations is hard to see, and the misconception that plants reproduce like familiar animals, i.e. that there is no alternation of generations, that the only haploid cells are egg and sperm, is often assumed. The male gametophyte of seed plants is pollen, an organism of 3-6 cells that initiates its development from a spore on one sporophyte plant and completes its development on another sporophyte plant, in a location near that of the female gametophyte. For some groups, pollen releases a mobile, flagellated, sperm, but for the familiar groups, flowering plants and conifers, the male gametophyte is comparable to fungi in the sense that the gametophyte grows to (as opposed to swims to) the egg cell of the female gametophyte, fuses with it, and donates a sperm nucleus that joins with the nucleus of the egg cell to form a diploid zygote. Although the size of the male gametophyte is much reduced, it may live up to a year in conifers, starting its life on one sporophyte and ending it on another sporophyte. The female gametophyte of seed plants is also severely reduced: it is only seven cells in flowering plants but may exceed one thousand cells in conifers. In all seed plants, the female gametophyte exists solely inside tissues of the sporophyte that produced it, having no independent existence whatsoever. Besides the reduction in size of the female gametophyte, there is also a reduction in the number of female gametophytes that are produced by any specific megasporangium. Remember that female gametophytes grow from megaspores that are produced after a meiotic 'cell division' (it actually involves two cell divisions) of a megaspore mother cell. In all seed plants, only a single megaspore mother cell is produced inside the megasporangium. And although, typically, a megaspore mother cell produces four spores after meiosis, in seed plants three of the haploid nuclei degenerate after meiosis, leaving a single megaspore inside the megasporangium. Its structure is not at all spore-like, having no special spore wall at all; it has no need for protection because it is always buried inside of sporophyte tissue. Similarly, the megasporangium, the container in which megaspores develop, is very different from the sporangia of non-seed pants because it is not a container exposed to the environment but instead is a container embedded in sporophyte tissue. The development of the female gametophyte of seed plants occurs in an ovule and inside the megasporangium that develops in the ovule. In seed plants, the megasporangium is called a nucellus, and in some groups, the nucellus remains as a feature of the fully developed seed. Retention There are multiple retention steps involved in the production of seeds and only the final steps are specific to just seed plants. First, there must be retention of the egg in the organism that produces it. In organisms that have gametes differentiated into a 'sperm' (a mobile, usually flagellated, cell that is released from the organism that produces it) and 'egg' (defined as a gamete that is larger and immobile), retention of the egg is often (e.g., Oedogonium, water molds), but not always (e.g., Fucus), the case. Retention of the egg requires that fertilization occurs in/on the egg-producing organism. This is the case for mammals. For organisms that show alternation of generations, this means that the egg is fertilized in the gametophyte. The next retention found is a characteristic of all plants and is why the group is sometimes referred to as 'embryophytes' . It is the retention of the zygote, and the embryo that grows from it, in the female gametophyte plant. The retention of the egg, zygote, and embryo in the gametophyte allows the early development of the diploid generation to occur in a more controlled environment, with resources provided by the gametophyte.Note that this retention results in a sporophyte growing from a gametophyte, again something that is found in all plants. The next retention step is the retention of the gametophyte on a spore-producing plant. Gametophytes develop from spores produced in a spore case (sporangium) present in/on a sporophyte plant. In seed-producing plants (and a very few non-seed producing plants, e.g., some spikemosses) gametophytes are retained on the sporophyte plant that produces them because the spore is retained in, not dispersed from, the sporangium of the spore-producing plant. For the female gametophytes of seed plants this retention is permanent, the female gametophyte is only found living on/in a sporophyte plant, in a megasporangium, the structure where the megaspores (the large spores that develop into female gametophytes) were produced. The male gametophyte also exhibits retention, but only temporarily; microspores (small spores that develop into male gametophytes) are retained in the microsporangium of the parent (sporophyte) plant and the initial development of the male gametophyte occurs there to produce a pollen grain. It is then dispersed and completes its development on another sporophyte plant, in the structure where the female gametophyte is found (the female cone of conifers, the flower of angiosperms). Arrested development An essential aspect of reproduction is dispersal. Especially for plants, with their indeterminate lifestyle, reproduction is of little significance unless there is a potential of dispersing to a new location. Dispersal is a significant aspect of sex as well. Although the processes of syngamy andmeiosis can generate variability even when self-fertilization occurs, it is far more effective in producing variation, the raw material of evolution, if genetically distinct organisms participate. For sedentary plants, this requires movement of one individual to another, i.e., dispersal. For non-seed plants, dispersal is affected by two dispersal agents, the spore and the sperm. Spores have a tremendous dispersal ability because they are small and can be (generally) dispersed by the wind over large distances. This is only possible because the living thing inside the spore, the single cell, is extremely 'life-less' ;that is, if one were to observe it, one would see very little biological activity. Metabolism is minimal, very few chemical reactions are occurring; it is a very stable structure and is in a state of 'suspended animation' , the normal functions of life have been suspended temporarily. These life functions resume if the spore reaches a habitat that can trigger spore germination, which returns the spore to the animated state. In contrast, the other mobile agent of non-seed plants, sperm, are highly animated, they have a very substantial metabolic rate, not just because of their mobility (metabolism is required in order for the flagella to move) but their overall structure, in terms of organization of the membranes and cytosol, is much more typical of living things than that of dormant spores. Sperm are consuming stored energy supplies ( 'food' ) in order to sustain their life functions. Since sperm have a very limited ability to acquire food, their lifespan is set by the amount of the stored reserves that they are provisioned with when dispersed. The consequence is that sperm do not live very long and do not move very far. Seed plants also have two dispersal agents: the seed and pollen. Both of them are 'in suspended animation' in the same way that spores are. This allows both of them to travel substantial distances. It is significant that both the seed and the pollen are not single cells, they are partially developed organisms that have begun their development on a 'parent' plant, yet have arrested their development and entered a 'resting stage' where they can survive adverse conditions and live without any additional resources. While producing dormant cells (e.g., spores) are found in diverse groups of organisms, arresting development of a multicellular organism and having it enter a dormant stage is much less common, but it is essential to the development of seeds. Male gametophytes start their development inside the sporophyte plant when microspores are produced and develop into pollen. They are then dispersed in a dormant state, only to be revived if they reach the site of a female gametophyte, located on/in a sporophyte plant. Here, their development resumes, and they are able to produce a cell that can fertilize the egg. Similarly, the new sporophyte generation found in a seed exhibits arrested development. After fertilization , the zygote that is produced generally quickly divides and develops into an embryo with a root/shoot axis, root and shoot apical meristems, and one or two leaves that are 'seed leaves' = cotyledons. Then the development ceases, no cell division or differentiation occurs , in spite of the fact that nutrients are available and environmental conditions are favorable, at least temporarily. The metabolic rate drops to very low levels and the tolerance o f the embryo to extremes in temperature, etc., substantially increases. In this state, the seed is dispersed , and it only resumes growth and development if conditions favorable to germination are met. Provisioning Seeds contain nutrients, both nutrients that can 'supply energy' , i.e. materials that can be used in cellular respiration, and nutrients that are building materials for the construction of more plant cells. These energy and material supplies are very significant to a young autotroph because 'it takes money to make money' : in order to feed itself a plant needs structure but the structure isn't possible without energy and material supplies. Provisioning allows an organism to produce a structure that can obtain matter and energy on its own. Provisioning is accomplished in spores, but to a lesser extent; they do possess some materials, but the quantities are limited because the spore is generally only a single cell and generally small in size to promote dispersal. Seeds are provisioned with materials that are stored in several different tissues: 1. Materials can be stored in the female gametophyte which sometimes is a component of the seed : in conifer seeds, the female gametophyte is a structure of roughly 1000 cells all of which can store materials, 2. Material can be stored in the embryo itself, specifically in the cotyledon(s), the 'seed leaf /leaves' produced by the embryonic plant while growing inside the seed. In many angiosperms, the cotyledon(s) enlarge during development and store a substantial amount of materials. Many of our crop species possess large cotyledons that take up most of the seed volume and possess most of the stored material. 3. Material can be stored in the endospermtissue, a unique tissue found in the seeds of angiosperms that are formed as a result of a second fertilization event, besides the one that created the zygote. The next chapter will discuss how this tissue is formed and develops. Although all angiosperms have endosperm tissue at some point in their development, some angiosperms lose their endosperm as the cotyledons expand and the seed is left with enlarged cotyledon(s) but little endosperm. Wherever /however they are stored, the nutrients come from the parent sporophyte plant via phloem tissue. Careful examination of developing seeds will reveal that each is attached to the parent plant via a vascular thread. Packaging Seeds are eventually dispersed as a package inside of which is an embryo and stored food. The outside of the package (the seed coat) develops from sporophyte tissues of the parent plant that are called integuments, one or several layers of sporophyte tissue that form the outer layers of the ovule. Part of the transformation of an ovule into a seed is the transformation of the integuments (or part of the integuments) into a seed coat. The seed coat develops through a process of cell division and differentiation to form what is usually a rigid outside coating of the seed. These cells usually have thick secondary cell walls. Thus, a seed is a package containing an embryo and stored food. The development of a seed, also known as the ripening of an ovule, involves three distinct developmental processes: 1. The development of a zygote into an embryo. The zygote is the new sporophyte generation. It divides to produce new cells and these grow and develop to produce an embryo with both a root and shoot apical meristem and one to several leaves, called cotyledons, or seed leaves. 2. The transformation of the sporophyte tissues of the ovule into a seed coat. This typically involves the production of new cells, allowing for the ovule to increase in size, and the differentiation of these cells to produce a protective container. 3. The development of nutritive tissue to supply materials to the seed after it has been dispersed. As mentioned above, the nutritive tissue develops from different sources in different seeds but it always involves a proliferation of cells and an expansion of these cells as the material is supplied to them from the parental sporophyte. Seeds are successful for multiple reasons including: (1) the early development of the sporophyte occurs in a very protected location inside of the previous sporophyte generation, (2) two items are dispersed: pollen, whose dispersal is focused on getting gametes together, and seeds, whose dispersal is focused on getting the next generation of sporophytes to new locations, (3) seeds are dispersed in a package that generally contains substantial quantities of nutrients, increasing the likelihood that the next sporophyte generation will be able to become established.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.14%3A_The_Development_of_Seeds.txt
Seeds are a remarkable innovation that have been highly important to the evolution of plant life. The vast majority of plants that we observe and utilize possess seeds and seed plants dominate most terrestrial habitats. The last chapter described, in general terms, what seeds are and what modifications in the general plant life cycle of alternation of generations had to occur in order for seeds to appear. This chapter fills in some of the details for the five groups of seed plants: • flowering plants, with 250, 000 species, by far the most diverse and ubiquitous plant group • conifers:, although with only 1000 species, they are very commonly encountered and ecologically and economically important • cycads: a small group of around 300 species with limited distribution and importance • gnetophytes: a small group of only three genera and around 100 species • Ginkgo: a single species that survives only where cultivated In additionto these five extant groups, there are several groups of seed plants well represented in fossilsbutno longer present. These extinct species are sometimes lumped as 'seed ferns, ' but both the lumping and the designation as a group are not thought to be accurate: they are not closely aligned with ferns and they probably represent a polyphyletic grouping. Most workers believe that seeds evolved more than once and therefore that there should be no phylogenetic entity corresponding to either seed plantsor to gymnosperms (i.e., seed plants lacking flowers) although these categories do persist. We will consider the details of the life cycle, in particular the form of the female gametophyte and the mechanisms associated with pollination and fertilization, for the five groups of extant seed plants. TOPICS • Conifer seed development • Seed development in other gymnosperms • Seed development in angiosperms • Flowers • Floral modifications • Fruits Conifers Pines are the most commonly seen conifers and the group that will be described below but the basic pattern holds for all of the group. The plants that are recognized as pines are diploid, sporophyte plants. All conifers, including pines, are heterosporous and produce two kinds of spores, both on the same tree. The sites of spore production are the cones. The cones that most people recognize as 'pine cones' are female pine cones. These are not only the site of megaspore production but also the site of megaspore germination to form a gametophyte, egg production by that gametophyte, egg fertilization and seed development. All these events take place in a location described as an ovule. These processes generally take multiple years and the structures one usually recognizes as pine cones have been living and developing over a time of two years or more, with many of the significant events occurring when the cone is much smaller and not as easily observed (Figure1). A female cone consists of an axis (stem) bearing scales subtended by bracts, with the scales thought to be derivatives of modified branches. Upon the upper surface of the scale are the ovules, the structures that develop into seeds. Male spores are produced in less familiar, but certainly easily observed, male pine cones, which grow more quickly than female cones but are present on the tree for a much shorter time. Typically, they are produced in the fall and are visible as a cluster of structures at the base of bud. These expand in the spring/early summer (Figure 2) and dry up and wither a month later. In contrast to the female cones, m ale cones are simple in structure: a branch with tightly packed spore bearing leaves (sporophylls) , each with a pair of relatively large sporangia on their lower surface. The gamet ophyte generation develops from microspores and megaspores produced and retained in the male and female cones. Gametophytes are highly reduced and, especially for the female gametophyte, largely invisible because of its small size and location. Male gametophytes are produced in t he microsporangia of the male cones. These initially contain cells that undergo meiosis to produce microspores. At first, t he spores are in clusters of four reflecting their origin in the two divisions of meiosis (one cell to two cells to four cells). The spores eventually separate and undergo a very limited period of development, producing a haploid organism with four nuclei, usually in three cells (i.e., one cell has two nuclei), and possessing two wing-like air sacks (Figure 3).. Particularly significant to the development of the pollen grain (aka male gametophyte), is the fact that its development is arrested. This, and the fact that the microsporangium breaks open, allows the pollen to be dispersed by the wind. Pollinationis the name of the transfer of the male gametophyte (pollen) from where it is produced to the location of the female gametophyte, in conifers, a movement from a male pine cone to a location inside thefemale cone. At the time of pollen release, female cones are very small and are 'open' withspaces above each individual cone scalethat are open to the outside (Figure 4).. Each female cone scale bears on its upper surface two ovules, each with a megasporangium imbedded in sporophyte tissue called integuments. Early in ovule development there is an opening, the micropylar canal, between the integuments that connects to a space between the cone scales. Pollen grains (male gametophytes) in the air can slide between the female cone scales and be deposited in the space next to the micropylar canal. The ovule secretes a liquid 'pollination drop' into this space and pollen grains end up in the liquid and rehydrate. In a mechanism not completely understood, the liquid with the pollen grains is withdrawn through the micropylar canal to a space on the inside of the integuments adjacent to the megasporangium. Soon thereafter the integuments grow to block the micropylar canal and the cone scales grow to seal the female cone off from the outside. At this time the megasporangium has a single megaspore mother cell destined to undergo meiosis. After meiosis, only one of the four daughter cells remains as a megaspore. The megaspore is not dispersed but develops within the megasporangium into a female gametophyte of several thousand cells that generally produces two or three archegonia, each of which produces a single egg. All of this occurs inside the female cone that is attached and is part of the sporophyte plant. The female gametophytes of conifers are highly reduced 'organisms' found within the ovulate cones, imbedded inside sporophyte tissue of the plant. At the time of pollination there usually is no female gametophyte, only a megaspore. Inside the cone, the male gametophytescontinuetheir development, albeit very slowlyin pines, requiring 12 months between pollination and fertilization. As the megaspore produces a spore that slowly develops into a female gametophyte, it goes through a 'free nuclear' stage where mitotic divisions are not accompanied by cell wall formation (the organism is coenocytic). Eventually cell walls form and the female gametophyte forms structures described as archegonia, each with a single egg. As the female gametophyte develops, t he pollen germinates and a single cell elongates from the grain, growing through the megasporangium (the nucellus) towards the female gametophyte (Figure 6).. A little over a year after pollination t his tube cell fuses with the egg cell and two sperm nuclei are released, one of which fuses with the egg nucleus, forming a zygote while the other nucleus disintegrates. During the time between pollination and fertilization, the female cones grow only a small amount and they remain closed to the outside. Note that no swimming sperm is produced, the male gametophyte grows to the egg by means of an elongate cell. Following fertilization, the zygote develops into embryo, imbedded in, and nourished by, the female gametophyte. Tissues surrounding the female gametophyte develop into a seed coat, often producing a wing structure that allows the seed to be dispersed by the wind. As the seed develops, the cone surrounding it also develops, often growing substantially. Following fertilization, seeds may mature in as short a time as one year but for most species it is two years or longer. In most pines, the cones eventually re-open, allowing the seeds to fall out and be dispersed by the wind. Sometimes the cones remained closed and only open following the intense heat of a fire. The female cones of junipers and yews develop fruit-like features that attract animals who facilitate seed dispersal by consuming the 'fruits' and defecating the seed in a new location. Other gymnosperms The three other groups of seed plants without flowers, Gnetophytes, Cycads and Ginkgo exhibit the same basic pattern of seed production: male spores develop into pollen grains which are dispersed from the sporophyte to finish their development in the structure that produces female spores and hence the female gametophytes. Pollination in at least some cycads and in some gnetophytes involves insects; in ginkgo and most gnetophytes pollination is by the wind. Gymnosperm literally means 'naked seed' and one feature that unifies the non-flowering seed plants is that, at the time of pollination, the ovules are accessible, not buried in tissues that the male gametophyte must grow through; instead, the ovulesare available, at least for a brief period of time, because the cone scales have not fused with each other and the micropylar canal is open. However, the male gametophyte generally DOES have to growthrough the megasporangium (the nucellus)to reach the egg. In cycads, the male gametophyte actually develops a type of feeding structure (called an haustorium), a branched filamentous structure permeating the nucellusand apparently obtaining nourishment from it. Eventually a flagellated, mobile sperm is released and swims through the fluid of an 'archegonial chamber' , an area of fluid between the nucellus and the female gametophyte. Flagellated sperm are also found in ginkgo. Flowering plants The basic process of seed development in flowering plants is the same as in conifers. The major differences include the following: • Male (pollen producing) and female (seed producing) organs are usually found together in the same structure, the flower, not separated on two distinct branches as they are in conifers. • The ovules are produced inside a structure called an ovary , that is not open to the outside, thereby requir ing the male gametophyte grow through a substantial distance of sporophyte tissue in order to contact the female gametophyte • The transfer of pollen (pollination) often involves biological agents (insects, birds, rarely mammals) and a variety of floral features enhance pollination. • The female gametophyte , which is called an embryo sac (Figure 7). because it eventually contains the embryo, is even morereducedthan in other seed plants, drastically so, usually consisting of only seven cells, six haploid cells, one of which is the egg, and one larger central cell with two haploid nuclei. • Both of the spermnucleiproduced by the male gametophyte participate in a fertilization (syngamy) event. One fuses with the egg to form a zygote and the second fuses with the central cell. This sperm nucleus combines with the central cell 's two nuclei to form a triploid' endosperm 'nucleus. The central cell then proliferates, forming a tissue, endosperm, that has a limited development and is only found during seeddevelopment and often, but not always, in the mature seed. The initial stages of endosperm development involve a' free-nuclear 'stage where nuclei divide with no cell wall formation, creating a multinucleate, all triploid, (coenocytic) cell. This materialis called' liquid endosperm'and is familiar as coconut milk, which is actually cytosol. • In angiosperms the female gametophyte, which is very limited both in size and lifespan , is not the nutritive tissue for the developing embryo as it is in other seed plants, e.g., the conifers. In angiosperms the nutritive tissue for the developing embryo is the endosperm, the tissue resulting from a second fertilization event. The flower The flower is a highly modified stem, typically with four whorls that are bunched close together at the end of the branch. The components of each of the four whorls is thought to represent modified leaves, with the inner two whorls being highly modified spore bearing leaves (sporophylls) (Figure 8-9).. The elements of outermost whorl (sepals) are the most leaf-like, although often quite small. The elements of the next whorl (petals) are often leaf-like in form but usually are large and colorful structures that lack chlorophyll. The next whorl are stamens that often consist of a stalk (a filament) terminating in a structure called an anther in which pollen is produced. Initially, the anthers possess microsporangia containing microspore mother cells. These produce microspores by meiosis and these spores germinate and develop into male gametophytes, aka pollen grains, composed of only two or three cells. When pollen is mature the anther generally opens up to make the pollen accessible to pollinators or the wind. Pistils are the innermost whorl and often are fused together so the central structure of the flower is a single (compound) pistil. Pistil(s) generally consist of an enlarged base (the ovary), with a stalked structure (the style) emerging from its top that terminates with a surface (the stigma) that receives pollen. Inside the ovary are produced one too many ovules that eventually become seeds. Prior to this, the ovules are sites of megaspore production, female gametophyte (= embryo sac) development, fertilization and finally the process of seed development. Following pollination, the two-or-three celled male gametophyte (pollen) germinates on the stigma and grows through the style and then gains access to an ovule by growing through the micropylar canal, an opening between the integuments that surround each ovule. Pollen tube growth involves the expansion of a single cell, called the pollen tube, that delivers two male gametes to end of the embryo sac with the egg cell. The tube cell fuses to the embryo sac and delivers two sperm to bring about double fertilization, allowing for the subsequent development of the zygote and endosperm. Floral modifications The variations in the basic plan of flowers are one of the amazing stories of botany and of all biology. In general , the changes can be attributed to the forces of natural selection acting on the interaction between pollinators and plants. Some of the common transformations from the pattern described above include: • fusion of the parts of a whorl , e.g., all the petals fused together to form a cup or funnel • fusion of the members of two whorls (e.g., fusion of stamens on to the petals) • reduction in the number of members of a whorl, in particular a reduction from many pistils to a single pistil as found in the flowers of Asteraceae flowers • change from radial symmetry (all parts of a whorl being the same size and oriented in a similar fashion, Figure 9-10 ) to bilateral symmetry with flowers having two sides that are mirror images of each other (Figure 11), or sometimes to have no symmetry at all. • placement of the ovary below the point of attachment of the other whorls • elimination of multiple parts, sometimes forming unisexual flowers (Figure 12). The fruit After fertilization, the ovule transforms into a seedin a process that involves the coordinated development of three distinct tissues: 1. the zygote grows into an embryo; 2. the endosperm proliferates, first in a 'free-nuclear' pattern (nuclear divisions are not accompanied by cell wall formation) and subsequently by producing new cells, and finally, in some groups, the endosperm disappears as the embryo enlarges its cotyledon(s); 3. the tissues surrounding the embryo and endosperm develop into a seed coat. Note again that the genetic makeup of these three components differs—the embryo is a 'new generation' and is diploid, the endosperm is triploid and the surrounding tissues are diploid but are of a generation before that of the embryo. While the ovule transforms into a seed, the ovary, and sometimes other tissues surrounding the ovary, develop into a structure called the fruit. The transformation of the ovary into a fruit generally involves the production of new cells, the growth of these cells and the development of features specific to plant being observed. The fruit generally has features that enhance the dispersal of seeds and often has features that protect the seed. Although it is generally easy to distinguish the seed from the fruit, occasionally there is no obvious demarkation between themorthere may be a demarkation that is deceiving. For example, almonds are derived from a fruit that is like a cherry (in fact cherries and almonds are very closely related). We eat the fleshy part of cherries, which is part of the fruit. The 'pit' is not actually a seed but rather it is the seed surrounded by the innermost layer of the fruit. When you 'shell' an almond you are cracking open fruit tissue to reveal a single seed inside. In this case the protective role of the seed coat has been taken over by a portion of the fruit (Figure 13). Similarly, asunflower 'seed' is actually a one-seeded fruitand shelling the 'seed' is actually splitting open the fruit (Figure 14).	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.15%3A_Sex_and_Reproduction_in_Seed_Plants.txt
Reproductive/sexual behavior and the life of the organism Even for the simplest of unicellular organisms, reproduction requires a shift in the 'normal' activities. The 'cell cycle' (Figure 1) describes the pattern of activities that the cells go through in order to reproduce (i.e., undergo mitosis). As the cell goes through this cycle its activities change. Changes in gene expressionresult in changes from 'growth and synthesis' activities (G1, S, G2 stages) to mitosis activities. Even more changes need to take place if a unicellular organism is to participate in sex. At some point in the sexual cycle meiosis has to be induced, requiring cells to drastically reorganize themselves in a manner that will halve the number of chromosomes in a very specific way. At some other point cells with unique abilities, the ability to fuse with one another, need to be produced. For multicellular organisms the required changes to bring about reproduction or to bring about the sexual process usually involve profound changes. New structures may appear and the and the behavior of the multicellular organismoftenshifts, sometimes in drastic ways, ways that may even end the life of that particular organism. The patterns and the control of these developments are considered in this chapter. TOPICS • Reproduct ive structures: production patterns in time and space • Developmental control of sex and reproduction—general cues • Patterns of reproduction in flowering plants • Photoperiodism Reproduct ive structures: production patterns in time and space For most organisms, the normal activities involve the acquisition of matter and energy and the act of reproduction shifts resources from structures that acquire matter and energy to those that are involved in reproduction. For a plasmodial slime mold the shift in structure and behavior is dramatic and involves the whole organism: the coenocytic film that has been spreading across the substrate, finding food, suddenly shifts to a completely different structure, one that is immobile and unable to feed but is able to produce propagules. For other organisms, the processes of both sex and reproduction are involvespecific structuresthat are continuously or periodically produced that are specialized for those purposes. For example, normal fungal growth produces hyphae that areable to explore the medium it is growing in and obtain materials needed for growth. To reproduce asexually, e.g., with conidia, a fungal filament grows in a different direction (usually upwards)and producesa series of small, easily detached cellsthat can be dispersed. Thus, the fungus has shifted some of its activities from its normal growth mode to reproductive mode. Another example would be dimorphic fronds in ferns (Figure 2, see also sensitive fern) and horsetails; the plant makes one kind of leaf for reproduction and another type of leaf for photosynthesis–consequently its ability to photosynthesize is reduced as its ability to reproduce increases. For some plants, sexual reproduction involves a dramatic reorganization comparable to the slime mold. Remember that a flower is a transformed branch and thatbranchesare 'new modules' , significant not only for their growth but also because of its potential to produce even more modules. The transitionof that branchto a flower changes all this — it converts an indeterminate structure, capable of growing and producing more modules, into a determinate structure that produces a flower or flowers and then a fruit and then dies, eliminating that module, and removing its potential to produce any other modules. If all the shoots of a plant transition to flowering at the same time, thenthe plant as a whole becomes determinate and will die after fruiting. This is what happens in wheat (Figure 3). We can identify two 'extremes' in the pattern of allocation of resources to reproduction, one involves partitioning the organism in space and the other involves partitioningitin time. Some organisms, like cinnamon ferns, most algae and many fungi, simultaneously produce parts for reproduction and parts that conduct 'normal' activities. While the degree of partitioning may vary with time, the organism grows and reproduces more or less continuously. At the other extreme are organisms that spend part of their life growing and and then transform into a different type of organism in order to reproduce. Examples include butterflies, mayflies, carrot (Queen Anne's lace), burdock, beetand mullein, allof which produce a very short stem with multiple leaves and no branches in the first year of life. In the second year the stem elongates, branches form and flowers and fruits are produced. Most ofthe material stored from the first year of growth is directed to the developing seeds. In addition, the leaves are dismantled to provide additional resources. Consequently, the ability of the plant to photosynthesize disappears and the plant dies in the process of floweringand fruiting. In the first year the plant focuses on growth (acquisition of materials), in the second, on reproducing. Control of reproduction and sex In most organisms the ability to reproduce is controlled by cues from the environment that are sensed and bring about changes in structure and allocation of resources. Although it is often assumed that reproduction (and hence population growth) is dictated by resources, there certainly are situations where resources are available but organisms do not utilize these resources to reproduce. Instead of being tied to resources, many organism s ' reproduction is tied to specific cues in the environment–they respond to these cues by reproducing. Stated another way, although adequate resources may be necessary for reproduction, they are often not sufficient to bring about reproduction. Among other things this makes predicting population growth more difficult. This topic will be considered more when discussing the behavior of populations. Here we will discuss the particular cues that organisms utilize to trigger the reproductive process, sexual or asexual , and then consider the (primarily sexual) reproductive patterns found in flowering plants and some specific cues that control many plants' reproductive patterns. Cues to initiate reproduction and /or sex Growth/developmen t For many unicellular organisms reproducing by mitosis, reproduction simply involves the achievement of a particular stage in cellular development. This is generally somehow tied to growth, i.e., the accumulation of enough materials that the cell can be partitioned in two. Growth is connected to time ( 'cells have to reach a certain age to reproduce' ) but only as mediated by material acquisition. Bacteria that divide every 20 minutes are not timing the intervals, there are processes taking place, some of them fundamentally tied to the acquisition of materials, that take 20 minutes to occur. If you change the temperature or change the availability of materials bacteria will take a longer time to divide. Also, as noted above, organisms have the ability to change their rate of material acquisition, i.e., they control how fast they grow, and because of this, they can control their rate of reproduction. Time Although all eukaryotes appear to be able to keep time, very few (?none?) have reproduction or sex cued specifically by time (i.e., have a stopwatch that is initiated and then reproduces at the end of a specific time). However, it is common, especially for plants that have been selected for cultivation, that an integration of time and temperature determines flowering. Plants need to grow to a certain stage in order to reproduce and this requires time and favorable temperatures. Many seed packets for home gardeners state something like 'flowers in 60 days' — this is assuming a 'normal' temperature regime; if temperatures are cold, it might take 70 days. This idea of integrating time and temperature is discussed more in Chapter 26. Nutrients As discussed above, nutrition (i.e., the acquisition of resources required for growth) clearly can be a factor influencing growth and development , but sometimes nutrition plays a more specific role. Chlamydomonas sex is triggered by low nitrogen levels; fung al reproduction often requires a specific media formulation different from the medium that brings about growth; slime molds can be induced to sporulate (a phase of sexual reproduction) by specific nutrient regimes. The ability of some perennial plants to respond to flowering cues has been associated with carbon/nitrogen ratios in the plant that can be affected by both photosynthetic activity and nutrient availability. Adverse/favorable conditions Surprisingly, both good and bad conditions may trigger sex or reproduction, depending on the species. A number of organisms change their activities when conditions become unfavorable (e.g., high or low temperatures, drought, high or low pH, toxic levels of certain chemicals) and often the change involves reproduction and/or sex. For example, slime mold plasmodia (the multinucleate giant cells) are induced to form sporangia when the conditions are poor. A number of tree species are known to flower particularly well when they are about to die. Thesebehaviorsmight be considered adaptive since it produces structures (seeds, spores) that are resistant to harsh conditions at a time when conditions are deteriorating. Such structures may also be beneficial because they also provide for dispersal and movementto new, and possibly more favorable, conditions. At the same time, a cessation or reduction in the production of propagules during adverseconditions can be justified because the resources are needed to keep the organism alive and not used onthe 'frills' of reproduction and sex. Cues that are useful in predicting upcoming conditions Many species live in environments that vary seasonally and that havecertain portions of the year that are much more favorable to activities related to reproduction/sex than other periods. The most obvious activity related to reproduction/sex is material acquisition but other factors might include: availability of dispersal agents (e.g., wind or perhaps specific pollinators or fruit eaters), lack of predators for offspring, etc. The most common cue that predictsupcoming conditions isphotoperiod. Photoperiodic control of floweringwill be considered after describing the patterns of reproductive effort found in flowering plants. Patterns of reproduction and sex in flowering plants Angiosperms can be divided into two groups based on their flowering behavior: monocarpic plants, that flower a single time and die, and polycarpic plants, that flower multiple times. Monocarpic plants will die after flowering because all of their meristems have been converted from indeterminate vegetative shoots into determinate flowering shoots. After flowering, the flowers develop into fruits and the plant dies both because thereare no more vegetative shoots to produce more leaves and because the leaves that were already present have been 'scavenged' as a source of materials for the developing seedsand consequently have been destroyed. This was discussed above and is found in a number of crop species including corn, wheat, soybean (Figure 3 and 4) Many monocarpic plants are annuals, living for only a year. Whatever it takes to get the plant to flower occurs within a year of the germination of the seed. If a specific cue is involved then within a year the plant develops a sensitivity to the cue and can respond. Note that some of the annual plants of this area, especially those grown in gardens, may be annuals only because of the elimination of favorable conditions in the fall—they simply are killed by frost and cold and would live longer if the conditions were more favorable. Most of these plants are not native to this area; most of the annuals that are native to this area kill themselves off in the flowering process. In temperate North American habitats, most monocarpic annuals germinate in the spring and flower during the summer but some, called winter annuals, germinate in the fall, overwinter and flower in the spring.Most of the wheat grown in the northern U.S. would be considered a winter annual, although in central and southern parts of the country the wheat grown is a regular annual and planted in the spring. Monocarpic plants may also be biennials, sometimes defined as plants that live for two years but more accurately described as plants that live for two growing seasons. These plants are generally found in habitats that are seasonal, i.e., have part of the year favorable for growth and part unfavorable for growth, usually because of low temperatures, but occasionally because of lack of moisture. Biennials behave the way they do because during the first growing season they are not responsive to the cues that induce flowering, while in the second season they are. An example would be beet s, a species that need s a cold winter in order to be able to respond to the cues (photoperiod, see below) that trigger flowerin g. I t does not flower the first growing season even though it receives the cue to flower but does flower the second year after being exposed to cold. Biennials are monocarpic and generally exhibit a substantial dimorphism between the first and second year, often having a very short stem and no branches the first year and elongating and branching stem the second year. As mentioned earlier , one might think of the form the first year being associated with acquiring resources and the form the second year being associated with reproduction. Although uncommon , a few monocarpic plants are perennial, living for multiple years and then flowering once (Figure 5). Examples include century plant ( Agave), bamboo , and some gentian species . The case of bamboo is particularly significant to panda bears because they feed almost exclusively on the vegetative (i.e., non-flowering) bamboo plants which can grow for up to 70 or more years while forming an extensive clone. When the plant flowers, acres of bamboo, the product of 70+ years of growth, produces seeds (which pandas do not eat) and in the process the bamboo dies, leaving the panda with no source of food. Polycarpic plants are perennial. They potentially live forever because only some modules are turned into flowering shoots on any particular year. Since all of the plant is exposed to the same set of cues, the different behaviors of different meristems, some producing flowers and some not, is the result of differing sensitivity to cues. A common pattern is that only stems that are one-year-old respond to the flowering cue (see coltsfoot). Thus, a plant will have two groups of shoots, shoots of the current year that do not respond , and shoots of the previous year that do respond , and therefore produce flowers and fruits and die. Hence, in the spring of the year, these plants are composed solely of the shoots that will become flowers. But before they flower, they produce branch shoots that will not become flowers until the next year. A version of this pattern is seen in many varieties of raspberry/blackberry. Although the plant is perennial, this is the result of underground stems. The vertical stems, called canes, are biennial, the first year growing vegetatively, the second year producing flowers and fruits and dying. A raspberry patch is perennial but the stems you see only live for two years, each cane behaving like a biennial. Flowering plant cues for reproduction While a few plants , especially plants selected for cultivation, require no specific environmental cue to induce flowering, they simply flower after the plant has grown sufficiently, the majority of plants require specific environmental cues to trigger flowering. However, for many plants, the cue alone is not sufficient to trigger flowering; the plant itself must be able to respond to the cue, i.e., the plant initially is not responsive and does not respond to particular cues. W ith time, the plant develops a sensitivity to the cue and can respond when the cue occurs. Thus, when we consider what makes a plant flower, we must consider the possibility that two processes are involved: one triggering responsiveness and a second triggering the flowering itself. A good example of this is the flowering of beet: in order to flower it must first be exposed to cool temperatures for a period of time; this develops its ability to respond to a specific cue that induces flowering, which is photoperiod, a particular combination of light and day in a 24-hour period. Beet will not respond to photoperiod unless it has first been exposed to cool temperatures. Hence, it grows the first year without flowering, and only during the second summer, after a period of cool temperatures during the winter, will it be induced to flower. Photoperiodism A wide variety of organisms, including plants, animals, fungi and protists, respond to the photoperiod, relative amount of light and dark in a 24-hour period. For many organisms, including many plants, it is one of key determinants influencing reproduction (Figure 6). Specifically for flowering plants, photoperiod often determines when a plant flowers and photoperiod has probably been most extensively studied in this context. But it is important to appreciate that photoperiod often affects physiology, structure , and behavior and that its mechanism of action is at the molecular level, i.e., by influencing which genes are being expressed. Photoperiod is a significant cue for organisms living north or south of the equator because the photoperiod predicts upcoming conditions. The approaching winter can be sensed by the shortening photoperiods; an upcoming spring can be sensed by lengthening photoperiods. Plants have turned out to be excellent organisms to study photoperiodism because, for some of them, a single day of a particular photoperiod can result in a measurable response. In contrast, for some organisms, and indeed for most plants, a response is only apparent after prolonged exposure to particular photoperiods. Early studies established the fact that it is the night period that is critical. An interruption of the dark period can change a response while an interruption of the light period does not alter behavior. The ability to respond to photoperiod requires two abilities: the ability to sense light vs. dark, i.e., a photosensor, and the ability to keep time. I n all organisms studied the timing mechanism appears to be associated with an internal 24-hour rhythmicity, something described as the circadian clock because the rhythms in behavior have a periodicity of around (circa = around) 24 hours. Circadian rhythms are probably found in all eukaryotic organisms, certainly they seem to be a feature of most eukaryotic organisms where it has been looked for. The actual photoperiodic response is the result of a particular pattern of light and dark that is imposed on an organism's internal 24-hour rhythm. As a result, the behavior observed after giving an organism 12 hours of light and 12 hours of dark depends upon what portion of its 24-hour cycle that the 12 hours of dark is applied. The timing mechanism is not a stopwatch that times the dark period, what is critical is how periods of light/dark interact with internal rhythms that have a 24-hour periodicity. Stated differently, there is a periodicity in plants response to darkness. The most commonly encountered photoperiodic responses involve reproduction but more generally photoperiod can be an organizing factor determining the patterns of growth and development that an organism exhibits. Some of these are listed below: In flowering plants: • flower production • temperature tolerance • production of vegetative buds • activation of buds • activation of lateral buds • formation of tubers (Figure 7) • seed gemination In non-flowering seed plants: • production of cones • formation and activation of buds In dinoflagellates: • cyst formation In both red and brown algae: • pattern of growth and formation of reproductive structures In animals: • development of ovary and testes in birds and other animals and consequent changes in behavior For flowering plants, the photoperiodic flowering response is generally put into one of three categories: • long-day plants, which flower only if daylengths (periods of light) are longer than some critical value. • short-day plants, which flower only if daylengths (periods of light) are shorter than some critical value. • day neutral plants whose flowering is not obviously tied to photoperiod See Figure 8. Short-day plants (black line) need night periods longer than some critical value in order to flower. Long-day plants (red line) need night lengths shorter than some critical value in order to flower. The actual critical daylength (i.e., the vertical part of the line) may shift to the right or left depending upon the particular species (or variety within a species). Note that neither of the two plants illustrated here would be flowering with night lengths between 15 and 12 hours. Similarly, if the red line were shifted enough to the right, or the black line enough to the left, one would have situations where both long-day and short-day plants would flower at the same photoperiod. Although the names refer to periods of light in a 24-hour period it is actually the night period that is critical. Hence long-day plants might better be called short-night plants and short-day plants might better be called long-night plants (but they aren ' t!!). Another confusing factor to appreciate is that although we might consider that any day with more than 12 hours of light is a ' long-day ' (and ' short-night ' ), what is critical is the actual length compared to the critical value. Hence, one can have both long-day and short-day plants flowering under the same photoperiod: a photoperiod of 10 hours light and 14 hours dark would trigger flowering in a long-day plant with a critical value of 9 hours of light and also a short-day plant with a critical value of 11 hours of light. While plant responses fall into these three general types, the actual responses are often complicated by two factors. One is that a plant response to a particular treatment may not necessarily 'all or nothing' (described as a 'qualitative response' ), meaning that the plant will not flower unless it receives the appropriate stimulus. For many plants the response to an appropriate stimulus is 'quantitative' meaning that the plant flowers more quickly or with more flowers if receiving a particular stimulus (the transition lines on the graph above may not be vertical but instead have a slope). A second complicating factor is that photoperiodic sensitivity may involve multiple sequential signals, including ones that do not involve photoperiod. For example, some plants will only respond to long-days after short-days or respond to long-days only after a period of time under cool temperature conditions. In plants there appears to be two pigments, phytochrome and cryptochrome, that can interact with circadian rhythmic phenomena and produce photoperiodic responses. While both of these pigments interface with several different physiological processes, the flowering response appears to be the result of changes in gene expression resulting from signal transduction systems that influence protein/DNA interactions. Specifically, the appropriate photoperiodic stimulus appears to result in production of specific mRNA molecules that are important in transforming vegetative shoot apical meristems into floral meristems.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.16%3A_Reproduction-_development_and_physiology.txt
Sex, Evolution, and Species Although for many organismssex is crucial to the ability to reproduce, sex is an important concept to biology for more reasons than this. Sex is critical to two other highly significant biological topics: the process of evolution and the concept of species, two things that are in fact interconnected. Evolution describes changes through time. What is it that changes? It is notan individual organism, whosechanges are described as 'development' . What evolves are groupsof organisms, i.e., populations ((Figure 1). Populations are usually described as a group of organisms of the same species. The criterion that puts individuals together into a group called a species is the ability to interbreed, i.e., species are groups of organisms united by the fact that they can potentially interbreed, and the only way to interbreed is through sex. Sex is the process that connects individuals together into something called aspecies, a group of interbreeding organisms. Species, i.e. interbreeding groups, are thought to be the biological entity that evolves. Additionally, sex is significant to the process of Darwinian evolution because: • sex can be an important process that generates variation within a population and variation is significant to the evolutionary process, providing the 'raw material' upon which the process of natural selection can act. • sex provides a mechanism to spread particular features within a population, allowing favorable characteristics to spread. It should be pointed out that sex is certainly notrequired for the process of evolution. There are a number of groups (e.g., bacteria) that evolve readily and have no sexual process(although bacteria DO have processes that allow characteristics to spread within a population, it is not sex) (Figure 2). Moreover, groups that do not have sex cannot be categorized as having species (although oftentimes they are!) because sex is what delineates an 'interbreeding group' , which is the criterion usually used to define species. Thus, although sex and species are significant to evolution, they are not essential to evolution. As noted earlier, several of the groups considered here (e.g., dinoflagellates) do not have sex, but the groups'diversity clearly point to the fact that evolution has been, and presumably still is, operating. Even within groups that are considered to be sexual, e.g., flowering plants, there are groups that do not participate in sex. Dandelions produce seeds but do so in a manner that does not involve sex. Such groups might be considered evolutionary 'dead-ends, ' yet, as noted above, sex is not essential to the process of evolution. The process of sex is significant to the grouping and naming practices discussed in Chapter 2. To deal with diversity, biologists group organisms that are phylogenetically connected (reflected in the fact that organisms within the group 'look alike' ). There are different levels of relatedness that correspond to different 'levels' in a biological classification: phylum, class, order, family, genus, species, variety. Except for the species level(and perhaps not even there!), all of these levels are not defined, e.g., there is no rule about what constitutes a family, about how similar organisms have to be to put them together in family grouping. As a consequence, there certainly can be some workers who will take a group, e.g., the pea family, and say that it should be considered as three families, making three groups, each of which is more uniform than is the group when considered as a single family. The species level is unique in having criteria that define who should be in any particular group. However, in spite of the fact that there IS a concrete definition of species, i.e., an interbreeding group, this does not mean that it is easily appliedor that when it is applied the appellation is based on the definition. It is not that easy to discern who is breeding with whom and this is especially the case with plants and fungi. Studies to determine mating behavior are time consuming and the overwhelming majority of species (even in the animal groups) have not been checked to see if what is being called a species actually is an interbreeding group. And many, many groups that are known to be asexual (all prokaryotes, most dinoflagellates, many fungi, some flowering plants) are grouped into entities called 'species.' Thus, at every taxonomic level workers still rely on subjectivity to delineate the extent of taxonomic groups;and one finds both 'lumpers' (people who tend to lump groups together and have fewer groups with more variationin each) and 'splitters' (people who tend to split groups up and have more groups with less variation in each). Consider again the example of asexual dandelions (Figure 3). The entity Taraxacum officinale is asexual, and is generally considered to be a species represented by its Latin binomial. But should it really be considered a species? Some workers consider the T. officinale to be an assemblage of several hundred 'microspecies' , each of which is a clonal population. For sexual populations, who breeds with whom is controlled by a number of parameters specific to the species being considered. Collectively, these factors describe a 'breeding system' and it turns out that flowering plants offer a rich diversity of breeding systems. A 'closed' breeding system is one where outcrossing (breeding with another individual) unlikely. An 'open' breeding system is one that encourages outcrossing. One might think that flowering plants, the vast majority of which produce bisexual flowers with male and female parts in close proximity, would have closed breeding systems. But there are a number of processes that can make their breeding system more open. • being dioecious, having unisexual flowers on plants that bear either male or female flowers but not both (Figure 4). About 5% of flowering plants are dioecious including aspen, cannabis and holly. • being monoecious, having unisexual flowers, but both male flowers and female flowers are on the same plant , for example corn, cattail and most species of squash. • having bisexual flowers with parts that mature at different times , e.g., having flowers where first the pollen matures and is disseminated and then the stigmas are produced and are able to receive pollen. • having incompatibility systems that prevent pollen from being able germinate and/or grow on stigmas of the same plant and therefore unable to fertilize its own flowers • an inabilityto form seeds unlessthe sexual process is accomplished It is significant that each of these features is not 'all or nothing' –there are plants that are generally unisexual but may have a few flowers of the second sex; there are plants that mostly have unisexual flowers but have a few bisexual ones; there are plants which have separate maturation times for the male and female parts of the flower but have multiple flowers so that on any one plant there can simultaneously beboth functional male and female parts; there are plants that have flowers whereself pollen can grow on but just not as fast as non-self pollen; there are plants that will produce seeds without sex but only if sex didn 't happen (e.g., pollination didn' t occur); there are plants that almost always produce seeds asexually but occasionally will go through the sexual process; there are plants that produce megaspore mother cells that undergo meiosis to make haploid megaspores which then fuse with each other to form a diploid cell that behaves like a zygote! Breeding systems are important because they influence plant evolution, patterns of variability and the reality of things that we identify as 'species.'	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.17%3A_Sex_evolution_and_the_biological_species_concept.txt
One of the activities that define organisms is that at some point in their life, or throughout it, they grow. Growth requires the acquisition of matter and both the acquisition of matter and the incorporation of this material into a living form (i.e., into biomolecules) involves energy. Both matter and energy are needed but it is important to keep in mind that they are two distinct entities that are NOT interconvertible. The energy transformations that organisms carry out involve manipulations of matter but they DO NOT involve converting matter into energy. Energy is obtained by rearranging matter, mostly by converting carbohydrates and oxygen into carbon dioxide and water. What complicates understanding is that matter is needed in two ways (Figure 1): (1) materially, providing the materials that become part of the larger organism: organisms are made of carbohydrates, (2) energetically, because energy can be made available as matter is rearranged, e.g., converting carbohydrates and oxygen into carbon dioxide and water. Although matter is being rearranged, it is not being transformed into energy. Matter, Energy and the Laws of Thermodynamics Matter and energy are key players in the process of life at all levels : cell, organism, and ecosystem. Both matter and energy are familiar ideas, yet misconceptions are common, especially about energy and the interplay between matter and energy in biological systems. Matter is straightforward: it has mass , occupies space and can be categorized into elements (e.g., carbon, hydrogen, oxygen) that often are usually present in specific mixtures termed molecules (e.g., carbon dioxide, glucose) that have a characteristic composition of elements and are arranged in specific ways. Living things are made of matter and have a characteristic material composition, being made of biomolecules such as proteins, carbohydrates, and nucleic acids. Life may be partly defined by the ability of living things ( organisms ) to acquire matter and incorporate it into themselves , i.e., to grow. Life can also be defined on the basis of its ability to manipulate matter in characteristic ways that involve energy transfers. While matter is an easy concept, e nergy is much more elusive ; consider the following: 1. Energy has the ability to affect matter by rearranging it or moving it from one place to another. 2. Energy is dynamic and the energy associated with a given bit of matter, e.g., a molecule, depends on circumstances ; it is a function of the situation matter finds itself in, the speed it is moving, the location that it is in , in particular its position relative to other matter or relative to electric, magnetic and gravitational fields (which are controlled by matter). 3. Energy is a property of systems, i.e., an assemblage of matter in a particular place and with specific relationships with each other. 4. Energy describes the ability of a given assemblage of matter (a 'system' ) to change the organization of another bit of matter (another 'system' or perhaps 'the surroundings' ). 5. Energy could cause atoms or molecules to move in relationship to each other, e.g. a chemical reaction, or cause an object to change position in a gravitational field (rise or fall), or cause a charged molecule or object to change position in an electrical field. 6. Just as energy can cause movement of matter, the movement of matter (i.e., matter changing position) changes the energy content and allows energy to be 'transferred' from one system to another or one molecule to another 7. Energy can also be transferred to material via electromagnetic radiation, waves of electricity and magnetism that are given off by any bit of matter with a temperature above absolute zero (i.e., every bit of matter!!!). 8. Electromagnetic radiation is a 'form' of energy that is important to all forms of life but especially so for photosynthetic organisms. Electromagnetic radiation has a dual nature and can be described as (1) a rhythm of electric and magnetic fields, a series of waves with a certain frequency and wavelength , moving at a constant speed, the speed of light , or (2) packets of energy called photons. The energy in a packet (a photon) is relate d to the wavelength of the wave s of electricity and magnetism. Note that these photons/waves of electricity and magnetism are able to interact with matter and transform it, thereby transferring energy to the matter. 9. Two o ther concepts related to energy are heat, which can affect matter by changing its kinetic energy, changing the average speed that molecules are moving, and work, which can change the position of objects in a gravitational field, or perhaps concentrate chemicals in a particular spot (chemical work). While both heat and work are connected to energy and are sometimes considered 'forms' of energy, they might better be described as interactions between systems or between a system and its surroundings. A common feature of both matter and energy is that both are conserved, something described in what is known as the first law of thermodynamics. Although modern physics has demonstrated that matter can be converted into energy and it is their collective entity (matter + energy) that is conserved, in biological systems matter and energy are NEVER converted one to the other and consequently we can consider each to be conserved—there is always the same amount of matter and the same amount of energy, neitherone is created, destroyed or 'used up.' The conservation of matter is easily understood, mattercan be moved from one place to another, e.g. accumulated in an organism, lost (or gained) by diffusion from (or to) an organism. Elements can be rearranged, e.g. carbon transformed from carbohydrate to carbon dioxide in the process of cellular respiration, but the amount of matter is constant—the same number of carbons, hydrogens and oxygens. Similarly (and much less appreciated), energy is conserved. It can be 'moved' from place to place, or transformed from one form to another (as molecules are rearranged or moved relative to each other and relative to gravitational, electrical and magnetic fields), but the amount of energy is constant, unchanging. Living systems, non-living systems and combinations of living and non-living systems rearrange matter, and by rearranging matter they redistribute energy. But the first law of thermodynamics states that in all these rearrangements there is a constraint: after any rearrangement, the amount of matter and the amount of energy must be the same as it was in the beginning. Living things constantly reorganize matter: molecules combine, molecules separate into pieces, molecules move from one place to another. In all of these transformations, matter must be conserved. In addition, the energy must be conserved; consequently, organisms may release energy during some transformations (because the final arrangement of material in the organism has less energy than the initial arrangement); or, if the final arrangement has more energy than the initial one, the organisms must somehow have acquired energy to bring about the transformation. Since matter and energy play in zero-sum games then one might think that their transformations are rather tedious and potentially circular, with losses in one spot being exactly matched by gains somewhere else, and the potential of ending up exactly where you started. This is not the case, there is a direction to the transformations and it is strictly a one-way flow: you can never return to the starting point. This constraint is dictated by the second law of thermodynamicswhichstates that in spite of the fact that energy is conserved, the amount of energy that can be used to do work is always decreasing. To most, this statement is startling because they assume that all energy can be used to do work; but some energy is not 'useful' and the second law states that the amount of 'useless' energy is always increasing. The second law of thermodynamics is extremely powerfulandthis is reflected in the fact that it can be defined in a variety of ways. Fundamentally, its utility rests in the fact that it puts an arrow on rearrangements of matter. Given two possible arrangements, A to B, each with the same amount of matter and energy, the second law dictates that the direction of the rearrangement will always be to a situation that has less useful energy. The second law points out what rearrangements of matter will be 'spontaneous' , i.e., occur 'on their own.' Rearrangements in the opposite direction (the non-spontaneous direction) will only occur if energy, useful energy, is supplied. The second law adds a second constraint on transformations; not only must matter and energy be conserved but the amount of useful energy must decrease. Consider a system A with a certain amount of matter and energy at a time, one and the same system, now called A ', a time later; the second law dictates that, barring interaction with the surroundings, the only change in A that is possible as it transitions to A' is one where there is a decrease in energy available to do work; thus once you leave situation A, you can 't return to it (i.e., get from A' back to A). A lthough the energy in both is the same, the amount of energy available to do work is diminished as it transitions from A to A. 'This reflects one of the common ways that the second law can be stated: there are no perpetual motion machines. A device can' t get back to where it started without energy from the 'outside' . Organisms, matter and energy How is all of this significant to organisms?? Organisms are defined in part by their ability to grow and since growth requires the acquisition of matter, all organisms need to be able to acquire the specific materials that they construct themselves with. Moreover, growth requires useful energy because work is done in the construction of most new molecules for growth. What complicates understanding is that matter ( 'food' ) plays a dual role: (1) materially, providing the materials that become part of the larger organism, (2) energetically, providing energy that is made available as matter is rearranged. The transformations of matter and the transfers of energy performed by organisms are intertwined in ways that allow misconceptions to easily be acquired but it is important to remember that matter and energy are two different entities. But growth isn 't the only reason that organisms need matter and it isn' t the only reason why organisms need energy. Why organisms need energy 1. In addition to needing energy for growth organisms need energy because they 'do work' in a physical/chemical sense. They create electrochemical potentials, they develop pressure, they generate forces that result in movement. Particularly significant is that they perform chemical work as they grow: many biomolecules consist of arrangements of matter that contain more useful energy than the materials these molecules are constructed from, and therefore energy is needed to synthesize them. The process of growth requires organisms to rearrange material, reposition it, in ways that cause the new material to possess more useful energy than what it was made from. This is only possible if organisms have a 'supply of energy' and the work that they do is possible because part of the energy in this supply is 'used' to allow for the rearrangements of materials. Note that energy is conserved, but the amount of useful energy, the amount that can be used to do work, is diminished. 2. But even in the hypothetical situation where an organismisnot growing (making more biomolecules) and not doing work (e.g., moving itselfor materials within itself), it would still need energy simply to maintain itself. Organismsexist in an organized state thatspontaneously degrades to a less organized state. The maintenance of the organized state requires energy. An easily understood example of this involves the charge difference found across the cell membrane, with the inside being negative relative to the outside. This organized situation spontaneously 'breaks down' to a less organized one because electrical forces push negative ions out across the membrane and positive ions in. Maintenance of the organized state requires energy because the process of organizing (in this case moving ions across a membrane so they are more concentrated in one place than another) requires energy. How organisms obtain energy Organisms 'energetic needs are largely satisfied by acquiring biomolecules (food), generally carbohydrates, and processing them in a group of reactions called cellular respiration. Cellular respiration (Chapter 19) is a controlled' burning 'process whereby carbohydrates reactwith oxygen (the carbohydrates are oxidized), producing carbon dioxide and water. If one compares the energy content of equivalent amounts of carbohydrate plusoxygen to that in carbon dioxide pluswater, there is substantially less energy in carbon dioxide plus water. If you burn carbohydrates in a fire the difference in energy is released as heatand light, but in cellular respiration, less energy is released as heat, and none as light, because some energy is' captured'in chemicals, in particular one called ATP. Because the products of the reaction (carbon dioxide and water) are invisible gases many believe that cellular respiration converts matter to energy. But this is impossible, the first law forbids it! The original carbon, oxygen and hydrogen are still present, just now in different forms. Similarly, the original energy remains but is now present in the ATP that is formed and the heat energy that is released. Why organisms lose material because of their energetic needs As an organism carries out cellular respiration it produces two materials (water and carbon dioxide) that are easily lost and sometimes 'purposely' eliminated (e.g., in humans where breathing , i.e., ventilation , facilitates the loss of water and carbon dioxide). As a consequence of cellular respiration , organisms are continually los ing matter as carbon dioxide and water and consequently are also los ing weight. Thus, in order to maintain its weight, a respiring organism must acquire more 'food' . Obtaining matter and energy In order to satisfy theirenergetic needs, an organism requiresa supply of carbohydrates (or other biomolecules) to utilizein cellular respiration. These carbohydrates may be obtained in two basic ways: (1) by consuming biomolecules that have been produced by other living things—carbohydrates or molecules like proteins that can be metabolized to produce carbohydrates or (2) by consuming 'self-constructed' carbohydrates that are produced in reactions (usually photosynthetic reactions) that synthesize carbohydrates from carbon dioxide and water. Such reactions utilize 'sources' of energy (e.g., sunlight) that allow a chemical reaction to occur where the products have more energy than the reactants. The synthesized carbohydrates are then used to power cellular respiration, i.e., they are converted back to carbon dioxide and water. The group that consumes carbohydrates that other organisms have produced are termed heterotrophs (hetero-other, troph-eat; literally 'eat others' ), and the organisms that make their own carbohydrates to 'eat' are termed autotrophs (auto-self, troph-eat; literally 'self-eaters' ). It is important to realize cellular respiration occurs in both groups, they differ only in how they acquire carbohydrates to be oxidized in cellular respiration. It is critical to keep in mind that matter and energy are two different things but they are intertwined. Energy that is present in carbohydrates and oxygen can be 'released' when the material is rearranged into carbon dioxide and water. The 'released energy' might end up as heat, or as work, or in a new arrangement of molecules (e.g. ATP is a rearranged version of ADP plus inorganic phosphate). However, the second law requires that the total amount of energy in the new arrangement (e.g., carbon dioxide, water and ATP) must possess less ability to do work than the earlier arrangement (in this example, carbohydrate plus oxygen plus ADP plus inorganic phosphate). Appreciate that the 'food' that organisms obtain, either by finding it (heterotrophs) or making it (autotrophs) serves a dual function, providing (1) energy (through cellular respiration) and (2) material (through a variety of metabolic pathways where carbohydrates are reconfigured to produce other biomolecules (proteins, fats, nucleic acids). If food provides energy through the process of cellular respiration it is transformed into carbon dioxide and water and thesecannot be used materiallyto make biomolecules. Alternatively, food can provide 'building materials' that are used to make more cell membranes, cell walls, cellular enzymes, but this food will NOT be 'providing energy' . Food cannot provide both energy and building materials at the same time! You cannot 'have' your cake (build with it) and 'eat' it too (use it for cellular respiration). The major topics to be covered in this section on the growth of organisms are outlined in bold below. Growth has both material and energetic needs. As described above, almost all energetic needs of almost all organisms are accomplished by cellular respiration(Chapter 18)the oxidation of carbohydrates by oxygen, producing carbon dioxide and water. Satisfying the material needs of heterotrophic organisms is a relatively simple story; however it is more complicated for autotrophs, where it involves both photosynthesis(Chapter 19)and mineral nutrition(Chapter 22), the acquisition of mineral elements like nitrogen and phosphorus. Although most prokaryotes satisfy their material and energetic needs in typical heterotroph or autotroph fashion, we will also consider some of the metabolic diversity (Chapter 21)found in some prokaryotes that revealvery different patterns of satisfying energy and material requirements. This diversity is an interesting contrast to the familiar, normal ways of life and also plays a significant role in the nutrition of plants by influencing the availability of plant nutrients. We will briefly consider how organisms move materials throughout their bodies(Chapter 24), a process that usually (but not always!) 'requires energy' . We will alsoconsider the nature of soils(Chapter 23), which serve as reservoirs for the nutrients and water that plants require. A final aspect of growth that we will consider is therhythms of growth(Chapter 25)that organisms, especially plants, exhibitand how this growth might be modeled.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.18%3A_Matter_Energy_and_Organisms.txt
Although most bakers don 't realize it, they work with explosive material. Flour is highly flammable and under appropriate conditions flour dust can explode. On several occasions flour mills have exploded, perhaps the most famous being near Minneapolis in 1878 when a recentlybuilt mill, one that at the time was the largest in the world, was totally destroyed and 18 workers killed (Figure 1). More recently, in 2008, a sugar mill in Georgia exploded, killing 14 and injuring 40 more. These examples demonstrate that there is energy present in carbohydrates, chemicals with the general formula of CH2O, i.e., a' hydrated 'carbon. Often the carbohydrates are polymers of six carbon sugars with a formula of C6H12O6. Cane sugar, what exploded in the Georgia mill, is made up of two hexoses, glucose and fructose, bound together. Starch, the main component of flour, is made up of long chains of glucose molecules bound together. Glucose, fructose and starch are all carbohydrates and like all molecules they' contain'energy. If carbohydrates react with oxygen to form carbon dioxide and water, energy is released. The energy of carbohydrates and its release when interacting with oxygen is central to the biology of most organisms. And understanding how the energy is obtained and utilized is significant not only because the energy released is essential for the functioning of organisms but also because it represents a unifying feature of all living things, every living organism carries out this process, or part of this process, or something similar to this process. Organisms need energy for growth, maintenance, and for the performance of work such as the motion of the whole organism, e.g., swimming, or internal motion, e.g., pumping materials within the organism or moving materials within a cell, that are essential for the organism 's livelihood. Many, but certainly not all, of these energy-requiring processes ' run ' on energy ' supplied by ' adenosine triphosphate, ATP, and most of an organism' s supply of ATP is provided by the cellular respiration, a process that synthesizes ATP while carrying out a chemical reaction that runs on carbohydrates. Exactly how ATP participates in metabolism varies and its action is often not direct and obvious in the way that the energy of falling water allows a mill to 'do work.' The action of ATP often involves 'coupling' different chemical reactions (examples below) with the consequence being that the participation of ATP makes unlikely events more likely to happen and/or events that occur slowly more likely to proceed rapidly. ATP 's participation in cellular activities causes the molecule to lose one or two of its three phosphate groups, forming either adenosine diphosphate (ADP) or adenosine monophosphate (AMP). Obviously, the regeneration of ATP is significant to an organism' s functioning and for most organisms, this regeneration is the result of a group of reactions described as cellular respiration. TOPICS • Overview of cellular respiration • Four parts of cellular respiration • glycolysis: glucose to pyruvate • pyruvate decarboxylation • citric acid cycle (Kreb's cycle) • oxidative phosphorylation • Mechanisms of ATP synthesis • Summary Overview of cellular respiration Cellular respiration describes a set of chemical reactions that together convert carbohydrates and oxygen into carbon dioxide and water. Collectively, these reactions allow a cell to obtain chemical energy in the form of ATP from the same basic process that allows causes a flour mill to explode and allows campers to obtain heat and light (other forms of energy) when wood (which is largely carbohydrate) is burned in a campfire (Figure 5). The chemical process of burning is an oxidation, or more properly a reduction/oxidation, a type of chemical reaction where an electron is transferred from one molecule to another. The molecule that loses electrons is said to be 'oxidized' ;the one that receives electrons is 'reduced' . The process is generally 'driven' by the fact that some molecules/atoms have a higher affinity for electronsthan others. In a thermodynamic sense, this is similar to the fact that rocks move downhill in response to gravity; one might say that 'low spots' (in a gravitational field) have a higher affinity for rocks than 'high spots' .It takes energy to move rocks up in a gravitational field and (most of) the energy expended moving a rock up 'ends up' in the rock now in its new, higher position. If the rock then rolls down it 'gives up' energy and, after descending, the rock ends up with less energy than it at the bottom than before. The first law of thermodynamics tells us that the energy is somewhere, where is it? One can state that the energy hasbeen 'released' as rocks move downhill and also that this energy can be 'captured' in various ways, i.e., work can be done in the process(can you think of a way to capture the energy of a falling rock?). In a similar manner, electrons move 'downhill' , from molecules that have less affinity for them to molecules that have a greater affinity for them, and as they move 'downhill' work can be done. Keeping track of electrons and the affinity of different compounds for electrons is sometimes challenging and we won't pursue it in detail here, except to say that the task is made easier when what is transferred is an electron plus a proton, i.e., a hydrogen atom and in these cases the oxidation/reduction is easy to trace by seeing what loses hydrogens and what gains hydrogens. The summary equations, in words and formula, for cellular respiration are: • carbohydrate plus oxygen forms carbon dioxide plus water • specifically, glucose plus oxygen forms carbon dioxide plus water • C6H12O6 +6 O2 ——>6 CO2+ 6 H2O In cellular respiration what is oxidized are the carbons ina carbohydrate molecule of the general formula CnH2nOnand what is reduced is O2. The carbons of the carbohydrate have lost hydrogens while forming carbon dioxide (CO2). The oxygen has gained hydrogens while forming water (H2O). It is important to realize that the carbohydrate does NOT react with oxygen(although it does if a log is burned in a fire); the equation merely summarizes a group of reactions occurring simultaneously andhave the net effect of converting carbohydrates and oxygen to carbon dioxide and water. We can split these reactions into four basic parts: 1. Glycolysis A process that converts a glucose(six carbon sugar with six carbons, 12 hydrogens and six oxygens) into two pyruvic acid molecules, each with three carbon molecules and withthe formula C3H4O3 (Figure 6). Note that the carbons of the carbohydrate have been oxidized (lost hydrogens) as pyruvic acid has been formed. What has been reduced is a metabolite called NAD+which has been reduced to NADH. Because the NAD+has a higher affinity for hydrogens than the carbon in a carbohydrate, this group of reactions is 'downhill' . Also occurring in glycolysis is the synthesis of some ATP from ADPand phosphate ion (iP). Thus, some energy present in the hexose is now present in the forms of NADH and ATP (andsome has been released heatand some is present in the pyruvic acid molecules). 2. Pyruvic acid decarboxylation Each of the two pyruvic acid molecules is 'oxidatively decarboxylated' , removing a carbon as a carbon dioxide and producing atwo carbon ( 'acetyl' ) fragment attached to the metabolite coenzyme A. The lost carbon has been oxidized as NAD+ is reduced toNADH. Because NAD+has a higher affinity for electrons than the carbon in the pyruvic acid this reaction is 'downhill' . 3. Krebs cycle The remaining two carbons derived from each pyruvic acid are added to a four-carbon compound making a six carbon compound that is then oxidatively decarboxylated twice and then goes through a series of oxidative steps to regenerate the original four carbon compound that can receive another two-carbon unit. This is what is known as both the Kreb's cycle or the citric acid cycle. The net effect of steps 1-3 is the total oxidation of the carbohydrate to carbon dioxide, accompanied by the reduction of a number of NAD+molecules to NADH and also the reduction of a similar molecule, FAD, to FADH2. Some ATP has been synthesized in both glycolysis and the citric acid cycle, but the majority of the ATP generated in cellular respiration comes from step 4 below where the 'reducing power' of NADH and FADH2 is utilized to 'power' an elaborate mechanism that 'utilizes' energy from the reduced molecules to accumulate protons and create a charge and concentration gradient across a membrane. This gradient is then used to synthesize ATP. 4. Oxidative phosphorylation (electron transport chain) Like the citric acid cycle, oxidative phosphorylation occurs in a mitochondrion, an organelle with two membranes with two aqueous spaces: in between the two membranes and inside the inner membrane (Figure 7). Oxidative phosphorylation transfers electrons, donated by NADHand FADH2, through a series of membrane bound carrier molecules located in the inner membrane, ultimately delivering them to oxygen. Oxygen simultaneously picks up protons andformswater molecules, H2O. Oxygen is essential to the process because it is oxygen 's affinity for electrons that drives the electron movement. To again use a gravitational analogy, oxygen is a' low point 'to which electrons move. If there isn' t a low point there would be no movement. The movement of electrons through a membrane operates an 'electrogenic pump' : it causes protons (H+) to accumulate in the space between the two membranes, creating an electrochemical gradient, a charge and concentration difference, across the membrane. In an energetic sense, the pumping is 'uphill' and it is made possible by a coupling to the 'downhill' movement of electrons to molecules with higher affinity for them. Theproton gradientthus created is a source of energy that can be utilized to synthesize ATP from ADP and iP. In oxidative phosphorylation there are two things moving 'downhill' in anenergetic sense: (1) electrons move from NADH 'downhill' to oxygen because it has a higher affinity for them, (2) protons that have been 'pumped' uphill then move 'downhill' across a membrane, from a place where they are in high concentration to a place where they are in low concentration. If one 'follows' the energy it goes from glucose to the reducing power of NADH/FADH2, to a proton electrochemical gradient, to ATP. Besides producing ATP, another very important consequence of the process of oxidative phosphorylation is the regeneration NAD+and FAD, compounds that are needed in glycolysis and the citric acid cycle. These processes cannot proceed unless NAD+and FAD are available (this point will be discussed further in Chapter 21 on metabolic diversity). Mechanisms of ATP synthesis During cellular respiration ATP is formed in two very different ways, both of which involve energy transfers and the concept of 'coupling' , in these cases the coupling of ATP synthesis to other reactions that 'provide energy' . Examining these reactions is not only important to the energy relations of a cell, but they also provide examples of 'coupling' . ATP is formed when a phosphate group (PO3) is added to ADP. Under most circumstances, this reaction is very unlikely. Most of the ATP formed by living things occurs in organelles called mitochondria where the electron transport chain discussed above results in a high concentration of protons on the outside of a membrane (remember that membranes are generally impermeable to charged items like protons). Embedded in the membrane, with openings to both sides, is a large enzyme, a polymer of amino acids, that has a very specific and complicated three-dimensional structure, a structure that is a consequence of the sequence of amino acids in the polymer. This enzyme binds ADP and phosphate and has a path, a channel, through which protons can flow through the protein (and also through the membrane) from high concentration to low. The movement of electrons through the protein causes the enzyme with attached ADP and phosphate to be bent in a way that makes it much more likely that phosphate binds to ADP, thereby forming ATP. Note that the charge and concentration difference of protons across the membrane represents a 'source of energy' that can be used to do things, in this case, bend the molecule and synthesize ATP. The energy from the proton gradient makes an unlikely reaction, ATP synthesis, much more likely. Stated another way, ATP synthesis is coupled to protons moving from high concentration to low. A second way to synthesize ATP from ADP and phosphate is seen in glycolysis. Instead of directly transferring a phosphate group to ADP it is first added to GAP (Figure 1). This reaction by itself is unlikely (uphill) but it can be made more likely if the GAP is simultaneously oxidized while NAD + is being reduced, a reaction that is favored (downhill) because NAD + has a higher affinity for electrons than GAP. The combined reaction results in the conversion of GAP to 1, 3 bPG, with the GAP being simultaneously oxidized and phosphorylated. And while the attachment of a phosphate group directly to ADP is 'uphill' (unlikely), the transfer of a phosphate group from the 1, 3 bPG to ADP is 'downhill' (likely), thus there is coupling between oxidation of GAP and ATP synthesis. A similar mechanism operates where ATP is formed in the citric acid cycle. Coupling is an important aspect of both ATP synthesis and hydrolysis and represents ways that energetically unfavorable (uphill) reactions can be made more likely by coupling them somehow (and there are multiple ways) to favorable (downhill) reactions. Summary Thus the net effect of cellular respiration is the complete oxidation of carbohydrates to form carbon dioxide and water. In the process, ATP is synthesized from ADP and iP. Although the process as described above 'starts' with glucose, a number of other molecules can provide six carbon sugars to be utilized in glycolysis, e.g., starch (a polymer of glucose), sucrose (a disaccharide containing glucose and fructose), galactose (a six carbon sugar), lactose (a disaccharide made of glucose plus galactose), mannitol (a six-carbon sugar alcohol). In plants, sucrose and starch are the most important sources of substrates for glycolysis. Besides hexose/hexose polymers, other materials can be 'burned' in cellular respiration, including fats and the carbohydrate portion of the amino acids of proteins. These 'food sources' enter the metabolic pathways of cellular respiration in several different places. Although cellular respiration is generally thought of as being a degradative process (catabolism), it can also be synthetic (anabolism—the making of biomolecules). When this happens the material entering the cellular respiration exits the process before being completely oxidized and thereby providing metabolites that are used to construct biomolecules. For example, intermediates of cellular respiration can be used to synthesize fats and amino acids. When this happens less (or no) ATP energy is obtained because less of the process of cellular respiration is occurring.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.19%3A_Cellular_Respiration.txt
Plants grow out of thin air. While a small portion of their (dry weight) mass comes from the soil, approximately 98% comes from the atmosphere. A typical serving of potatoes is 6 oz = 170 grams. Since potatoes are roughly 80% water a serving of potatoes is about 34 grams of dry weight. This weight is nearly pure starch which has a chemical formula (C 6 H 12 O 6 ). Carbon atoms represent 40% of the weight of starch (or of any hexose or hexose polymer) so that 34 grams of potato has 13.6 grams of carbon = 1.13 mols of carbon. This has been derived from the air which is roughly 400 ppm carbon dioxide. In order to acquire the carbon needed for a serving of potatoes the plant has to extract carbon from approximately 67 thousand liters of air. This photosynthetic ability is even more remarkable because it involves a transfer of the energy of light (electromagnetic radiation) into chemical energy present in the carbohydrate that is produced. The synthesized hexoses have considerably more energy than the raw materials (carbon dioxide and water) used to produce them. TOPICS • Overview • The light dependent reactions • The carbon dioxide assimilation reactions • Photosynthetic constraints: the photosynthesis/transpiration compromise • C4 photosynthesis • CAM photosynthesis Overview Photosynthesis produces carbohydrates. The name reveals what they were originally considered: hydrated carbons (i.e., water added to carbon), but research has revealed that a more accurate description of carbohydrates is reduced carbon dioxide. This is illustrated in the overall equation for photosynthesis: CO2 + H2O —> (CH2O)n + O2 Hydrogen is added to the carbon dioxide, i.e., it is reduced, and hydrogen is being removed from oxygen, i.e., it is being oxidized. Note that, as in the case for cellular respiration, the overall equation is a summary of the net effect of multiple reactions taking place simultaneously. Specifically in photosynthesis, carbon dioxide does NOT react with water. Instead, both water and carbon dioxide are consumed in a group of reactions that ultimately produces oxygen and carbohydrates. The overall reaction as written is exceptional because oxygen is a highly electronegative atom, one that attracts hydrogens strongly, much more strongly than the carbon atom that the hydrogensare transferred to. For this reason, the reaction is 'uphill' and unlikely to occur, while the reaction in the opposite direction is much more likely to occur, with carbohydrates being oxidized by oxygen to produce carbon dioxide and water(see the previous chapter). The last chapter illustrated that cellular respiration (carbohydrate oxidation)is 'driven' by the electronegativity of oxygen; this electronegativity 'pulls' electrons through the inner mitochondrial membrane, ultimately uniting them with oxygen. Thus asignificant question concerning photosynthesis is what pulls electrons away from the oxygen of a water molecule–what has a stronger 'pull' for hydrogensthan oxygen (i.e., what is a more powerful oxidant than oxygen)? Light interacting with the pigment chlorophyll plays a critical role in generating the strong oxidant. Also critical is the structure of the chloroplast which, like mitochondria, consists of a complex structure of membranes separating aqueous compartments. The membranes contain chlorophyll (Figure 1) as well as other pigments and proteins, organized in very specific ways. The light-dependent reactions of photosynthesis Light 's role in photosynthesis is in rearranging specific chlorophyll molecules, causing them to lose electrons (oxidizing them) and thereby making them oxidants that remove electrons from other molecules and ultimately form water.Light is a form of energy and consequently is able to change the circumstances of the material that it interacts with. In particular, light changes the electron configuration of chlorophyll, shifting an electron from its normal position to a situation where it is more likely to escape from the chlorophyll molecule, i.e., after absorbing light, the chlorophyll is more likely to be oxidized. The oxidation of chlorophyll is made even more likely because there is a molecule nearby in the inner membrane of the chloroplast that is capable of accepting the electron. The electron lost from chlorophyll ultimately(after many steps) ends up associated with the carbon of a carbon dioxide molecule, forming carbohydrates. The oxidized chlorophyll molecule (i.e., the one missing an electron) is not a strong enough oxidant to extract electrons from water. But it can act on the' oxygen evolving complex', an enzyme complex that contains four manganese atoms. A chlorophyll lacking an electron is capable of oxidizing one of the four manganese atoms. Afterthis process is repeated three more times and all four of the manganese atoms are oxidized, the molecule is now a strong enough oxidant to act on two water molecules, removing four electrons, one each from the four hydrogens, and producing four protons (H+) and one molecule of O2. The electron lost from chlorophyll follows a path through a membrane similar to the flow of electrons through the inner mitochondrial membrane in the process of 'electron transport' (= oxidative phosphorylation) of cellular respiration, sometimes utilizingsimilar electron carriers. And, similar to some of the steps in oxidative phosphorylation, some of the electron transfers have the effect of moving protons from one side of the membrane to the other. Moreover, the 'splitting' of water, performed by the manganese-containing protein, adds protons to that same side of the membrane. The accumulation of protons on one side of the membrane creates an electrochemical gradient across the membrane. And, because of the electrochemicalgradient, ATP can be synthesizedas it is in the electron transport chain of cellular respiration. But in this case the electrons are not flowing to oxygen. They move first to a different chlorophyll atom, but only after it, like the chlorophyllmolecule described earlier, has been oxidized by the action of light. When this second chlorophyllreceives an electron from the electron transport chain itis converted back to its normal state, and in this state thechlorophyll can once again absorb light, be excited, and lose an electron, thus continuing the process. Note that we have identified two distinct chlorophyll molecules, both of which absorb light and lose electrons. One chlorophyll molecule (called chlorophyll 680) obtains 'replacement' electrons from a manganese containing protein; the second chlorophyll (called chlorophyll 700) obtains replacement electrons from the electron transport chain. The flow of electrons described so far is: water—> manganese enzyme complex—> chlorophyll 680—> electron transport chain —> chlorophyll 700. But they haven 't finished their journey yet! Ultimately these electrons will be reducing carbon dioxide, but before getting to the carbon of a carbon dioxide they are transferred to another important intermediate, NADP+ (Figure 2), a compound very similar to the NAD+that operates in the mitochondria during cellular respiration. Like NAD+, NADP+can accept two electrons and a proton to form NADPH and can lose the same elements to reform NADP+, i.e., it is an electron carrier that (as NADP+) can oxidize compounds and (as NADPH) can reduce compounds. NADP+receives electrons from carrier molecules that receive them from an' excited' chlorophyll 700 molecule. NADPHis a relatively stable molecule and is water-soluble, unlike many of the electron carriers involved in photosynthesis that are soluble only in the lipids of the chloroplast membrane. In total, what we have described so far is a light-driven flow of electrons from water to NADP+, forming NADPH and O2 (Fig 3). The flow occurs in the inner chloroplast membrane and involves two steps where the energy of light is significant in making electron transfer(i.e., redox reactions) more likely. The flow of electrons through a membrane is capable of creating a proton gradient, as it does in the inner mitochondrial membrane. And, as is the case in mitochondria, this gradient in protons can be used to synthesize ATP. This group of reactions, powered by light and creating NADPH and ATP from NADP+, ADP and inorganic phosphate, is called 'the light reactions' and is summarized as: H2O + NADP+ + ADP + iP —> NADPH + ATP + O2 The carbon dioxide assimilation reactions of photosynthesis The products of the light reactions, NADPH and ATP, are used to synthesize carbohydrates from carbon dioxide, a process called carbon dioxide fixation. Carbon fixation fundamentally involves the use of the 'reducing power' of NADPH to reduce carbon dioxide, and the process is summarized in the following equation: NADPH + ATP + CO2—> (CH2O)n + NADP+ + ADP + iP Note that one of the extremely important aspects of these reactions is that it regenerates metabolites needed in the light reactions: NADP + , ADP and iP. Since the supplies of these metabolites are limited , it is critical that they be recycled. The reactions of carbon fixation can be summarized in three steps: carboxylation, reduction and regeneration. Carboxylation Carboxylation describes the incorporation of carbon dioxide into an organic molecule. Interestingly, this can be accomplished without involving any of the products of the light reaction. Carboxylation occurs when carbon dioxide is added to a metabolite called ribulose bisphosphate (RuBP), a five-carbon sugar with two phosphates, in a reaction catalyzed by an enzyme called ribulose bisphosphate carboxylase (rubisco). The resultant 6-carbon compound rapidly breaks down to two molecules of a three-carbon compound called phosphoglycerate (PGA). Reduction Although carbon dioxide has been assimilated , the PGA is not a very useful compound because it is too oxidized. To be useful the PGA needs to be reduced. It can then be used as a precursor molecule to make a variety of biomolecules such as sugars, amino acids, nucleic acids and many others. In addition, the reduced compound can be used to make more RUBP and thus allow more carbon dioxide to be assimilated. The reduction of PGA is accomplished using NADPH and ATP produced in the light reactions of photosynthesis and produces a three-carbon sugar called glyceraldehyde-3-phosphate (G3P). PGA + NADPH + ATP —> G3P + NADP++ ADP + iP Regeneration of RuBP In order to sustain photosynthesis the plant needs to regenerate RUBP, the 5-carbon sugar that is used to acquire CO2. This occurs when RUBP is synthesized from G3P. Obviously, you can 't make a five-carbon sugar out of a three carbon sugar. You might do it usingtwo G3P moleculesbut there would be one' fixed 'carbonleftover. However, the synthesis can be accomplished tidily if one starts with five G3P molecules (fifteen total carbons) and makes three RUBP' s (also 15 carbons). These reactions are called the Calvin-Benson cycle and they require one ATP made in the light reactionsfor each RUBP produced. At the same time, G3P can be used to make six-carbon sugars, in particular glucose and fructose and from them, sucrose, starch, cellulose and a wide variety of polysaccharides. Putting both these activities together, if six molecules of carbon dioxide are fixed by carboxylating six RUBP 's, then 12 G3P can be produced after reduction utilizing12 NADPH and 12 ATP. Ten molecules of G3P canbe used to regenerate the sixRUBP' s and this process requires six more ATP. The remainingtwo molecules of G3P can be used to form a fructose or a glucose. This is how allplants carry out photosynthesis. Each carbon dioxide assimilated requires two NADPH and three ATP. Note that ALL of the above equations are summaries of multiple reactions occurring simultaneously. There is a great deal of chemistry taking place in chloroplasts, although the net effect can be expressed simply as 6 CO2 + 6 H2O —> (C6H1206) + 6 O2 Note that the netequation does not include ATP, ADP, iP, NADP+, NADPH, RuBP, PGA or G3P. All of these reagents are produced at the same rate that they are consumed. The net equation also hides the fact that that actually 12 H2O are needed as reactants and that 6 H2O are products (the net effect is simply the consumption of 6 H2O). Part of the elegance of photosynthesis is that in spite of the myriad of reactions taking place, the net effect is very simple. Another aspect of its elegance is that the product of the process, carbohydrate (CH2O)n, can be used to make all of the diverse chemicals that the plant produces, not just the obvious ones (starch, cellulose, hemicellulose, pectins) but the less obvious ones (amino acids, nucleic acids, lipids, lignin, etc, etc). Moreover, carbohydrates are also used as a source of energy to power these synthetic reactions: In cellular respiration.carbohydrate is consumed to produce carbon dioxide and water while producingATP and NADH, chemicals that are needed in many of the synthetic reactions. Carbon dioxide acquisition, problems and solutions The carbon dioxide fixed in photosynthesis is derived from the atmosphere. Over the last 150 years, atmospheric carbon dioxide levels have increased by over 40% but they are still very, very low at 0.04% or 400 ppm (parts per million;for every million molecules in the air only 400 of them are carbon dioxide). Carbon dioxide enters the leaf by diffusion, but since the maximum concentration outside is 400 ppm and, for most plants, the minimum concentration inside is about 100 ppm. This minimum is the result of the fact that rubisco cannot carboxylate RUBP if carbon dioxide concentrations are below 100ppm, hence the [CO2] can't go below 100 ppm. Consequently, the driving force for diffusion (the difference in [CO2] between the inside and the outside of the leaf) is low and potentially is limiting carbon dioxide flux into the leaf and consequently photosynthesis. Considering the flux equation (Chapter 3), carbon dioxide flux into the leaf can be increased by decreasing the resistance to movement, i.e., by making the leaf more porous to the atmosphere by opening stomates, the regulated pores in the leaf epidermis. Unfortunately for most plants, this exposure to the atmosphere results in water loss, termed transpiration. The lost water needs to be replaced with water from the soil, water that is sometimes in short supply. This leads to what has been termed the photosynthesis/transpiration compromise: to the extent that the plant gains carbon dioxide for photosynthesis, it loses water in transpiration. The low carbon dioxide concentrations in the air aggravate the problem: to allow more carbon dioxide to enter the leaf can open its stomates more fully but this results in the loss of more water. In moist environments, where water is readily available, there is no problem with have very porous leaves (i.e., open stomates), but when water is scarce the plant must balance carbon gain with water loss. Stomatal behavior reflects this compromise: they generally close at night, when photosynthesis is impossible, and during times of drought, when acquiring water toreplace that which has been lost is difficult. The additional carbon dioxide in the atmosphere in the last 200 years probably accounts for the observation that the earth is 'greener' (increased leaf cover) now than 50 years ago. More carbon dioxide can act as a 'fertilizer' and/or allows plants to survive under conditions of low water supply. While there are a number of features that allow some plants to survive under dry conditionsthere is one that directly involves the photosynthetic reactions discussed above. This modified photosynthetic pathway, called the C4 pathway, allows some plants to acquire carbon dioxide while losing less water than a normal plant would. C4 plants concentrate carbon dioxide in a relatively small portion of the leaf, called the bundle sheath cells. The pathwayutilizes two carboxylations.The first occurs in leaf mesophyll cells and utilizesan enzyme, PEP carboxylase, that adds a carbon to a three carbon compound, phosphoenolpyruvate (PEP). PEP carboxylasecan operate at carbon dioxide levels down to around10 ppm, roughly 1/10th of the concentration neededfor rubisco to operate. Thefour carbon compound produced by PEP carboxylaseis transported via plasmodesmata to a sheath of enlarged cells (Figure 4) that surrounds vascular strands of the leaf. Here the four-carbon compound is decarboxylated, releasing carbon dioxide that is subsequently fixed in normal photosynthesis using rubisco. The remaining three carbon fragment is transported back to the mesophyll cells. Using this system of two carboxylations allows plants to produce an environment (the bundle sheath cells) where there is a higher concentration of carbon dioxide. It is only in this location where rubisco is present. Because of the CO2 concentrating mechanism, the [CO2] can be greater than 100 ppm in the bundle sheath cells while the [CO2] of the air inside the leaf is close to is less than 10 ppm. Because the concentration of CO2is substantially lower than in a normal leaf, there can be a greater driving force for diffusion into the leaf. This allows the resistance to be higher (stomates more closed) while still achieving the same amount of carbon dioxide flux (photosynthesis) as a plant that didn't utilize this pathway. Thus the leaf can function photosynthetically while being much less porous to carbon dioxide, thereby losing less water in transpiration. Plants that utilize this dual carboxylation pathwayare called 'C4 plants' because the first carboxylation produces a four carbon compoundas opposed to the pattern in most plants, called C3 plants, where carboxylation produces a three carbon compound. The C4 pathway is outlined below: • in the mesophyll cells of the lea f a three carbon compound, PEP, is carboxylated by PEP carboxylase, to form a four carbon compound • the four carbon compound is transported to the bundle sheath cells that surround the vascular bundles (the veins of the leaf) • the four carbon compound is de-carboxylated, releasing CO 2 and pyruvate, a three carbon compound • the pyruvate is transported back to mesophyll cells where it is converted by into PEP in a process that requires energy in the form of NADPH and ATP • the CO 2 that was released in the bundle sheath is fixed utilizing rubisco in the normal pathway Note that C4 requires all the machinery and reactions of C3 photosynthesis, it is just that there is an additional set of steps prior to the C3 pattern. C4 photosynthesis is less efficient than C3 photosynthesis because it requires more ATP energy. However, it is more efficient in terms of water use and this is of greater significance in drier regions. Also, for reasons that we won't go into, C4 photosynthesis is favored at higher temperatures. There is a second group of plants that utilize the dual carboxylation pathway but in a modified way. They are called CAM plants. CAM refers to crassulacean acid metabolism because t he pattern of behavior shown by this group was first discovered in succulent plants in the Crassulaceae family. CAM plants have several peculiarities: they are usually succulent, i.e., have thick fleshy leaves (Figure 5), or no leaves and a thick, fleshy stem (e.g. cactus). They typically show a marked daily pattern of tissue acidity with the highest acidity at dawn and decreasing acidity during the daylight hours and increasing acidity during the nighttime. Most peculiar is that they open their stomates at night, not during the day whereas most plants only open their stomates during the day when they can photosynthesize. Basically, these plants operate just as C4 plants do but instead of having a spatial separation of the two carboxylations as C4 plants have (mesophyll vs. bundle sheath), they have a temporal separation (daytime vs. nighttime). The initial carboxylation occurs at night when stomates are open. The four carbon compound is an acid and causes tissue acidity to increase. During the day the stomates close, carbon dioxide is provided by the decarboxylation of the four carbon acid and tissue acidity declines. The released carbon dioxide is re-fixed via rubisco to form carbohydrates. Do these plants photosynthesize at night or during the day? It depends on how one might want to define photosynthesis : carbon acquisition is at night but sugar synthesis is during the day. CAM photosynthesis is associated, but not obligately, with succulence. CAM plants are generally found in habitats that are dry, either climatically , e.g., deserts , or because of microhabitat , e.g., epiphytes, plants that are not rooted in the ground but that grow on other plants. E piphytes are often exposed to drought because of their lack of connection to the soil. Cactus and other leafless succulents are commonly CAM plants. CAM photosynthetic rates are very low and CAM plant growth rates are also low. The association of succulence and CAM probably reflects the fact that plants in arid habitats often develop succulence to store water and that succulence is more conducive to CAM because succulent tissues can store more carbon as the four-carbon acid. Patterns of both CAM and C4 photosynthesis reveal that these pathways have evolved multiple times, i.e., the pathways say little about phylogeny. C4, C3 and CAM are mixed within genera, families and orders. Apparently, it is relatively 'easy' for C4 and CAM to evolve.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.20%3A_Photosynthesis.txt
Lessons from eccentrics Sometimes understanding a process is aided by looking at variations on the process. We are studying how organisms satisfy their energetic and material needs. The primary material we are considering right now is carbon, but it generally brings with it hydrogen and oxygen as a carbohydrate molecule. We will get to other materials in a subsequent chapter, but carbon, hydrogen and oxygen make up 95% of most organisms. We will first review the common patterns found in most organisms. We will then consider several groups of organisms whose energy and carbon processing is eccentric in various ways. TOPICS • Review: 'normal' patterns involving matter and energy • Acquiring energy—cellular respiration • Acquiring food—heterotrophs and photosynthetic autotrophs • Acquiring carbon—heterotrophs and photosynthetic autotrophs • 'Eccentric' organisms • Obtaining energy when there is no oxygen • fermentors • using alternative electron acceptors • Chemoautotrophs, making food (carbohydrates) without light • Photoautotrophs, separating matter and energy 'The norm' — the most common processes 1. Acquiring metabolic energy Nearly all organisms utilize the reactions discussed in the chapter on cellular respiration to supply their energetic needs: cellular respiration provides energy in the form of ATP as long as a supply of carbohydrates and oxygen is available. Oxygen is readily available in all terrestrial habitats due to the fact that the atmosphere is 20% oxygen and local depletions are rare because the atmosphere is continually mixed by winds. In contrast, in some aquatic situations (including soils saturated with water), oxygen may be in short supply. Present in such situations are a number of organisms, both prokaryotic (bacteria or archaea) and eukaryotic, that can obtain ATP energy in the absence of oxygen, in a manner that utilizes only the glycolysis part of cellular respiration. Alternatively, there also are organisms, solely prokaryotes, that have mechanisms to make ATP that don't rely at all on the pathways of cellular respiration. 2. Making your own food: energy flow in photosynthetic autotrophs If you consider it closely, the energetics of photosynthetic organisms seems unnecessarily involved: the light reactions produce ATP and NADPH in order to synthesize carbohydrates from carbon dioxide. Then the carbohydrates are broken down in cellular respiration to produce NADH (for our purposes the same as NADPH) and ATP. Why bother making carbohydrates; why not just use the light reactions to obtain 'energy currency, ' ATP and NADH? T o a limited extent, photosynthetic organisms DO satisfy some of their energetic needs directly off of the light reactions, i.e., not all of the ATP and NADPH produced is used to make carbohydrates, some power other processes. But for the most part, the flow of energy in photosynthetic organisms goes from light to ATP and NADPH, to carbohydrates and then back to ATP and NADH; and the amount of energy available is diminished along the way because the energy transfers are not 100% efficient. There are several justifications to this behavior of photosynthetic organisms: • cellular respiration evolved first and photosynthesis appeared as a means to allow organisms to avoid having to 'beg and steal for food' • the need for energetic compounds is continuous but nighttime prevents photosynthesis from happening., ATP and NADH cannot be readily be stored and, while they are constantly recycled, the absolute amounts of ADP/ATP and NADP/NADPH are small. In contrast, carbohydrates can stored and can be present in much greater amounts. • for vascular plants, the below-ground parts need energetic compounds yet can't photosynthesize. The labile nature of ATP and NADH means that they cannot be transported, while carbohydrates can. But we will see that there are some organisms who use light in a strictly energetic role, not using it to make carbohydrates that are subsequently be used to obtain energy. 3. Material needs, specifically carbon As to material needs, for the most part (or you might say 'for most of their parts' !), organisms are composedof carbohydrates, or molecules that are made from carbohydrates, e.g., the amino acids of proteins, which basically consist of a carbohydrate with nitrogen group(s) and occasionally also a sulfur group attached, or fats, which are made from carbohydrates that have had most of their oxygens removed. Thus anyorganism must obtain carbohydrates to construct more of themselves, i.e., to grow. For photosynthetic autotrophs, carbohydrate needs are supplied by photosynthesis but note that whatever carbohydrates directed towards material needs are not available to be used for energetic needs. For heterotrophs, carbohydrate needs are satisfied by appropriating part of what is consumed to whatever 'building projects' a heterotroph may require, but, as a result, reducing the amount of energy that can be obtained. Nearly all organisms are either heterotrophs, whose consumption of organic material (bodies or parts of bodies of organisms) provides them with both energy and with carbon materials or photosynthetic autotrophs who use light to make their own carbohydrates out of carbon dioxide and water and then, like heterotrophs, use this 'food' for both material and energetic needs. However, there are some organisms (all prokaryotic) who are non-photosynthetic autotrophs, i.e., they are able to make carbohydrates without sunlight, using chemicals as an energy supply. There also are organisms, again prokaryotes, whose dietary habits include or require some materials that are not obviously 'organic' , i.e., made by organisms, e.g., formaldehydeor 'plastic' (polyethylene terephthalate). There also are some organisms that 'eat' solely for carbon nutrition and have other mechanisms, that are not based on carbohydrate food, to obtain energy. Below are some groups of eccentric organisms, organisms that differ from the more usual patterns discussed above. Eccentric organisms I: anaerobic organisms—use of alternate electron acceptors Remember that oxygen 's role in cellular respiration is to be an ' electron magnet ', a low point to which electrons flow. Electrons obtained from carbohydrates are transferred to form NAD+ (forming NADH) and from it electrons flow through a series of carriers of the electron transport chain. Oxygen' s role is essential both because it 'drives' the electron flow that in turn allows ATP to be synthesized, and also because the process regenerates NAD + which is required for both glycolysis and the citric acid cycle to continue. I n most of the earth 's habitats, oxygen is plentiful and has been ever since photosynthesis became popular roughly 2 billion years ago. But there are situations where oxygen becomes scarce, generally as the result of cellular respiration coupled with physical factors, e.g., waterlogged soils, that make oxygen replenishment unlikely (Chapter 26). One solution to an oxygen deficit is to find another atom or molecule that will serve the same role, i.e., be a ' downhill situation' to which electrons can flow. There are a number of bacteria that do this, utilizing a number of different molecules as substitutes for oxygen. A particularly important group to plant nutrition is called denitrifying bacteria. They use nitrate (NO3) as the electron acceptor that receives the electrons from NADH produced in glycolysis and the citric acid cycle. In the process, they convert nitrate, a form of nitrogen that most plants can assimilate (i.e., utilize) into dinitrogen gas (N2), a form of nitrogen that plants cannotassimilate (although some can with the aid of a symbiont). Moreover, N2is volatile and can escape the soil; in contrast, nitrate is an ion and consequently unable to leave the soil solution, although the soil solution itself may leave the soil, taking ions with it (i.e., leaching). The process of converting nitrate to dinitrogen gas is called denitrification and in some situations, it causes a substantial loss of nitrogen from soils. Another substitute for oxygen is sulfate (SO42-), which, after accepting electrons, is converted to hydrogen sulfide. As was the case with denitrification, these reactions adversely affect plant mineral nutrition by eliminating a form that the plant can assimilate (sulfate) and putting sulfur into a form that plants are less able to acquire and also a form that is volatile and can be lost from the plant's habitat. Eccentric organisms II: anaerobic organisms—fermentation One solution to a scarcity of oxygen, and one that is the closest to the normal patterns, is a process called fermentation ( 'anaerobic respiration' ) which involves an addendum to glycolysis, the first stage of cellular respiration, and necessarily the elimination of the remaining parts of cellular respiration. The pyruvate produced by glycolysis does not go through the citric acid cycle but instead is used directly or indirectly to accept electrons from NADH, allowing NAD+ (Figure 1), which is essential to glycolysis, to be regenerated. Significant to the fermenting organism is that this allows glycolysis to proceed, although much less ATP is obtained in the process than would be formed if the citric acid cycle and oxidative phosphorylation were able to occur. Also significant is that, while the end products of cellular respiration are water and carbon dioxide, benign substances that are easily dispersed, the end products of fermentation, commonly ethanol or lactic acid, are more toxic and more difficult to eliminate. Fermentation is extremely important in human affairs, both in the production of alcoholic beverages (generally by fungi but occasionally by bacteria) and in the production of desirable food products, e.g., sourdough (Figure 2), sauerkraut, sour cream, yogurt, all of which are influenced by lactic acid production. Some fermenting organisms are facultative anaerobes (i.e., they can live with or without oxygen). Most of these switch to fermentation if oxygen is not present but some carry out fermentation regardless of oxygen availability. Some are obligate anaerobes, meaning that they cannot live in the presence of oxygen. Eccentric organisms III: making food without sunlight- chemosynthetic organisms Most autotrophs ( 'self-eaters' ) make food through photosynthesis and then eat themselves. The energy of light is what makes an unfavorable reaction, the reduction of carbon dioxide by water, more likely. A vague but common description of the process is that some of the energy of light is captured by the plant and stored as carbohydrates. A more specific description is that light is able, in the organized structure of a membrane, to move electrons in a way that NADPH is formed from NADP+using electrons derived from water. In the process, ATP is formed as a result of the electron flow. In the Calvin cycle, these products, NADPH and ATP, can cause carbon to be reduced with electrons provided by NADPH and with ATP promoting the reactions. Light is essential to photosynthesis because it provides a mechanism to obtain NADPH and ATP. But these metabolites can be made in other ways and there are non-photosynthetic autotrophs that do exactly that. They are described as chemosynthetic organisms and they make their own food in ways that do not require light. What is needed is a chemical that can donate electrons to reduce NADP+to NADPH and a membrane system that allows ATP to be synthesized as the electrons flow from the donor to NADP+. Chemosynthetic organisms are uncommon and are only found within bacteria and archaea, but they can be very significant in certain habitats and in carrying out processes that are important to global biogeochemical cycles. From a plant perspective, the most important group of these organisms are the nitrifying bacteria, a group that oxidizesammonia (NH3) to nitrite (NO2), and a group that oxidizes nitrite to nitrate (NO3). The result ofthe two reactionsis that ammonia is converted to nitrate, which is the preferred nitrogen source for most plants, and, unlike ammonia, cannot escape the soil as a gas. Note that both these reactions are oxidations(this is obvious in the NH3to NO2reaction as hydrogens are removed from nitrogen, but is also true in the NO2to NO3conversion). The electrons removed from the nitrogen compound are used to reduce NADP+to NADPH and provide for an electron flow (through a membrane) that allows ATP to be synthesized. These reagents are then used to reduce carbon dioxide in the reactions of the Calvin cycle, 'fixing' it into a carbohydrate form. The nitrifying bacteria, like photosynthetic plants, make their own food and then use it for synthetic reactions (as a building material) or as a source of energy (as it is oxidized to carbon dioxide in cellular respiration). There are other chemosynthetic organisms besides the nitrifying bacteria, including bacteria in deep-sea vents, that utilize hydrogen sulfide as an energy source to fix carbon, methanogens, that use energy from dihydrogen gas (H2) to fix carbon (and at the same time producing methane), and methane 'eaters' that oxidize methane to dinitrogen (N2) while reducing carbon. Many, but not all, chemosynthetic organisms are archaebacteria, although nitrifying bacteria are not. Eccentric organisms IV: separating matter and energy For most organisms 'food' , i.e., what heterotrophs absorb or ingest and for photosynthesizers, the carbohydrates that they make, plays a dual role: as an energy source (producing ATP and NADH) and as a carbon source, providing 'reduced carbons' that are used in a variety of biosynthetic reactions that ultimately can make the organism bigger. The pathways for the two processes are initially the same but if the carbon is to be utilized as building material much less energy is obtained and less carbon dioxide is produced. If used for energy, 'food' i.e., carbohydrates, ends up as carbon dioxide and the amount of energy obtained is maximal; if used for material, the carbons of the carbohydrate end up in any one of the thousands of biomolecules found in the organism, in fats, proteins, nucleic acids, etc., and the amount of energy obtained is reduced compared to what would happen if all the carbons were totally oxidized to CO2. However, there are some organisms who have distinct pathways for obtaining energy, pathways that generally don 't involve carbon at all and their' eating 'is solely to obtain carbon atoms for biosynthesis. The easiest group to understand is photoheterotrophs. They include both archaea and bacteria that are capable of using sunlight in a process that allows them to synthesize ATPbut not in a manner that produces carbohydrates.Thus they must' eat food'(absorb carbohydrates/organic molecules) NOT necessarily for their energetic needs (i.e., to supply ATP) but rather to satisfytheir carbonneeds. This lifestyle is found in a few Archaea, for example, Halobacteriumwhich possesses a pigment, bacteriorhodopsin, related to the rhodopsinfound in vertebrate eyes. Bacteriorhodopsin is a membrane-spanning protein that can acquire protons in the cytosol, change conformation due to the absorption of light, and release protons on the outside of the membrane (Figure 3). Protons then flow into the cell, down their electrochemical gradient and, as is the case in the light reactions of photosynthesis and oxidative phosphorylation in cellular respiration, the proton movement causes ATP to be synthesized from ADP and inorganic phosphate. Most of the photoheterotrophs are bacteria that use a form of chlorophyll to absorb light energy and again create a proton gradient that can be used to synthesize ATP but need a source of reduced carbon for material needs. In a similar manner there are chemoheterotrophs, organisms that 'eat' for their material (i.e., reduced carbon needs) but generate ATP by chemical means that doesNOT involve the cellular respirationand oxidation of carbohydrates. Table 1 below summarizes the different modes of acquiring matter (carbon) and energy (reducing power and ATP). Table 1. energy carbon source groups heterotroph energy (reducing power and ATP) from oxidation of collected biomolecules carbon (reduced) from collected biomolecules all animals, all fungi, slime molds, water molds, some dinoflagellates, most bacteria, most archea photosynthetic autotroph energy (reducing power and ATP) from oxidation of self-made biomolecules carbon from carbon dioxide reduced in photosynthesis and used to synthesize biomolecules all plants, green algae, red algae, brown algae, diatoms, some dinoflagellates, cryptomonads, cyanobacteria, green sulfur bacteria chemosynthetic autotroph energy (reducing power and ATP) from oxidation of self-made biomolecules carbon from carbon dioxide reduced in photosynthesis used to synthesize biomolecules some, but not many, bacteria (nitrifying bacteria, sulfur-oxidizing bacteria, iron-oxidizing bacteria, some methanogens) and some archaea (methanogens). photoheterotroph energy (some reducing power but mostly ATP) from light-driven reactions carbon (reduced) from collected biomolecules Some, but not many, archaea (Halobacterium), some green non-sulfur bacteria, some purple non-sulfur bacteria. chemosynthetic heterotroph energy (reducing power and ATP) from electron flow driven by inorganic sources of electrons carbon (reduced) from collected biomolecules some, but not many, bacteria (Beggiatoa) and some archaea (methanogens).	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.21%3A_Metabolic_diversity.txt
In order to grow, an organism has to acquire materials to make itself bigger. These materials are sometimes considered 'food' (Figure 1-2) or may be described as nutrients and this chapter considers what nutrients are required by organisms and how they are acquired. We have already considered three nutrients, carbon, hydrogen and oxygen that play a role in the energetics of organisms, but they also are important materially. Organisms are built of more than just these three and need others in order to grow. The acquisition of required materials (i.e., organismal nutrition) is something that distinguishes most of the organisms considered in this book from animals. Nutrition is highly significant, not just to the success (i.e., growth and reproduction) of organisms but also to ecology and to interactions with other organisms and specifically agriculture. For reasons that should be obvious already and that are elaborated on further in this chapter, the nutrition of organisms is strongly affected by their lifestyle, in particular, whether they are an autotroph or heterotroph, and also by their evolutionary history. TOPICS • Chemical (molecular) composition of organisms • Chemical (elemental) composition of organisms • How nutritional requirements are met by heterotrophs and autotrophs • Mechanisms of nutrient acquisition • Vitamins Chemical (Molecular) Composition of Organisms One of the properties that define organisms is their chemical composition, both in terms of compoundsand in terms of elements. The compounds that make uporganisms aredistinctive in comparisonto the world they live in, with most of the chemical compounds(biomolecules) being unique to living things, although some (e.g., silicon dioxide, calcium carbonate) can be produced in non-living situations. A general classification of the molecular composition of organisms is shown below. Table 1. The chemical compounds (molecules) of organisms type chemistry elements examples functions carbohydrates (C6H12O6) C, H, O glucose, fructose metabolites, energy sources carbohydrate polymers polymers of simple sugars C, H, O starch, cellulose, hemicellulose, pectin energy storage, cell wall components amino acids carbohydrate with an NH2 group C, H, O, N, S glycine, leucine, aspargine components of proteins, means of transporting nitrogen atoms proteins polymers of amino acids C, H, O, N, S rubisco, DNA polymerase enzyme catalysts, structural molecules lipids chains of carbon and hydrogen, often with a phosphate attached. C, H, P fats, phospholipids, glycolipids, partitioning the cell into compartments, energy storage in seeds nucleiotide nitrogenous compound attached to sugar plus phosphate groups C, H, O, N, P ATP, GTP energy metabolites, components of nucleic acids nucleic acids polymers of nucleotides C, H, O, N, P DNA, RNA information storage and processing Elemental Composition of Organisms The elemental composition of organisms reflects their molecular composition. Typically around 98% of the mass of any organism is composed of four elements, C, H, O, and N. But other elements are present and many of these are 'essential' , i.e., the organism must have them in order to survive, grow and reproduce. Table 2 lists those elements that are considered essential for all organisms and are also found in high enough concentrations to be considered 'macronutrients' . Table 2. Essential 'macronutrients' , elements considered to be essential (with known required roles) and needed in 'large amounts' , typically more than 0.1% of the dry weight of an organism. C (carbon) carbohydrates, lipids, proteins H (hydrogen) everywhere!! also important when present as protons (H+ ) O (oxygen) carbohydrates, proteins, electron acceptor in respiration N (nitrogen) amino acids (proteins), nitrogenous base of nucleiotides, thus in nucleic acids; also present in metabolites such as ATP, NAD, NADP, and many others P (phosphorus) phospholipids, nucleic acids, ATP, and others K (potassium) used exclusively as a cation unbound to an anion; important in effecting changes in membrane charge and influencing water diffusion Mg (magnesium) present in chlorophyll, an important ion in many enzyme reactions Ca (calcium) A component in cell walls often serves as a messenger in signal cascades, often plays a regulatory role within cells S (sulfur) found in two amino acids, and thus in proteins; also a component of several important metabolites, including some considered as vitamins Fe (iron) found in cytochromes and other iron-sulfur proteins important in the electron transfer processes of both photosynthesis and respiration Note that sodium (Na) is not on the list. Sodium is required by animals, where it plays a role in membrane charge, electrolyte balance and nerve transmission. But it is not required by most plants and fungi. Sodium is common in the environment and is absorbed by plants. Typical sodium concentrations in plants are high enough, in spite of the fact that it is not required, to supply herbivores and other heterotrophs with sodium sufficient for their needs. In addition to macronutrients, organisms require additional elements but only need very small amounts; these are called micronutrients. Table 3 lists micronutrients known to be essential in plants and thought to be essential in all organisms. Table 4 lists micronutrients that are not essential to plants but are thought to be essential to at least some organisms. Table 3. Essential 'micronutrients' , elements considered to be essential (with known required roles) and needed in small amounts, typically less than 0.1% of the dry weight of an organism. Cu (copper) co-factor in multiple enzyme systems; in normal (oxygenic) photosynthesis, copper is involved in electron transport between the two photosystems Mn (manganese) a component of several essential enzymes and also in the 'oxygen-evolving complex' of the oxygenic photosynthesis process found in plants and cyanobacteria Zn (zinc) required by several enzymes and also is a component of regulatory proteins involved in gene expression B (boron) probably plays a role in several enzyme systems; also present in plant cell walls, important in plant cell elongation Cl (chlorine) important as an electrolyte; in plants, chlorine is also involved with water splitting and the oxygen-evolving complex of oxygenic photosynthesis Ni (nickel) involved several essential enzymes Mo (molybdenum) involved in several essential enzymes; in plants, Mo is essential to processes involved with nitrogen assimilation Table 4. Common micronutrients required by some or many heterotrophs but not required by plants. The first four (sodium, iodine, cobalt, selenium) have known roles for substantial numbers of organisms. Na (sodium) not required for most plants but commonly present in them; required by animals where it plays a role in electrolyte balance, membrane charge and nerve transmission I (iodine) a component of thyroid hormones, not required by plants Co (cobalt) a component of vitamin B12, which is essential for animals and many protists (including some photosynthetic protists), also required by bacteria and cyanobacteria that carry out nitrogen fixation Se (selenium) part of several enzymes, including some that eliminate oxidant molecules, required by few plants where it is generally is a component of antiherbivore compounds Vn (vanadium) component of antioxidant enzyme found in diatoms and red, brown and green algae; needed in nitrogen-fixing bacteria and cyanobacteria Cr (chromium) essential role debated, some cite a role related to insulin Fl (fluorine) essential role debated but is known to strengthen bones and teeth As (arsenic) essential in rats and mice; essentiality not established for humans, role not known Sn (tin) essential in rats and mice; essentiality not established for humans, role not known Tables 2 and 3 list the 17 essential elements required by plants. The elemental composition of plants, andorganisms in general, is not reflective of the abundance of elements in the atmosphere (80% nitrogen, 18% oxygen) or the solid earth (46% oxygen, 28% silicon, 8% aluminum, 5% iron ~ 3% calcium, sodium, potassium, magnesium) or dissolved in the water (chlorine 19.1 g / kg of seawater, sodium 10.7 g/kg, magnesium 1.3 g/kg, sulfate 2.7 g/kg) ). Clearly, organismsare not in equilibrium with their environment and somehow acquire elements to higher levels than found in their environment. Acquisition of nutrients —how nutritional needs are met For the groups that are covered here, nutrition is strongly influenced by lifestyle. For heterotrophs, their chemical composition and how they acquire it arerelatively easy to explain — 'you are what you eat;' the composition of heterotrophs reflects their absorption of biological molecules that are derived from the organisms that they ingest. And since all life is made of the same materials, the consumption of biomolecules by heterotrophs should allow heterotrophs to acquire the material required to make more of themselves and consequently to grow. Recall that some heterotrophs are 'ingesters' (e.g., lions, caterpillars, humans) swallowing organisms or parts of organisms into a tube inside their body where digestionoccurs that breaks down the large biological molecules (e.g., proteins) into smaller ones (amino acids) that can be absorbed bythe organism. Other heterotrophs are 'absorbers' (e.g., fungi, many bacteria, water molds) and do the digestingoutside of the body. Thebasic process is the same in both groups: large molecules are broken down into smaller ones that can be absorbed. Three key factors influence the nutrition of heterotrophs: food choice (what they choose to eat), digestive abilities (what biomolecules they can break down into smaller units, and absorptive abilities, what molecules they can transport into their cells. These factors vary tremendously, especially within the archaea, bacteria and fungal groups. Also note that for absorbers, digestion may be partly or largely the result of other organisms living in the same habitat. A similar situation exists within ingesters because they usually harbor organisms within their gut track that participate in digestion. Note that for heterotrophs the acquisition of the nutrients shown in Table 4 may be problematic because the element may not necessarily be in the ingested food, e.g., iodine is not required by plants so heterotrophs may not necessarily acquire it from the food they eat. The same is potentially true for sodium, but in practice, most plants contain sodium even though they do not require it because sodium is common in the environment. The nutrition of autotrophs is very different. They need the same elements that heterotrophs do (Tables 2 and 3) but they do not acquire these in a 'prepackaged' form. Moreover, many autotrophs can 't utilize nutrients in a prepackaged form. While some photosynthetic protists (algae) and many photosynthetic prokaryotes do have the ability to absorb organic compounds, plants have no ability to ingest materials (i.e., no mouth and digestive tract), nor can they break down large organic molecules outside their body, or even to absorb breakdown products like amino acids, should they happen to be present. In fact, thematerials that plantsabsorb are not' organic '(= biological), they are elements or simple compounds found in the environment, such asCO2(carbon dioxide), NO3(nitrate), SO42-(sulfate), PO4(phosphate)or elementalions (e.g., Ca2+, Cl). Autotrophs have the ability, which heterotrophs lack, of transforming these elements and simple compounds into biological compounds. By far the most extensiveprocess is the conversion of carbon dioxide and water into carbohydrates, but many other reactions are essential: adding nitrogen groups to carbohydrate molecules to produceamino acids, synthesizing nucleotides, nucleic acids, assorted metabolites (e.g., NADP+, assorted vitamins), etc. This process is made all the more challenging by the fact that the raw materials used by autotrophs are all dilute and scattered in the environment. This is in contrast to the materials that heterotrophs consume, where allthe needed materials are usually found together in' food'. In order for autotrophs to acquire the minerals, they need these minerals must be in a form that dissolves in water and in a form that autotrophs can acquire (i.e., will pass through a membrane or through a channel/carrier protein imbedded in a membrane).For aquatic autotrophs, all of the nutrients that they acquire come from the solution they are immersed in. For terrestrial autotrophs (plants), carbon is the sole element acquired directly from the air, as carbon dioxide. All other nutrients come from the 'soil solution' , the water held in the soil. Not only must nutrients be in soil solution they also have to be in a form that the organism can assimilate. For example dinitrogen gas (N2), readily dissolves in water, and readily enters into organisms, but it can only be assimilated, i.e., incorporated into an organic form, by a relatively small group of organisms in both the Bacteria and Archaea groups. Plants, other eukaryotic autotrophs, and most prokaryotic autotrophs cannot assimilate N2and need to acquire nitrogen as either ammonia or nitrate. The role of heterotrophs in autotroph nutrition A common bumper sticker used to be 'Have you thanked a green plant today?' —the message being that green plants are essential to all life on earth because they form the base of the food chain. A comparable message is also significant— 'Have you thanked a heterotroph today?' As essential as green plants are, they in turn are dependent on heterotrophs. Heterotrophs are essential to autotrophs (and thus to heterotrophs themselves, i.e., this is circular) because heterotrophs put nutrients into a form that autotrophs can use. Without heterotrophs, green plants would be unable to acquire the carbon and other elements that they require. When viewed by autotrophs the general role of heterotrophs is to break down organic material into simple 'inorganic' compounds that they can utilize, a process described as 'mineralization' . Because nutrients are diluted in the environment and concentrated in organisms, absorption of elements involves accumulation—the concentration of elements inside organisms. And this accumulation requires energy and is an 'active' process. Somenutrients are absorbed in the charged (ionic) state.Since the inside of the cellis negatively charged relative to the outside of the cell, nutrients that are cations (positively charged) may actually be accumulated by moving down their electrochemical gradient. In such a situationthe accumulation might be considered 'passive' (down an electrochemical gradient) but this is ignoring the fact that energy is requiredto make the insideof the cell negatively charged. For both autotrophs and heterotrophs, a variety of cellular mechanisms account for the absorption of nutrients. They include the following: • diffusion across the membrane:since most nutrients are charged and since charged molecules do not readily penetrate the phospholipid bilayer of the cellular membrane, this is relatively rare; however, occasionally it can account for the absorption of uncharged molecules, e.g., ammonia (NH3) • passive diffusion through channels:Cations are sometimes acquired by diffusion down an electrochemical gradient through protein-structured 'pores' in the phospholipid bilayer. Generally, these pores are selective and only allow certain cations to pass through them. • pumps : some nutrients move across the membrane in a process that requires an energy source, typically ATP. This movement involve s proteins (enzymes) whose conformation changes in response to some process that is energetically driven. Generally, pumps account for the accumulation of nutrients against an electrochemical gradient, but they could also could also account for enhanced movement of cations down their electrochemical gradient. • coupled ion transport:Since cells are negatively charged, the movement of charged molecules can be coupled to the passive movement of cations into the cell or anions out of the cell. Most commonly, anion movement into the cell is coupled with the inward movement of protons. Coupled ion transport also involves proteins and generally is quite specific with regard to nutrients, i.e., there are separate carriers for different ions. Absorption mechanics are significant because all of the elements required by autotrophs may actually become toxic (with levels high enough to inhibit growth) if they become overly abundant in the environment (e.g., chlorine toxicity in saline soils). It is also significant that autotrophs often take up elements that they do not require and this may be beneficial (e.g., sodium) or detrimental (e.g., arsenic) to the heterotrophs down the food chain. Acquisition mechanisms for essential nutrients Carbon For all autotrophic organisms carbon is acquired as carbon dioxide, either from the atmosphere ordissolved in water. Carbon dioxide dissolves in water and then can be transformed into a variety of compoundsby (mostly) abiotic chemical reactions. The most significant reactions are the formation of carbonic acid from carbon dioxide and water; the formation of bicarbonate ion as carbonic acid loses a proton; the formation of carbonate ion as bicarbonate ion loses a proton. Carbon is readily exchanged between these pools and all of them can be considered 'biologically active' forms of carbon. H 2 O + CO 2 — > H 2 CO 3 (carbonic acid) H2CO3 —> H++ HCO3 (bicarbonate ion) HCO3> H++CO32- (carbonate ion) For heterotrophic organisms, carbon is acquired in a variety of biomolecules: carbohydrates, proteins, lipids. The exact mix of compounds depends on the dietary preferences of the organism. Heterotrophs can only absorb relatively small molecules (simple sugars, amino acids, nucleotides) and therefore often have to break down polymers (e.g., starch, proteins) before absorption actually occurs. Once inside the cells of the organism, these small molecules (e.g., glucose, amino acids) may beoxidized in cellular respiration, decomposing them to carbon dioxide, water, and (for amino acids) some nitrogenous compounds like ammonia. Absorbed nutrients may also be 'reassembled' into polymers or metabolites like NADHthat are used for growth or to replace moleculesthat have been broken down. Hydrogen For autotrophs , hydrogen is is acquired in water molecules and occasionally in other compounds. For heterotrophs , hydrogen is acquired in water, carbohydrates, proteins and lipids. Oxygen Oxygen plays two roles in organisms: a structural role, being a part of most biomolecules (carbohydrates, proteins, nucleic acids) and a dynamic role, being an essential reactant in cellular respiration that is subsequently lost as water. For autotrophs, oxygen for the structural role is acquired as carbon dioxide that is incorporated into carbohydrates and subsequently into other important biological molecules. For heterotrophs, structural oxygen is acquired in the food that they consume. For both autotrophs and heterotrophs, oxygen for respiration is acquired as molecular oxygen (O2) which, for terrestrial organisms, can be acquired directly from the atmosphere where it accounts for nearly 20% of the air's molecules. In aquatic systems, oxygen is obtained from the water where it usually is present as a dissolved solute. Oxygen concentrations in water are variable, depending primarily on biological activity. Photosynthetic organisms produce oxygen but this effect is limited to the region of the water column that receives light. Throughout the water column, oxygen is consumed by all aerobic organisms. How much the oxygen levels are lowered by this action depends on the amount of living things, their rate of oxygen consumption (this is a strong function of temperature), and the rate of oxygen delivery to the system. Nitrogen For heterotrophs, nitrogen is obtained from the food that they eat, primarily from proteins, but also from nucleic acids and nucleotides. Some fungi, bacteria and archaea can acquire nitrogen as nitrate (NO3) or ammonia (NH3)/ammonium ion (NH4+). For plants, nitrogen is always acquiredas nitrate orammoniadissolved in water. Although nitrate and ammonia are considered to be 'inorganic' molecules they are almost always produced from biological molecules as a consequence of the following biological processes: ammonificationis the production of ammoniaand can be considered to be a type of 'decomposition' . Itoccurs as amino acids are used as a source of energy; the carbohydrate component of amino acids isoxidized in cellular respiration and the amino group is either directly excreted as ammoniaor as some other small nitrogen-containing molecule (urea, uric acid). All heterotrophs participate in ammonification, either by directly producing ammonia, or indirectly by producing compounds like urea and uric acid that are readily converted (mostly by bacteria) to ammonia. How much a particular heterotroph participates in ammonification depends upon their diet, specifically how much protein they consume. nitrification is the production of nitrate. Nitrate is produced by the action of a small group of chemosynthetic organisms (previous chapter) that use ammonia as a source of energy; as ammonia is oxidized to nitrate , an electron flow is created that can result in the synthesis of ATP. Additionally, some chemosynthetic organisms use the reducing power of ammonia to reduce carbon dioxide to carbohydrate. The process first involves the conversion of ammonia to nitrite (NO 2 ) by one group of bacteria followed by the conversion of nitrite to nitrate (NO 3 ) by a second group of bacteria. Ammonia is uncommon in most soils because it is usually quickly converted to nitrate by nitrifying bacteria and also because it is volatile and can be lost from the soil by vaporization unless acidic soil conditions transform it to ammonium ion, which is not volatile. Most plants take up nitrate more readily than ammonia, but a few prefer ammonia. Ammonia is a toxic compound and is rapidly metabolized by plants (and other organisms) if it is absorbed. Phosphorus For heterotrophs , phosphorus is obtained as phospholipids, nucleic acids and other metabolites in the food that they acquire and break down. For autotrophs, phosphorus is generally acquired as the phosphate anion (PO 4 ) which is made available by the action of heterotrophs who break down organic material and release phosphate. Phosphate is a key nutrient in aquatic systems and often regulates the amount of autotroph biomass and primary production. Calcium, magnesium and potassium These ions play multiple roles in organisms, generally being present as dissolved cations but occasionally being permanent parts of molecules (e.g., magnesium is part of the chlorophyll molecule). F or heterotrophs, these elements are obtained as cations dissolved in the cytosol of the cells that they digest. Plants absorb Ca 2+ , Mg 2+ and K + as cations dissolved in the soil solution. These ions are generally derived from the breakdown of organic material (decompositions) and as soil minerals are weathered (dissolved) and put in solution. Fungi are unusual compared to most eukaryotes because they generally require much lower levels of calcium. Sulfur For heterotrophs, sulfur is obtained primarily from protein digestionreleasing the two sulfur amino acids, cysteine and methionine and their subsequent absorption. While some heterotrophs can utilize either cysteine or methionine as a sulfur source, humans and some other animals cannot synthesize methioninefrom cysteine and therefore methionine must be obtained in theirfood. For autotrophs, sulfur is acquired as the sulfate anion (SO4) and subsequently needs to be reduced to produce all biologically active forms. Iron For heterotrophs, iron is obtained from organic material, where it is a universal cellular constituent, albeit in low concentrations. Iron absorption into the heterotroph is sometimes deficient and iron deficiencies may result from an inability to absorb rather than from a lack of iron in food. For plants, iron is acquiredas boththe ferrous (Fe+2) or ferric (Fe+3) ion. The ferrous ion is much more soluble in water but is much less common under normal (high oxygen) conditions which causeiron to be inthe more oxidized ferric state. In this state, the availability of iron is strongly influenced by pH with less available iron at higher pH 's (over 6). Consequently, although iron is very common in soils it is often unavailable to plants because it is not in solution, especially at high pH' s; however if the soil becomes waterlogged and anaerobic, iron becomes readily available in the ferrous state and may become toxic. Sodium Sodium is unusual because it is not an essential element for most plants but it is essential for animals. In spite of not being essential for plants, sodium is generally present in plants amounts sufficient to supply the needs of most heterotrophs. Sodium is common in most water sources, even 'fresh water' sources and sodium is essential for CAM and C4 plants. Micronutrients (molybdenum, chlorine, boron, copper, zinc, manganese, nickel) For both heterotrophs and autotrophs these elements are absorbed either in elemental ionic forms (Zn 2+ , Mn 2+ , Cu 2+ , Ni 2+ , Cl ) or as simple molecules (MnO 4 2- ), H 3 BO. Vitamins A final nutritional category is 'vitamins' . These are molecules, not elements, that play a critical role in specific chemical reactions and, for a variety of reasons (inability to synthesize, inability to absorb, metabolic disorders), may be deficient. Bacteria and archaea, whether autotroph or heterotroph, do not have vitamin requirements, generally because they make these metabolites themselves from the 'raw materials' that they require, or, less commonly, they have alternative biochemical pathways that avoid thevitaminrequiring step. (There are, however, multiple bacterial strains found (or developed) to have specific vitamin or other nutritional requirements and these turn out to be very useful tools for research). Among eukaryotes, plants, like prokaryotes, generally have no vitamin requirements, generally because they can synthesize vitamins along with the many other molecules that they manufacture. In contrast, eukaryotic heterotrophs often do have vitamin requirements, i.e., molecules that they cannot make and therefore that they must acquire from the food that they eat. For example, humans, and a few other animals, require vitamin C because they are unable to synthesize it. Plants and most animals, including cows, make vitamin C. But although cows can make the vitamin, meat provides very little to consumers, so a diet containing fruits and vegetables is important in preventing vitamin C deficiency in humans Among other roles, vitamin B3 (niacin) is a precursor to the metabolites NAD and NADP discussed earlier. Although humans and other animals can make niacin from the amino acid tryptophan, they can develop niacin deficiencies if eating a diet low in niacin and tryptophan. Plants can make both niacin and tryptophan from mineral elements and the carbohydrates produced in photosynthesis. They therefore never have niacin deficiency and can provide these nutrients to heterotrophs. The vitamin requirements of heterotrophs apparently reflect a loss of metabolic abilities through evolutionary time, presumably the result of the fact that the vitamins are generally present and in the organic matter that is consumed. Plants, who do no consuming, must manufacture any required metabolite. Surprisingly, a number of autotrophic algae groups do have vitamin requirements for several B vitamins. It probably is significant that these organisms are aquatic and B vitamins are water-soluble and hence commonly found in aquatic environments, the result of decomposition of organic matter.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.22%3A_Nutrition_and_nutrients.txt
If people had a longer life and a larger perspective more would appreciate that soils (Figure 1) are living things and that they demonstrate many of the properties that we associate with organisms. They are dynamic entities that develop through time in an orderly and predictable way and are characterized by a number of processes that involve matter and energy transformations. However, they do not have boundaries in space or time and , since they are not discrete , they do not reproduce. In an ecological sense, they are communities possessing a variety of living components that collectively, in conjunction with physical processes, carry out a variety of functions. Observers often consider soils to be an abiotic medium in which organisms grow, but the actions of the organisms in the soil are often so intertwined with the physical processes occurring there that it is pointless to try to separate them, other than to acknowledge that the relative importance of the activities of organisms in the soil vs. the physical processes varies greatly between different types of soils. Although most consider soils to be an assemblage of debris (i.e., 'dirt' ), soils are better understood if viewed as being composed of the four basic elements that the Greeks and other cultures described: earth, air, water and fire. The earthis a solid material, derived both from inorganic sources, ultimately rock, and from organic sources, pieces of material that are derived from living things. Waterpervades the soil as its adhesive properties assure that it sticks to all the particles. Depending on the amount of water, airpermeates the soil to a greater or lesser extent. And finally, the fireof the soil is the living creatures, mostly small and highly dominated by fungi and bacteria but also including a variety of invertebrates, protists, occasional vertebrates and a dynamic population of plant roots. All four of these components are critically important to plants: the solid material is the ultimate source of most nutrients and provides surfaces where significant events occur; water is needed by all plants and also is the medium from which they obtain nutrients; air provides the oxygen that plants and many other living things in the soil require; the living things in the soil carry out a variety of processes significant to plants, in particular, the degradation of large molecules into units that can dissolve in the solution and be available to plants. Each of these four components, earth, water, air and fire, interacts with the others: living things change the gas composition, the gas composition affects living things; water moves and organizes the solid phase; the solid phase controls the water content; the solid components change water chemistry;changesin water chemistry can add or subtract tothe solid phase. Soils are a web of interactions, and while components can be listed, the whole is much more than the sum of the pieces and the functions of soil are hard to attribute to specific components. The D's of Dirt—Deeds, Dynamic, Diverse Biologists (and non-biologists!) should be aware of three key aspects of soils: what they do—their deeds ; how they are dynamic , and how diverse they are. TOPICS • Deeds of the soil — what soils can do • Dynamics of the soil — how and why soils change • Diversity of soils Deeds What do soils do? A great deal more than we can enumerate here but some of the most important to organisms, populations and communities are: holding water, holding nutrients, and changing the chemistry of the water in the soil. Soils hold water , usually very significant quantities of water , and this vastly enhances the possibilities for life outside oceans, lakes and rivers. While some living things exist in areas with no soil (i.e., on bare rock) , their activities are strongly modulated by the availability of water, and water is only available when it is raining and for a short period thereafter. Unless rain is frequent , the activity of living things is limited because organisms require water and when it is not available they must shut down, becoming inactive and thereby able to tolerate the dry conditions. In contrast, a soil holds and stores water, greatly prolonging the time that water is available to living things and making possible a vast diversity of lifestyles and organisms that would not be present otherwise. Because the soil can absorb and store water, soil s moderate the pulses of water flowing overland when precipitation occurs, diminishing the erosion and flooding that would occur without a mantle of soil. This fact is very apparent if one is in a large paved parking lot when rain is falling, or on a parcel of land once the soil has been filled to capacity and can no longer absorb water , or in a situation when rain is falling faster than the soils can absorb. The amount of water held by a soil is greatly influenced by the size of the particles that make up the soil. A term that describes the sizes of particles in the soil is texture . Most soils are composed of particles with a variety of sizes, but soils made up mostly of very small particles are called clay soils, and soils composed primarily of larger particles are called sandy soils. There are two main reasons why texture affects the amount of water held by a soil. The first is obvious but often not that significant: texture affects pore space : the total volume between the solid particles which is where water can reside. Obviously, a soil with more pore space has more volume available for water. Surprisingly, the total pore space of different textured soils is not all that different: sandy soils have about the same total pore space as clay soils. What is different between clay soils and sandy soils is the size of the spaces and this turns out to be particularly important. Clay soils have many small spaces where water can reside while sandy soils have fewer spaces for water but they are considerably larger. Consider two soils that occupy the same volume, both with 'no' water (although it turns out to be impossible to get rid of all the water). The soil can be filled with water so that all the pore space (spaces between the solid particles) are occupied with water. A soil at this state is said to be saturated (Figure 2) and one could determine the total pore space by keeping track of how much water had to be added to the soil to saturate it. A soil can only be saturated if it is in a closed container, one that gravity cannot pull water out of. If holes are opened in the bottom of the container then the force of gravity can pull out water. Significantly, gravity cannot pull out all of the water, but it can pull out some of it. It turns out that gravity can remove much more water from the sandy soil than from the clay soil. This is because water is held in small pores much more tightly than water held in large pores and the force of gravity is only strong enough to pull water from the largest pores. A soil holding all the water that it can against the force of gravity is said to be at field capacity (Figure 3). To remove more water from the soil one needs to add plants. One could also wait for evaporation to remove more water but this is generally much slower than allowing plants to do it and allows one to see another critical point in soil moisture. Plants, like gravity, can only remove some, but not all, of the water remaining in the soil. This is because eventually the soil becomes so dry that plants cannot survive. Soil at this degree of dryness is said to be at a permanent wilting point (Figure4). Plants do differ in how much dryness that they can tolerate but most plants, in particular crop species, have quite similar tolerances. Both field capacity and permanent wilting point define degrees of dryness in the soil and actually can be defined in terms that relate to the force holding water in the soil and to a thermodynamic term defined as water potential. And the amount of force present is related to the size of pores holding water: as it dries the water remaining in the soil is in smaller and smaller pores and is harder and harder to remove. Knowing how much water is in a soil is not particularly useful: a clay soil with 15 grams of water per 100 grams of soil(percent moisture = 15%) is so dry that few plants could live in it. A sandy soil with a water content of 15% may be saturated and gravity could remove water from it. Consequently, the 'wetness' of a soil is monitored not by water content (percent moisture) but in energetic (water potential) terms. The amount of water held by a soil between its field capacity and the permanent wilting point is important because it represents the storage capacity of the soil that is useful to plants. Water added to a soil that is a field capacity will drain out of the soil due to gravity (how quickly this happens depends on the texture of the soil). Water held in the soil below the permanent wilting point is unavailable to (most) plants. Sandy soils dry out quickly because they store little water between field capacity and permanent wilting point. Clay soils can hold much more but because water moves slowly through the clay soils are generally not desirable for agriculture and the best agricultural soils are described as loams, with a mixture of sand and clay. In addition to water, soils also hold nutrients . Remember that all the nutrients that plants acquire, with the exception of carbon, come from the soil solution. Thus the water held by the soil represents not only a supply of water but also a supply of nutrients. Exactly how much of each nutrient (and other solutes) are present depends partly upon the amount of water but also on chemical interactions in the soil. A simple view of soil chemistry is that nutrients can be in one of two situations: solids (i.e., part of the soil particles) or solutes, dissolved in the water. T here are a variety of mineral salts that can disassociate, putting ions in the soil solution , e.g., Na + and Cl . The reality is more complex. T he soil is a three-phase system with chemicals not just in the solid-state (precipitated state) and in solution as dissolved ions. The third phase in between these two described as 'ion exchange surfaces' that is the result of solid components of the soil breaking down (weathering) and losing (generally) cations, producing a negatively charged surface that can electrostatically bind cations, forming a 'cation exchange surface' . The movement of ions from the soil solution onto this surface is less specific and more dynamic than the precipitation of ions from the soil solution into specific minerals. While precipitation to a specific minerals requires a match between cation and anion, any positively charged ion (cation) can associate with a cation exchange surface. Which cations are actually held depends on their abundance in the soil solution, their size, and the amount of charge. For plant nutrition, the key parameter is abundance in the soil solution. Consider a soil solution in equilibrium with a cation exchange surface and consequently having a certain ratio of Na + to K + in the soil solution. If plant roots remove K + from the soil solution, the lowering of the K + concentration in the soil solution increases the Na + /K + ratio and causes Na + ions to be exchanged for K + ions on the cation exchange sites. This replenishes the supply of K + in the soil solution. A common application of cation exchange surfaces is in water softeners, devices that remove the calcium and magnesium from water and replace them with sodium, thereby making the water 'softer' . This results in a number of favorable consequences, e.g., more effective washing with soaps. A water softener operates by moving water through an ion-exchange 'column' that has been 'loaded' with Na + (i.e., all the ion exchange sites are filled with Na + ). As the water moves through the column the Na + replaces the Ca 2+ and Mg 2+ in the solution. Eventually one needs to replace the ion exchange material because it has become 'filled' with calcium and magnesium ions. Hence there are three 'pools' of plant nutrients in the soil: specific solid materials, both organic and inorganic, the soil solution, and ion exchange sites. Ion exchange can help buffer changes in nutrient supply and explains why soils with higher cation exchange capacity often are generally better soils for agriculture (i.e., can grow better crops). Most ion exchange surfaces are negatively charged and hence are cation exchange surfaces. The amount of ion exchange surfaces present in a soil is strongly dependent on the age of the soil. As soils age, specific minerals are produced by the weathering of the soil minerals and the decomposition of soil organic material. Remember that the soil as a whole , and the soil solution specifically, remains neutral: positive charges equal negative charges. This is also true of the solution that enters (e.g., rainfall) and exits the soil as groundwater, but the chemistry of the water flowing out of the soil may be quite different from that entering the soil. Ultimately the supply of nutrients (e.g., K+, Ca2+, PO4, SO42-) in the soil depends upon the balance between additions and losses. Processes that add nutrients include: additions from rain, snowfall and dust; decomposition of organic material into components that are able to dissolve in the soil solution; weathering of soil minerals into components that are able to dissolve. Processes that remove nutrients from the soil include erosion, leaching (the loss of solutes in water as gravity pulls water out of the root zone), and the harvesting/removal of plant or animal material. Dynamics of the soil Soils are continuously changing as a result of a variety of processes. Solid material is continuously being added, primarily from the plants that shed leaves, stems, fruits and entire bodies to the soil surface and continually add roots directly within the soil. Material is also added by animals and by mass processes e.g., wind and water deposition. Some of the material is readily decomposed, disappearing into the atmosphere (carbon dioxide) and soil solution (ammonia, 'dissolved organic matter' ) within a few days. Other materials (e.g., tree trunks, large woody roots) remain for hundreds of years. Water is continually flowing through the soil, usually being deposited on the surface by rain/snow and moving down with the pull of gravity. But occasionally water moves upwards because of evaporation from the surface of the soil. As water moves, it carries material with it, mostly in solution but sometimes in suspension(if there is a mass flow). Carried materials are not necessarily transported out of the soil but may be deposited, generally in lower layers, where the physical conditions (amount of oxygen, pH, size and type of particles) may be different. While the water balance of a soil is generally zero (i.e., inputs match outputs) over the course of a year, this is generally not the case for solid material and soils may be either accumulating or losing material. Even if the solid and liquid phases are in a steady-state, with losses matching gains, activities in the soil can change its structure. While we generally think of material in the soil as breaking down because of the processes of weathering and decomposition, sometimes larger molecules are made from smaller ones. Diversity of soils Because soils are dynamic, they are diverse and change through time in predictable ways, i.e., they develop over time. Young soils will have different features than old ones. T he age of the soil is one of the five key factors that determine the nature of a soil (Figure 5). The other four are parent material (what it is made of), climate, biota, and slope. Parent material can vary between solid rock (e.g., a lava flow), particulate mineral material (e.g., volcanic ash), or organic matter (e.g., in a bog ) with a wide variety in between. Parent material affects particle size, soil chemistry and what organisms are likely to occupy the soil. Climate, i.e., patterns of rainfall, temperature and the variation in these factors , is important for reasons that should be apparent: temperature controls the rate of decomposition and weathering; rainfall also influences decomposition and weathering and also controls the amount of water percolating through the soil. Biota, the forms of life present, influences the types of organic material that are deposited and the rates of decomposition. The remaining factor of importance, slope, is perhaps is surprising until one appreciates that all of the following are influenced by it: the amount of water running through the soil, whether or not water may be stagnant on/in a soil, the amount of erosion/deposition on a site. Because of variation in the factors described above, soils are diverse. Moreover, their features are changing continuously depending upon their age. One manifestation of this diversity is the existence of layers (horizons) in many soils. The horizons develop because of processes taking place in the soil. In the north central and northeastern U.S. glaciers played a very significant role by influencing three of these factors: In many areas, they eliminated whatever soil was present, thus many soils are relatively young; the glaciers deposited a variety of soil materials (ranging from sands to clays) on which new soils developed; and glaciers created a variety of topographies (slopes) upon which soils developed.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.23%3A_Soils.txt
In addition to needing materials, organisms need to move materials: materials need to be moved from where they are acquired or synthesized to other places where they are utilized; materials may need to be transported to storage sites and also retrieved from storage sites; chemical signals may need to move from a place of sensation to a place of response. Materials are moved in three basic ways in organisms, two of which occur in non-living systems as well: (1) materials move by diffusion, which is a consequence of the fact that all molecules at a temperature above absolute zero (i.e., all molecules!) are moving in a random thermal way; (2) fluid materials (i.e., gases and liquids) move by mass flow, from high pressure to low as long as there is an open pathway that allows the fluid to move; (3) materials move as the result of chemical interactions unique to biological entities, the so-called motor proteins, which can use chemical energy to do physical work (i.e., pushing or pulling a molecule, applying force over a distance) or the rotary motors of flagella that create a rotational movement that 'runs on' proton movement down an electrochemical gradient. Motor proteins are highly significant within cells where they can produce cytoplasmic streaming, a process that is significant to larger cells because diffusion is ineffective except over very short distances. The larger cells found in some of the algae, and especially in the coenocytic/siphonaceous cells are highly dependent on the ability of motor proteins to transport material within the cell. But for this course, we are more interested in the ability of larger, multicellular organisms, especially plants, to move materials within the organism, a process that is accomplished by a combination of diffusion and pressure flow. TOPICS • Diffusion • A simple but insufficient model • Osmosis—the diffusion of solvents, including water • Effects of pressure on diffusion • Combining the effects of purity and pressure • Plants and Fungi use manipulations of pressure and osmosis multiple ways • Structurally • Growth • Guard cell movements • Leaflet movements • Long-distance transport • In the phloem • In the xylem • the patterns • the mechanisms • the problem of cavitation and trade-offs in xylem anatomy • rare cases of pressurized xylem Diffusion A simple but insufficient model Diffusion is a process familiar to most. While the diffusion of gases and solutes is easily understood by simplistic models, the understanding of the diffusion of liquids, in particular water, is much more challenging and is often muddled by the imprecise application of terminology. The diffusion of gases and solutes is described as a spontaneous movement from regions of higher concentration to regions of lower concentration. The explanation for this spontaneous process is easily linked to kinetic theory—molecules move in a random way because of thermal energy. A s a consequence of this random movement, there is a net flow of matter from places where there are more molecules (i.e., higher concentrations) to regions where there are fewer molecules (lower concentrations). If dealing with mixtures (a gas with more than one component), each component will move independently of the others. Liquid water diffusion (osmosis) is NOT always from 'high concentration to low' However, this model (explanation) is not readily applied to liquid waterwith solutes, or tosolutions in general, largely because the idea of 'concentration' varies Concentration is not as precise a term as one might think, it can be expressed in several different ways (mass concentration, number concentration, molarity, molality, mole fraction). In the simplistic model of diffusion, the most appropriate measure would appear to be (number) concentration (number of molecules per unit volume) since random movement would move molecules from where they have more molecules per unit volume to where they have fewer molecules per unit volume. However, when considering the solvent (not the solute), the number concentration is not an accurate predictor of diffusion. For water and for most solvents the number concentration of the solvent changes very little as solutes are added, yet adding solutes can have a substantial influence on the diffusion of solvent. And while water volume changes little as solutes are added, the extent that it does change varies with different solutes, yet the effect on the diffusion of water is not controlled by the specific solute added but only on how much solute (number of particles) was added.Consider that while the addition of most solutes causes the water to slightly increase in volume (the number concentration goes down—the same number of water molecules are now in a largervolume), the addition of some solutes can cause water to contract (i.e., the number concentration goes up—the same number of water molecules are now in a smaller volume). If the (number) concentration of water is what directs its movement one would expect different solutes to have different effects on the diffusion of liquid, depending upon how much they caused the solution to change volume (and number concentration). And you actually would expect that some solutions (the ones that cause water to shrink) would have water diffuse fromthe solution intopure water. This never happens! Keeping all other factors constant, water alwaysdiffuses from where it is pure into any solution, regardless of the solute. And, at low concentrations, there is little to no effect of the particular solute—they all have the same effect on diffusion regardless of their impact on water 's number concentration.Itis the concentration of the solute NOT the concentration of water molecules that are directing diffusion: all other factors being held constant, water always diffuses from where there is a lower solute concentration to where there is a higher solute concentration. From this, one can conclude that itis the purity of water, not itsconcentration, that drives diffusion. This may seem like a subtle difference but it actually reflects some very profound features related to the laws of thermodynamics. Purity relates to entropyand entropy is known to' drive 'spontaneous processes. Moreover, our' mental image ', i.e., model, of what causes diffusion, doesn' t work—solventmolecules do NOT go from where there are more of them to where there are less of them, they tend to go from where they are purer to where they are less pure. The effect of pressure on diffusion A second key reason that the description/model that describes diffusion as occurringfrom 'high concentration to low' is deficient is that it fails to consider the effects of pressure. Pressure is the most familiar reason that fluids move (wind, water flow in pipes, blood flow in animals) but these movements are not diffusion, they are something called 'mass flow' , a movement that depends only on pressure differences, and a movement that will occur whenever there are pressure differences and an open path for fluid flow. But when mass flow is impossible (because there is no 'open path' ) pressure can also influence diffusional movement: water will diffuse from areas of high pressure to areas of low pressure. This is especially important for cells possessingboth a cell membrane and a cell wall. While the membrane allows there to be different purities of the solvent (water) inside vs. outside the cell, the wall allows there to be different pressures inside vs. outside the cell, and bothpurity and pressure are important in dictating the diffusion of water. Combining the effects of purity and pressure All other things being equal, water moves by diffusion from regions of higher pressure to regions of lower pressure and also from regions of high purity to regions of low purity. These two factors can 'balance' each other and it is possible to have NO diffusion between an area of low purity and high pressure connected toan area of low pressure and high purity. Looking at this another way, if you have water of low purity confined in a rigid container (i.e., a cell with a cell wall) and it is put into pure water, water will move into the cell, increasing the pressure in the cell. Eventually, pressure will be reached where there is no more diffusion into the cell. At this point, the pressure differences between the inside and outside are matching the purity differences between the inside and outside. Unfortunately, there is no easily conceptualized model for the diffusion of liquid wateras there is for the diffusion of gases and solutes. A rigorous model of the diffusion of liquid water requires the application of concepts from a thermodynamic parameter called water potential. The basic idea is relatively simple: osmosis (the diffusion of liquid water) is a spontaneous process and any spontaneous process must result in a decrease in the amount of energy available to do work (the 'free energy' ). Generally, two key factors affect the free energy of water (its water potential): thepressure (which increases its water potential) and the presence of solutes (which decreases its water potential). Liquid water diffuses from areas of high water potential to areas of low water potential just as heat flows from warm areas to cold areas. Forall organisms, and in particular those without a cell wall, the cell membrane and cellular activity allow solute concentration differences to develop between the inside and the outsideof the cell, resulting in differences in water purity between the inside of the cell and the outside. Whenpurity differences develop, water will flow in or out by diffusion. As long as the purity differences are small this movement can eliminate the purity differences by making the inside less pure(if water flows out)or more pure(if water flows in). However, such water movement will also cause the cell to change volume and if the cell swells or shrinks too much it can cause irreparable damage to the membrane, thereby destroying cell functioning. As a consequence, organisms without a cell wall must either live in areas where water purity is similar to what is found inside their cells or they must have structures/mechanisms that lessen diffusion and/or have the ability to either eliminate the water that diffuses in (e.g., the contractile vacuole of Paramecium) or to acquire water to replace that being lost by diffusion (generally this is accomplished by acquiring the 'salty' water and eliminating the salts). For cells with a wall (e.g., plants and fungi), the wall allows a new 'solution' to living in areas where the cell is more concentrated in solutes than the external environment (this is the normal situation for most non-marine habitats: fresh-water lakes and streams and terrestrial habitats where organisms are immersed partially or totally in soil whose water is generally quite pure, i.e., with few solutes). For these organisms, the rigid wall allows pressure to increase as water flowsinto the cells. This pressure acts to reduce the inward diffusion of water and eventually a dynamic equilibrium is reached where the high pressure and low purity inside the cell balance the lower pressure and higher purity outside the cell. Water moves (diffuses, i.e., moves by osmosis) in and out at the same rate. Plants and fungi use 'osmotic systems ' in a number of ways Structurally Water can be used as 'building blocks' when it is confined in a structure that will not expand. Living cells, with the combination of a cell membrane and a cell wall, are structurally strong and plants and fungi use them to form rigid structures that can withstand gravitational and wind forces (also discussed in chapter 3). Evidence for the structural importance of water comes from the observation of wilting: if plants are deprived of a source of water to replace that being lost by evaporation, they lose structural integrity. Some plants and fungi produce some structures (e.g., trees, bracket fungi) that don 't collapse when deprived of water, but for many plantsaccess to water is essential to' standing up'because it is the pressurization of cells that provides rigidity. Central to this ability is a cell wall that has high tensile strength and resists expansionand consequently allows for pressurization. Growth Cellular growth occurs when the internal pressures exceed the strength of the cell wall and thusyields to the pressure inside it. Organs (fungal filaments, roots and shoots) grow as a result of the expansion of individual cells and the internal pressure not only has to push out the cell wall but may also haveto push away (compress) soil in its path. Thus for plants (both roots and sometimes shoots)and fungi, growth may require the production of a significant amount of force. The force to power this growth comes from the diffusion of water (osmosis) and very significant forces can be created as the result of the movement of water down its water potential gradient. Pressures of 2-4 bars (= 0.2-0.4 MPa [megapascals] = 2-4 atmospheres of pressure = 30-60 pounds per square inch) are common and can be quite effective, as anyone who has observed a dandelion coming up through a sidewalk may have realized. Guard cells and stomates The opening and closing of stomates come about as a result of changes in the pressure of specialized cells, guard cells, that surround the pore. Pressurization of the guard cells, as a result of solute accumulation and subsequent water diffusion into the guard cells, causes the cells to swell and form an opening (a stomate) inbetween them. Adecrease in solutes in the guard cellswill cause a movement of water out of the cell, resulting in adrop in pressure and consequently stomatal closure. The triggers that stimulate guard cells to accumulate or lose solutes have been extensively studied and include light and the concentration of carbon dioxide. The exact controls may not be the same for all species. At least some plants are able to regulate internal carbon dioxide levels at a 'set point' that allows photosynthesis to proceed with little inhibition due to a lack of carbon dioxide, while at the same time minimizing the amount of water lost due to transpiration. Leaflet movement Similar to the action of guard cells, a number of plants have leaves or leaflets that move in response to environmental cues such as light, touch and drought, resulting in leaves or leaflets whose orientation varies depending upon circumstances. A common example is 'sleep movements' where leaves are horizontal during the day and vertical at night. These movements are the results of changes in the pressure of 'pulvinar' cells, located at pivot points. Relatively small changes in the size of these cells are leveraged as a result of their location and can cause substantial changesposition of organs involved. (see http://www.youtube.com/watch?v=U-PK13JEgk8 below) Watch A YouTube element has been excluded from this version of the text. You can view it online here: pb.libretexts.org/sdt34b/?p=302 Long-distance transport Phloem Both transport systems in plants, xylem and phloem transport, operate as the result of pressure differences created in the 'pipes' found in these tissues. The pressure differences are created as the result of the diffusion of water. In the phloem, pressures are created as a result of the addition of solutes (sugars) to the pipe cells, a process known as phloem loading, that occurs in regions of the plant called 'source' areas. As a consequence of the phloem loading, water flows into the sieve tube elements of the source area, and the pressure increases, triggering a flow in the pipes. The pressure differences and the flow are maintained because solutes are not just loaded at 'source' areas, they are also removed at 'sink' areas, the locations that solutes are being transported to;thus a continuous pressure gradient occurs in the phloem, from sources that provide sugars, to sinks that consume or store sugars. The exact locations that serve as sources or sinks can change depending upon whether a location is producing sugars (sucrose) or consuming them.Phloem movement can be up the plant (e.g., from storage sites in the root to shoot apical meristems) or down the plant (e.g., from photosynthesizing leaves to storage sites in the root). Loading of sucrose requires metabolic energy as ATP is used to move sucrose from where it is less concentrated to where it is more concentrated. As was the case in guard cells, water movement into the sieve tubes is passive once the solutes have been added. Because it is a mass flow, not just sucrose but any solute that is in the sieve tube will be transported to the sink. The most common of these other solutes are amino acids, but other nitrogen-containing compounds are transported in the phloem along with some mineral elements (e.g., K+, Mg2+, Ca2+) Xylem Water transport in the xylem is also the result of 'pressure' differences but these are actually differences in tension rather than differences in pressure. While pressure compresses fluids, the tension pulls liquids apart, just as pulling on a string exerts a force that acts to break the molecules of string. Surprisingly, in certain situations, water has substantial tensile strength and can indeed be pulled. The cell walls of all the cells in a leaf are infused and coated with water because of the adhesion of water to the cell walls and the cohesion of water to itself. When water leaves a leaf by evaporation the remaining water is 'stretched' , put under tension, because the remaining smaller volume of water is covering the same original volume of cells. This tension is transmitted to the water in the conducting cells of the xylem and creates a 'pressure' difference (actually a tension difference) that can pull water up the (non-living) pipe cells. What is generally driving the water movement up the pipes (trach ei ds and vessels) is a tension created as water is lost due to transpiration. However, water flow up the xylem can also occur even if there is little transpiration as long as growth is occurring: the diffusion of water into expanding cells can create a tension to pull water up plants in the spring when plants lack leaves and transpiration rates are very low. Water loss from the leaf is simple diffusion: water vapor at high concentrations (high humidity of the air inside the leaf) diffuses through open stomata to where the humidity is lower outside the leaf. The humidity of the air inside the leaf is maintained because liquid water in the cell walls of mesophyll cells evaporates and replaces water that has been lost. The tensions generated by water loss causes the tracheids and vessels to be slightly compressed as the pressure outside is 'normal' (one atmosphere) but the pressure inside is lower. Note that this is in contrast to the situation in living mesophyll cells which are pressurized because they have a membrane that allows them to concentrate solutes. If the tension in the water column of becomes too great cavitation occurs as air bubbles form when the water column is broken or when water breaks away from the sides of the tracheid or vessel. In either case, the cell is 'cavitated' and is no longer useful for water transport. In both transpiration-driven and growth-driven situations, and in phloem transport, there is a short-distance diffusional movement that creates a pressure difference that can result in a long-distance movement. In both the xylem and phloem the movement withinthe pipes is NOT diffusion, it is a much more familiar process called bulk flow. Bulk flow is a much more effective means to transport materials over long distances than diffusion, which is only effective oververy small distances (tenths of a mm for liquids). Bulk flow is blocked by cell membranes and is impeded, but not prevented, by cell walls. The pits found in the cell walls of tracheids and vessel tube elements provide a relatively low resistance path for water to move between adjacent cells. Water flows even more readily through the perforation plates of vessels because they are completely open. In the (living) conducting cells of the phloem, plasmodesmata connect the individual cells and phloem sap (which is essentially cytoplasm lacking organelles) bulk flow occurs from cell to cell through the plasmodesmata. Bulk flow is also significant in the soil where there are passageways for water to flow through and where both gravity and the 'pull' by movement into plants can create pressure differences. The pressures and tensions found in vascular tissue reflect these mechanisms. If a sieve tube is penetrated, phloem sap flows out because the pressure inside the cell is greater than atmospheric, just as you will bleed if your skin is severed. Under most circumstances, if a tracheid or vessel is penetrated water does NOT flow out , rather air flows in, reflecting the fact that the water inside the tracheid /vessel was under tension. In fact, if one measures the volume of a tracheid /vessel as tensions develop, it slightly decreases because of compression from the outside. Because of this, tree trunks exhibit a measurable decrease in circumference during the day as transpiration and tensions increase and they rebound overnight as the tensions are relieved and the plant is rehydrated during times of little or no transpiration. On rare occasions the water in the xylem is pressurized. This condition is described as 'root pressure' and only occurs under certain circumstances. 'Root pressure' is by the 'bleeding' (exudation) from a decapitated stem. Under these same special conditions, if one punctures an individual xylem vessel or tracheid it will also bleed, unlike the more normal situation described above. Root pressure only occurs if the soil is moist, roots are actively growing, and transpiration is low (at night or when no leaves are present). Under these conditions solutes (mineral ions) accumulate in the xylem of the root because of the actions of root cells, and because the endodermis collectively behaves like a membrane and is a barrier that prevents solutes accumulated in the root xylem from leaking back out of the xylem tissue. Hence, like a living individual plant cell which can pressurize because the cell membrane allows solutes to be accumulated, the entire root xylem can accumulate ions and pressurize. This phenomenon is rare, both because roots are generally not active enough to accumulate sufficient ions in xylem tissue and also because a pull from the top (created by transpiration or growth) prevents a pressure buildup from occurring. A final situation where the xylem is pressurized is the one that causes sap to flow (out) in maple tree trunks in the late winter and early spring. 'Tapping' , inserting a cylinder, into the xylem, results in the bleeding of sap that can be collected, concentrated and used as a source of sugar. Maple sap flow does NOT require root activity — it can be observed in stems removed from the root system. Maple sap flow DOES require freeze/thaw cycles because these somehow allow the xylem to become pressurized. The sugars found in the xylem sap are coming from xylem rays whose starch is converted into sucrose in late winter. Why only maples, and a few other species of trees, exhibit this behavior is generally attributed to aspects of their wood anatomy. Most tree species do not pressurize when exposed to freeze/thaw cycles. Although phloem tissue is penetrated when maple is tapped and although phloem tissue is pressurized and transports sucrose, extremely little of the sap collected from maples is derived from the phloem. The living cells (sieve tube elements) of the phloem tissue are capable of rapidly plugging holes to prevent 'bleeding' and consequent sugar loss. Maple trees that are tapped will bleed from the xylem tissue for several months, as long as they are exposed to proper conditions and as long as there isn 't a' pull 'from the top of the plant caused by growth or evaporation from leaves. Maple sap flows when leaves aren' t present and growth is not occurring. If one could tap into the phloem tissue it would be found to have a much, much higher sugar concentration (comparable to maple syrup) than maple sap, whose sweetness is barely detected by humans until it is concentrated.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.24%3A_Material_movement_and_diffusions_multiple_roles_in_plant_biology.txt
One of the marvels of life is growth, the ability of organisms to get bigger. This is especially the case for plants since they grow literally and figuratively 'out of thin air.' And while plant growth is a very ordinary phenomenon, its explanation is very much 'extra-ordinary, ' as they are able to accumulate scattered pieces of their environment and assemble them into an organic entity. In contrast, animals need only to find pre-assembled pieces of life, perhaps still living, perhaps not, and reconfigure them to their own use. And while the controls on animal growth are straightforward, being tied to ingestion, what controls plant growth is less obvious. When plants grow, they generally get bigger both in size and in weight and the process of growth can be linked to increases in either. However, for a variety of reasons, the growth of plants is defined as an irreversible increase in size, not an increase in weight. Part of the reason for this is because water absorption and loss can change plant (wet) weight substantially because of processes that most would not consider growth. For example, trees gain a considerable amount of water overnight to replenish that lost during the day; most would not consider the overnight weight gain to begrowth northe loss during the day tobe 'negative growth.' To avoid the dynamics of water, one might monitor growth with increases in 'dry weight' , a consequence of the accumulation of carbon, nitrogen, phosphorus, etc., and the synthesis of organic molecules such as carbohydrates and proteins. But defining growth by an increase in dry weight would lead to some counterintuitive results. Most would consider that trees grow in the spring when the shoots elongate and leaves appear. At this time the tree is actually decreasing in dry weight. During the summerin temperate areas, as trees photosynthesize and absorb nutrients, their dry weight increases, yet manyare not getting bigger in terms of longer shoots. Similarly, a sprouting seed, which most would consider to be growing, is actually decreasing in dry weight until its photosynthetic rate exceeds its respiration rate; thisgenerally doesn't happen until the seedling is a couple of weeks old and already of substantial size. Consequently, plant growth is typically defined as an irreversible increase in size. TOPICS • Growth processes • Limitations on plant growth • Growth models Growth Processes Increases in the size of plants come about as individual cells, produced by cell divisions in the meristems, expand. While this may seem at first a simple phenomenon , consider the following aspects of the process: 1. A ll plant cells, even small ones, are surrounded by a confining cell wall, whose most basic function is to prevent expansion. This allows the cell to pressurize and this is important to plant cell water balance and functioning. 2. As the cell expands the thickness of the cell membrane and the cell wall outside it do not diminish. In contrast, consider an expanding balloon: as you blow air into it, the 'skin' of the balloon is stretched thinner and thinner as the static volume of balloon material is spread over a larger and larger volume. This does not happen as plant cells grow–consequently, the expansion must be coordinated with the production of new material for the cell membrane and cell wall; this keeps the thickness of the boundaries of the cell constant. The significance of this, especially with respect to the membrane, should be apparent; stretching the plasma membrane is not possible, only the tearing of it, and this would destroy its ability to be a selective barrier, keeping some molecules in and others out of the cell. 3. Although the expansion of the cell is a consequence of water absorption, this is not a simple 'dilution' of the cell. Similar to what is happening in the membrane and wall, the cell is adding intracellular components at a rate that keeps pace with its expansion. 4. Although the cytosol does increase its volume as a cell grows, it is generally the expansion of the vacuole that accounts for most of the increased volume of the cell. Assuming that a larger cell is beneficial to the organism (because it allows it to penetrate more of its environment, important for both roots and shoots), the large central vacuole is a relatively 'cheap' way for a cell to get bigger because the contents of vacuole take less energy to obtain than the contents of the cytosol. T he enlarged cell is not simply a diluted and stretched version of the original one, it s walls and membranes are the same thickness as before and the cytosol is the same composition as before. The cytosol has increased somewhat in volume but the majority of the increase in overall cell volume is the result of a larger vacuole, which must have the same solute concentration as the cytosol, but the solutes are different and 'cheaper' ones are in the vacuole. 5. The region of growth of a plant is separated, often by very substantial distances, from the source of materials for that growth. What materials are needed for growth? We can identify three basic needs: water, which represents the biggest component of 'new plant' material; carbohydrates which are used both in cellular respiration, to provide energy for synthetic reactions, and also as building materials to make cell walls, cell membranes, internal membranes, proteins, metabolites, vitamins, etc; and mineral nutrients, phosphorus for membranes, nitrogen for amino acids, etc. Water and nutrients are coming from the soil and are thus very close to the growing cells of root meristems, but must be transported considerable distances to get to the tips of shoots, up to 350 feet in the case of a redwood tree. Carbohydrates are supplied by photosynthesizing leaves, which may be relatively close to growing shoots but may be 350 feet away from an expanding root meristem. Carbohydrates often do not directly flow from leaves to growth points but instead may flow from leaves to storage sites and then from storage sites to growth regions. Cellular expansion is resisted by the strength of the cell wall and expansion occurs when the pressure inside the cell, created by the inward diffusion of water, exceeds the strength of the wall. Growing cells have 'softer' cell walls, i.e., walls that yield (expand) at lower pressures than non-growing cells. And it is believed that plants control cellular growth by controlling the 'softening' of cell walls. To summarize, plant growth involves a coordinated process of the synthesis of membranes (both the cell membrane and the vacuolar membrane), (2) cell wall, (3) cytoplasmic materials (proteins, membranes, metabolites), and (4) vacuolar materials, along with the absorption of water. The size of a cell is determined by genetics and environmental conditions. Growth stops when the wall 'hardens' and no longer yields to the pressure generated by water diffusion. In those cells that have secondary cell walls additional cell wall material is deposited after cell expansion has ceased—note that while secondary wall materials are added the cell is not growing in size but is growing in mass. As described above the growth of plants is a result of the expansion of cells, not of cell division, which, as the name implies, simply partitions existing structures and does not produce anything that is bigger in size. However, cell division is essential to the growth process because it provides cells that have the potential to grow, i.e., cells that accumulate solutes and produce cell walls that will yield to the pressures that develop inside them. Cell division occurs in plants in isolated spots called meristems and the actual growth of plants generally occurs in areas adjacent to these meristems. The expansion of newly produced cells pushes the meristematic regions further away from the main body of the plant, expanding the total size of the plant. Thus there is a spatial separation between the region of cell division and the region of cell growth. Action generally occurs simultaneously in both regions. Growth occurs whenever the new cells produced by the meristem are allowed to expand. For some plants, growth is more or less continuous and steady as long as environmental conditions (in particular temperature, water and light) are steady. However, most plants exhibit episodic growth with bursts of cell production and expansion followed by periods of inactivity, even when conditions are constant and favorable. For many perennial plants living in areas with seasonal climates, growth is strictly seasonal, occurring for only a portion of the year. Often the growth period is only a very small portion of the 'favorable' time period. For example, most trees in this area grow only for two to four weeks in May. The patterns described above represent the extensional growth exhibited by apical meristems in roots and shoots (primary growth) and the expansional growth produced by the lateral meristems (secondary growth). The growth of leaves and fruits is slightly different; these determinate organs have a pattern similar to that of many animals where there is a period of cell division followed by a period of cell expansion. Often, there may be a period of overlap where both division and expansion are occurring but at some point, cells stop dividing and no more embryonic cells are produced. Growth is sustained as the new cells expand but eventually, the growth of the organ stops, and a structure of unchanging size remains yet it does continue to develop. In order to sustain growth, a supply of materials is needed, not just the water that powers cellular expansion, but the materials to make more cell walls, cell membranes and all the cytoplasmic constituents as the cell expands. Not only are materials needed to construct the enlarging cells, material is also needed to supply the energy that is needed for these processes. Every peptide bond requires the hydrolysis of an ATP, as does every additional glucose unit in a growing cellulose polymer. In addition to direct 'construction costs' energy is needed for other cellular processes, e.g., the transport of molecules across membranes. Limitations on growth Many people are interested in making plants grow more, producing more material in a shorter period of time. What is it that limits growth? Below are listed some significant factors, several of which operate in multiple ways. Although increases in all of these factors mayincrease growth, this response is not constant and often tapers off with further increases in the factor, leading to the phenomenon of saturation, where further increases in the factor cause negligible changes in growth. Moreover, for all of these factors, there can be 'too much of a good thing' and further increases actually diminish growth (toxicity). Nutrients All of the required mineral elements can potentially limit growth. The limitation can come about both because that element is lacking from the soil or because, although the element is present, it is unavailable because of soil conditions. For instance, iron is frequently unavailable in basic soils even though it may be present in abundance. The problem is that under aerobic, basic conditions very little iron is present in a form that readily dissolves. Somewhere on earth, there are soils that are deficient in all of the 14 mineral elements required by plantsand deficiencies can develop even for elements like molybdenum that are needed in very small amounts. In the early 19th century Carl Sprengel developed an idea later championed by Justus van Liebig called the 'Law of the Minimum:' that plant growth will be limited not by nutrient availability generally but by whatever nutrient is in the shortest supply relative to how much is needed. For example, although additions of nitrogen often increase plant growth, if there isn 't enough molybdenumavailablesuch additions will not result in any growth enhancements. One can think of growing crops to be like baking a cake: if the cake recipe calls for five ingredients, making a cake can be limited by any of the five ingredients, and a lack of one is not made up for by excesses in others. This is a very straightforward idea that applies in many situations. But it runs counter to the common idea that response to factors will always be the constant:' if a little bit is good then a lot must be better'is generally notthe case! While too little of the essential nutrients can limit growth, too many of the same elements (toxicities) can also retard growth. The most common toxicities are the result of saline soils that have high levels of K, Ca, Cl, SO 4 and Na but unique soil conditions (waterlogging) can also bring about toxicities in iron and manganese in non-saline soils. Water Water is probably the most important factor limiting terrestrial photosynthesis worldwide. Water plays multiple roles in plant growth: as a reagent in photosynthesis, as the main constituent of any new cell that is produced, as the transport medium which moves materials throughout the plant and in particular to the growing regions. While all of the above might potentially play a role, the effect of water comes primarily because of the interplay between water loss and carbon dioxide gain. In dry habitats, plants keep their stomates closed to avoid water loss. This lowers the carbon dioxide concentrations inside the leaf and lessens the amount of photosynthesis. Additionally, plants may reduce water loss by having smaller leaves or fewer leaves, both of which may limit growth because the total amount of leaf area determines the amount of photosynthesis that can occur. While lack of water can reduce growth, t oo much water is also damaging to most plants, primarily because waterlogged soils become anaerobic and the roots grow poorly and/or die. Light Without light, photosynthesis can't occur and without photosynthesis, growth cannot occur. Light can have a very significant effect on photosynthesis and growth but only when other conditions are favorable to sustain growth and only when dealing with light levels comparable to those typically experienced by the plant. Too much light can be extremely harmful for a number of reasons and plants adapted to the shade usually do very poorly if exposed to high light levels. For the home gardener, the proper location of ornamental plants is strongly influenced by light considerations. The amount of light a plant receivesis controlled both by the intensity of light and by the duration of light exposureand the effects do not always compensate for each other, i.e., short periods of very bright light are not equivalent to longer periods of less bright light. Most crop species are adapted to high light conditions and will do very poorly if grown under shaded conditionsand it is probably the casecrop growth can bereduced as a resultof prolonged cloudy conditions. However, such conditions are often associated with frequent rains and these might also be the cause of decreased growth if the soils become flooded. Leaf distribution and longevity are important plant parameters that are influenced by light considerations because of problems associated with self-shading. In general, leaves are produced in ways that lessen self-shading and allow for more photosynthesis. Older leaves, that are experiencing shaded conditions, are often abandoned (i.e., they senesce and abscise) because they no longer obtain enough light to be profitable in an energetic/material sense. This is reflected in the following equation: Net photosynthesis = gross photosynthesis – respiration Assuming that the maintenance cost (i.e., that the amount of respiration needed for a leaf to maintain its living condition)of a leaf is constant, shading will decrease gross photosynthesis to the point that net photosynthesis is negative, i.e., the leaf costs more to maintain than it 'makes' in photosynthesis. At this point it the plant can cut its losses by eliminating the leaf. Temperature Plants are poikilothermic, their temperature is not regulated internally but is determined by the environmental conditions. Moreover, plants have a range of temperatures within which they can survive (often this range of tolerance shifts seasonally). All biological processes, and in particular photosynthesis, respiration, and growth , are influenced by temperature (chapter 26) and, with a few important exceptions, the basic response is that that plant activities, including growth, increase at higher temperatures in the range of 0 to 20 C (32 to 68 F). However, all plants have a n optimum temperature for growth, above which growth diminishes with increasing temperature. Part of the explanation of this is that at higher temperatures respiration is more sensitive to temperature (i.e., increases more with increases in temperature) than photosynthesis–thus although gross photosynthesis might increase, respiration increases more and there is a decrease in net photosynthesis at higher temperature (see equation above). Interactions between water, light and temperature These factors are often intertwined: more light increases temperature and higher temperatures increase transpiration and can lead to complications from a lack of water. How tightly these three factors are linked depends upon a variety of factors. Leaf area As would be expected, plants with more leaves generally grow faster than plants with fewer leaves. This is discussed in the following section. Models of Plant Growth What limits plant growth is a critical question, one that has a multitude of practical implications. Clearly, plant growth can be limited by adverse environmental conditions, e.g., lack o f rainfall. But if conditions are ideal for growth, what limits it? Like all organisms, plants grow by acquiring material and incorporating it into their own structure. One might assume that the ability of a plant to acquire material is directly related to its size, with bigger organisms able to acquire more than little organisms. This would result in a positive feedback process of growth: acquisition of resources—>growth—> bigger plant—>greater acquisition of resources—> more growth—> even bigger plant, etc., etc. This idea can be modeled in a set of equations that are predicated on the idea that the growth rate is a linear function of plant size : more plant, more growth ; more growth more plant. In words, this idea can be expressed in two ways: 1. growth rate is determined by plant size 2. the growth rate, expressed per unit of plant, is a constant In mathematical terms these two statements are: 1. growth rate = ∆S/∆t = k * S, where ∆S/∆t is the growth rate, the change in size divided by the change in time, S is the total plant size and k is a constant 2. (∆S/∆t) * (1/S) = k, For most biology students this should be familiar because: (1) it sounds like 'exponential' population growth, or perhaps 'geometric' population growth, (2) it is starting to sound like calculus, a course that is often required for biology majors (and perhaps you now see why!) Calculus can lead to the following, putting these in differential form: $\dfrac{dS}{dt} = k S \tag{1a}$ $\dfrac{dS}{dt} (1/S) = k \tag{2a}$ The size ($S$) at any time ($t$) is given by $S(t) = S_o e^{k*t} \tag{3} \label{3}$ Note that while the jump to Equation \ref{3} requires calculus, the idea s of equation 1 and 1a , and their rearrangement in 2 and 2a , should make sense without it. Equation (3) follows from either of the first two. Thus, one might expect plant growth to be exponential, just as you might expect population growth to be exponential. Note that the meaning of the word 'exponential' has a mathematical meaning that is not equivalent to the one in general use. Exponential growth is not necessarily 'fast' , and indeed, fast is a subjective adjective. In a mathematical sense, exponential is described in equations 1-3, although only 3 has an exponent in it. One could develop similar equations based on leaf area (i.e., that the growth rate per unit leaf area is a constant), with the argument that leaf area, by controlling photosynthesis, dictates growth rates. However, a similar argument could also be made about roots since without water and nutrients photosynthesis isn 't possible. It is easiest to just assume that roots, leaves and everything else are all needed and let S simply be' total plant size'and work with the assumption that plants can acquire more materials at a rate that is a linear function of their size (i.e., equation 1). But the growth of plants, and the growth of populations, usually is not exponential, at least not for long. Why isn't plant growth exponential? A basic answer is that growth is not controlled by the rate of material acquisition. It is an internally regulated process and it is too simplistic to assume that the rate of growth is a simple function of the ability of leaves and roots to acquire the materials necessary for growth. The internal controls of the plant, including both hormonal controls and molecular controls (e.g., which genes are activated) regulate the processes of cell division and cell expansion and thereby the growth process. In a fundamental sense, this is no different than what was discussed earlier concerning the development of unicellular organisms (see reading on organism development). A second factor involves meristems or more generally regions of growth. If an organism only has a limited region where growth originates and this region has a finite capacity to produce growth, then growth will not be exponential. In the case of a filamentous algae, that grows from a single apical cell, it is easy to see why growth might not be exponential. Similarly, an unbranched stem with a single apical meristem might not be expected to show exponential growth although one with branches, and with branches that can produce more branches, might be expected to. An economic model of plant growth A useful analogy for plant growth is an economic, 'business' model. Gross income is first split between expenses (the costs of running the business) and net income ( 'earnings' , what is left behind after expenses have been paid). Earnings can be 'invested' in a variety of ways, investments that allow for more earnings, investments that protect existing structures, or in investments that are 'frivolous' , i.e., with no obvious benefit. For example, a baker earns an income from the bread he sells. Some of his income he uses for 'maintenance' covering the expenses of his bakery–to buy flour, to pay taxes, to pay for the power to run the ovens, to repair broken machinery, etc.The income left after maintenance costs have been paid can be invested in a variety of ways: (1) investments in additional ovens and mixers or perhaps in a whole new bakery. These investments would increase his earnings and would produce exponential growth. (2) in defenses, such as a sprinkler system to protect his bakery from fire, or perhaps a security system that makes robbery less likely. This might not increase his earnings at all but it does provide for protection against a variety of potential problems. (3) the money could be spent on 'frivolous' items, items that do not protect the bakery. Money might simply be stored under his mattress. Theoretically, plants operate in the same way, material acquired (primarily carbohydrates but also mineral elements) is used for maintenance and what remains can be 'invested' in structures (e.g., leaves)that will allow for the acquisition of more resources, or it might be invested in structures, (e.g., anti-herbivore chemicals), that protect existing structures, or perhaps the material acquired might not have been invested in anything 'worthwhile' at all.Note that as long as the baker(or a plant)invests a set portion of his earnings in ways that increase his capacity to earn more income (even if it is only a very small portion), the result will be exponential growth. T he exponential model of growth is overly simplistic and usually poorly reflects reality. It does, however, give a starting point from which to analyze growth and the basic idea that as organisms (especially plants) grow , their ability to grow (growth rate) increases simply because they are bigger.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.25%3A_Plant_growthpatterns_limitations_and_models.txt
A particularly significant and interesting aspect of organismal life is its interaction with its surrounding environment. As indicated by the term, interaction implies that both components affect each other: the environment affects organisms and organisms affect the environment. The 'environment' includes components that are living, i.e., other organisms (the biotic environment), and components that are non-living such as rocks, clouds, water, dead organisms or parts of dead organisms. The environment has properties or conditions, such as temperature and oxygen concentration thatare commonly considered 'the abiotic environment' or the 'physical environment' . Conditions are the consequences of physical processes such as radiation, diffusion, convection;and these processes are sometimes strongly influenced bybiotic processes (Figure 1), such as respiration (generates heat and carbon dioxide, removes oxygen)and photosynthesis (absorbs light, adds oxygen and water, removes carbon dioxide). The conditions present on a sitecan dictate whether or not an organism can exist, and if it exists, how it behaves. This is sometimes described as an interaction between organisms and the physical, or abiotic, environment. Because organisms can affect conditions, they can interact with other organisms as a result. In addition to the interaction between organisms mediated through conditions, there are more direct interactions between organisms, such as one organism eating another or an insect transporting pollen from one plant to another. Interactions are fundamental to the discipline of ecology. Indeed one definition of ecology is 'a study of the interactions between living things and their environment' . Another common definition of ecology is 'a study of the distribution and abundance of organisms' (Figure 2). The distribution and abundance of organisms are controlled by interactions between organisms and their biotic and abiotic environment. For example, the distribution of a plant might be limited by the intensity of light. The amount of light available is a consequence of both the physical environment (latitude, degree of cloudiness, whether the site is facing south or north, etc.) and the biotic environment (presence or absence of tree species to intercept the light). The distribution and abundance of a particular plant (species 'A' ) might also be limited to the presence or absence of an organism that eats the plant or perhaps by an organism that pollinates the plant. In either of the latter cases, one might consider the factors that determine the distribution and abundance of the second species to be controlling the distribution and abundance of species A. Another definition of ecology is “a study of biological organization above the level of individual.” As we have seen, organisms have a structure (form, size, organization of component parts), and also organisms have functions, they do things such as develop, reproduce, and exchange matter and energy with their environment. Similarly, groups of organisms (e.g. populations) have structural and functional features that can be described and categorized, and explanations can be sought as to what determines their organization. An important point is that life is not simply organized at the level of the cell and the level of an organism; there also is an organization involving groups of organisms and this is the level of study for the discipline of ecology. Two entities that ecologists study are populations (groups of individuals of the same species) and communities (assemblages of species in a particular area). A population could certainly be considered a 'living thing' and its distribution across the landscape is a manifestation of biological organization and is a structural feature of this entity. The abundance of a species (how many individuals are present per unit of the environment) is another structural feature of a population. The fact that populations have patterns of distribution and abundance represents an organization, a structure, and the processes determining this structure are the same processes discussed above: interactions between organisms and their physical and biotic environments. Similar arguments can be made concerning the organization of communities. I n our examination of the role of interactions in the biology of organisms , we will consider in this chapter the interactions between organisms and conditions, examining the key conditions that affect terrestrial and aquatic habitats, why these conditions affect an organism's function, and what factors cause these conditions to vary, including how organisms themselves may control conditions. In the next chapter, we will examine more direct interactions between organisms, trying to see fundamental similarities in the ways that organisms interact with each other. Finally, we will look at agriculture , an interaction that we all depend upon, and interactions (Chapters 28-30) that are critical to agriculture . Our approach will be centered primarily on organisms, although many of the topics overlap with ecology and approach the topics from a broader scale. TOPICS • Temperature • Temperature's influences • Organism tolerances • Organism growth • Psychophiles and thermophiles • Fruit ripening • Temperature as a cue • Temperature's influence on other conditions • Moisture • Terrestrial habitats • Aquatic habitats • Salinity • Oxygen • Light • Currents • Nutrients Temperature Temperature is of critical importance to all organisms–it affects whether they can survive and what they do. Even for organisms who regulate their temperature at a set point, (i.e., homeotherms), temperature has significant consequences. But temperature is even more significant for the vast majority of organisms who do not regulate their temperature. For such organisms, termed poikilotherms, the thermal conditions of their environment control their metabolic activity. Although the temperature is important in all habitats, it is of relatively less importance in most aquatic systems because the thermal properties of water buffer temperature fluctuations. But organisms in terrestrial habitat s are immersed in a fluid (air) that absorbs very little heat energy and has a low heat capacity (i.e., little buffering ability). This makes the temperature of terrestrial systems much more dynamic in time and space than in most aquatic systems. One of the key reasons why temperature is important in terrestrial habitats is because it affects evaporation and moisture levels. While there are some terrestrial habitats where temperature is not a key determinant of activities, from a global perspective temperature and moisture are the major factor controlling what organisms are present and what they are doing. Temperature's Influences on Organisms All organisms have a range of temperatures in which they can carry out the functions that define and sustain them. Temperatures above and below this range alter their structure and functioning in several ways. The most important alterations are listed below. Membranes and temperature Membranes are essential for life, they regulate molecular movement and perform a variety of other functions. The physical nature of membranes is between a solid and a liquid; they can be described as “liquid crystals” because part of their nature is rigid and ordered while other parts are fluid-like (Figure 4, discussed also in Chapter 3). This duality of structure is important to their function; they need to be partly rigid because much of their functioning depends upon the organization of its parts; if these parts are out of place, functioning is disrupted. At the same time, membranes need to be able to change shape and membrane components do need to be able to move laterally; this is only possible because of membrane fluidity. Temperature disrupts the balance between fluidity and rigidity–high temperatures make membranes more fluid and low temperatures make them more rigid (crystalline). Shifts in either direction are damaging. Membrane characteristics of organisms found in habitats of different temperatures are different in predictable ways that relate to the maintenance of a certain degree of 'fluidity' . At higher temperatures, the lipids are more likely to contain longer chains of hydrocarbon and these chains are more likely to be more saturated. Both of these features make the membranes that they are found in more 'solid-like' at any particular temperature. Along the same lines, it has been found that some organisms that experience yearly variation in temperature adjust their membrane chemistry in a way that maintains a constant degree of fluidity in spite of changing temperatures. Thus, the range of temperature tolerance is partly determined by the chemical nature of an organism's membranes. Coordinated chemical reactions and temperature A second factor involved in both high and low-temperature disruptions of organism function is the balancing of the myriad chemical reactions that are taking place inside cells. The rate of nearly all chemical reactions is strongly influenced by temperature, with the rates going up as the temperature goes up. Most of these reactions are in some sort of a balance so that, in general, there is no build-up or depletion of metabolites. This balance can be upset at both high and low temperatures because the temperature sensitivity is not the same for all reactions–thus reactions that are 'in balance' at some temperatures may not be at higher or lower temperatures. The biochemistry of cells is such that control process (e.g., feedback loops) can operate to achieve balance in metabolic pathways, but there are limits to these control processes, and at least some of the problems with high and low temperatures may be attributed to problems with reactions becoming 'unbalanced' . Enzymes and temperature Enzyme functioning is dependent upon a three-dimensional structure. This structure can be disrupted, a process called denaturing, by high temperatures because the thermal motion is significant enough to break the relatively weak bonding that accounts for certain aspects of the enzyme structure. The temperature at which denaturing occurs varies with proteins but is in the range where temperatures become lethal to most organisms (25-40 C). Problems with freezing Not surprisingly, freezing causes a variety of problems for living things. The expansion associated with freezing can burst cells, destroying membranes and walls in the process. For plants and fungi, which have a substantial volume of their structure (the apoplast) that is outside of the membranes, freezing (especially if it occurs slowly) generally occurs first outside the cytosol, i.e., in the apoplast, because of its substantially lower solute concentration. The freezing outside causes the diffusion of water from the inside to the outside, resulting in desiccation damage on the inside. Because of these effects, a wide group of plants and fungi have their lower thermal limit at 0 C, or slightly below it. In spite of this, plants and fungi do live in habitats where freezing occurs. For some, survival is the result of an overwintering part that is below-ground where temperatures are more moderate and never go below freezing. For others, e.g., trees and shrubs, the existence of perennial above-ground parts reflects an ability to withstand prolonged periods of sub-freezing temperatures. Tissues/cells may avoid freezing through two mechanisms, one involving freezing point depression and the other involving supercooling. Freezing point depression is one of the four 'colligative properties of solutions' — changes in the properties of a solution that occur with the addition of solutes, regardless of what solute is added. Although the presence of solutes in the cytosol does lower the freezing point, the effect is relatively small (up to -2 C, at the concentrations of solutes typically found in the cytosol), and protection against freezing by this mechanism is not significant for most organisms. Supercooling can result in much more substantial drops in the temperature at which freezing occurs. Supercooling describes a situation where liquid water exists at temperatures where it is usually frozen. Although supercooling can occur in pure, or nearly pure, water, especially if there are no sites for ice nucleation (e.g., under certain atmospheric conditions that cause supercooled raindrops), in living systems supercooling appears to be a consequence of specific antifreeze solutes, proteins or glycoproteins, that somehow prevent crystal formation. Such compounds are found not only in plants but also in fish and insects. The lower limit of supercooling is around -40 C (which is also -40 F!!!!), but for many species the limit of supercooling is well above this, in the range of -10 C. An additional problem of freezing, significant to vascular plants, is that when water freezes dissolved air is excluding from the ice, creating bubbles of air in the ice. Upon thawing these bubbles remain. This is potentially a problem for xylem transport because the tensions that develop during xylem transport will cause expansion of the bubbles and cavitation (air locking) of vessels and tracheids, disrupting xylem water transport. This problem may be avoided by the production of new water-conducting cells in early spring, by pressurization of the xylem ( 'root pressure' ) that occurs in at least some species as a result of solute absorption in the spring, or as a result of physical processes that can eliminate the bubbles. Tolerances All organisms have high and low thermal limits; if an organism reaches that temperature it dies. Chronic exposure to more moderate temperatures can also be lethal, in a manner connected to the length of exposure. Some plants will be killed by a short-term exposure at 38 C, while 36 C is lethal if exposure is longer than 60 minutes. Extreme tolerances The majority of organisms have high-temperature tolerances of around 40 C and low-temperature tolerances of 0 C but there are stages of many organisms that have a much wider range of tolerance. This tolerance is often associated with a stage in the organism 's life cycle that is devoted to dispersal, e.g., spores, seeds. These structures serve to perpetuate the organism through a time of unfavorable conditions. Along with tolerance to temperature extremes, there typically comes a tolerance to desiccation and to a number of' insults 'that would normally kill cells (e.g., ultraviolet radiation, extreme pH, lack of oxygen). This tolerance is a consequence of an altered cellular structure that simultaneously increases tolerance and decreases metabolic activity. In short, the structure of the cell(s) becomes more and more inanimate and less and less affected by extreme conditions. Usually this state of' suspended animation'involves several or all of the following: accumulation of materials such as starch or oils that serve as reserves of energy and reduced carbon, changes in membrane structure, changes in protein structure, changes in organelles (in eukaryotes), reduction in cytoplasmic volume, desiccation, and, for certain cells, a thickening of the cell wall (or sometimes the addition of a wall to a cell that previously lacked one). Generally, these tolerant structures are single cells but in some organisms tissues or the entire organisms undergo comparable changes in structure and function. In the plant kingdom, such tolerant tissues are usually present in seeds and sometimes present in apical meristems. Such tolerance can occasionally be found in other structures and can also be found in entire plants, especially those found in freezing environments or deserts. The table below lists prokaryote, protist, fungal and plant structures that are particularly tolerant of extreme conditions. Although the table only tabulates low-temperature tolerances, it is important to realize that, in general, high-temperature tolerance, as well as desiccation tolerance, correlates with low-temperature tolerance. For example, most seeds readily tolerate prolonged exposure to frozen conditions; they also tolerate desiccation and exposure to high temperatures (e.g., 50 C) that would normally kill plants. Table 1. group structure notes some bacteria endospores most are very resistant to high and low temperatures and survive for prolonged periods most bacteria microbial cyst (=exospore) bacterial cells increase the thickness of the cell wall and contract the volume of the cytoplasm cyanobacteria akinete an akinete is a specialized spore found only in some cyanobacteria euglenoids cyst cyst formation is often triggered by changes in nutrient levels dinoflagellates cyst cysts have no flagella and produce a cell wall with cellulose, features that are NOT normally present in dinoflagellates diatoms resting cells and spores spores have thickened silica walls, resting cells do not; these structures may have requirements for germination. Spores of marine forms may be important components of the fossil record zygomycetes spores, zygospores the zygospores that are associated with sex and are multinucleate have a much thicker cell wall and are more tolerant of abuse than normal cells basidiomycetes both asexual and sexual spores in addition to spores, some forms produce sclerotia, desiccated and modified hyphae that are inactive and tolerant of extremes ascomycetes both asexual and sexual spores (see above description for basidiomycetes) mosses whole plants, spores the spores of most species are tolerant of a variety of treatments; in addition, the entire gametophyte plant of many mosses tolerates both freezing temperatures and desiccation ferns and other seedless vascular plants spores, rarely whole plants unlike mosses and like most seed plants, ferns generally canNOT tolerate desiccation, although spores of ferns tolerate this and other extreme treatments. Only a few species have above-ground parts that overwinter in sub-freezing conditions. conifers pollen grains, seeds, whole plants as a group, many conifers are more tolerant of freezing than most flowering plants, evidenced by the presence of conifers at high latitudes and elevations; however, spores are NOT especially tolerant; they generally only occur in hydrated tissues; cycads seeds only for most species only a few can tolerate temperatures below freezing, most are restricted to warmer areas gnetophytes seeds only only Ephedratolerates freezing temperatures ginkgo pollen, seeds, above-ground parts the tree is tolerant to the USDA's zone 3, which has temperatures down to -40 flowering plants pollen, seeds, above-ground parts of some species quite a number of flowering plants have adapted to temperatures well below freezing; there are also a number of species that can tolerate temperatures above 40 C Temperature's Influences on Growth Because temperature affects the rate of chemical reactions and because chemical reactions determine what an organism does, and in particular the rate at which things are done, the temperature has a profound effect on organism functioning. The combined effects of an organism 's chemical activity are termed metabolism and metabolic rates commonly double to triple with a 10 C (18 F) rise in temperature. While most students generally assume that the opportunity to' do more 'as a consequence of a higher metabolic rate is a desirable thing, this isn' t always the case. Higher metabolic rates require more food because an organism's metabolism runs on cellular respiration. To a certain extent, poikilotherms survive periods of low temperatures because it costs very little to maintain them under these conditions. Lower metabolic rates mean lower oxygen needs;consequently, many plants can survive low oxygen conditions (typically brought about by flooding) much more readily if temperatures are low. Growth and growing degree days For any organism one of its most significant activities is growth, the acquisition of materials, and subsequent utilization of matter and energy to make the organism larger and ultimately coupled with the production of new organisms. The effect of temperature on growth is nicely seen in the concept of growing degree days, a statistic that integrates time and temperature and is used to predict the progress of a wide variety of crops during the season. While the details vary between crops, and even between different varieties of a specific crop, the basic idea is that you can predict the growth stage of a crop species by keeping track of the number of days that the crop has spent at different temperatures. For example, if the daily temperatures had a high of 86 F and a low of 70 F, corn might take 100 days to reach maturity (i.e., the time to harvest); if the temperatures were cooler, with a daily high of 80 F and the low of 60 F, it might take 140 days. Agronomists have developed models to predict how long the crop will take to reach maturity based on the accumulation of something called a 'growing degree day' . Based on its temperature, each day is assigned a certain number of growing degree days (GDD's), with warm days earning more than cold ones. A typical formula that calculates growing degree days is the following: GDD = [(Tmax + Tmin)/2 ] – 50 Given the days listed above, the warmer day is worth (86+70)/2–50 = 28 GDD, and the cooler day is worth (80+60) – 50 = 20 days. If corn needs 2800 GDD days to reach maturity it will do so in 2800/28 = 100 days at the warmer temperatures and 2800/20 = 140 days at the slightly cooler temperatures. This is an example of an 'empirical model' , one that attempts to predict things based on observations but not necessarily based on an understanding of how a system operates. The fundamental basis for the model is the observation that crops grow faster when it is warmer. The model is successful in spite of the fact that it has a fairly crude approach to the relationship between growth and temperature. There are a number of features of the model that are useful to appreciate: • a GDD represents a unit of growth and the basic idea is that plant development can be represented as an accumulation of these units of growth. • a GDD also represents the product of time and temperature; although this is represented in its units ( 'degree-days' ), it isn't obvious in the equation above because the time factor is always 1 day and is not included; the equation might be written: • GDD = [(Tmax + Tmin)/2 -50] degrees * [1.0] day • the temperature term has two components, the first represents a type of average, a representation of a dynamic (changing with time) variable, in this case, temperature. This particular average (sum the extreme values and divide by 2) is convenient, as it is commonly used by meteorologists to reflect daily temperature. Although it is a crude type of average, based only on two values, it works well. The other temperature term (50 in the above equations) might be described as a 'base temperature' , the minimum temperature at which no growth occurs. Although the equation potentially predicts an impossible 'negative growth, ' if the average temperature is below the base temperature, this prediction is rarely the case because in most situations crops aren't planted until after average temperature daily temperature exceeds the base temperature. • the GDD concept has been used successfully for a wide variety of crops and also with insects, generally with modifications of the 'base temperature' and/or changes in the average temperature term (e.g., letting the maximum temperature never exceed 86) If one tried to devise a 'mechanistic model' , one that operates based on the mechanisms of growth, it would be much more challenging. Growth is a complex process that is a consequence of a variety of chemical reactions occurring simultaneously. Most of these are clearly affected by temperature but predicting the net effect of temperature on all of them would be particularly challenging. Certainly, the processes associated with growth are controlled by temperature, but the interrelationships associated with growth would be difficult to elucidate. Variation in the temperature ranges for growth While the vast majority of fungi, plants and protists have an optimum temperature for growth in the range of 25-35 C, there are some exceptions. A number of plants have maximum rates of growth well below 35 C. Not surprisingly, these plants grow in cooler habitats. While there are a number of possible reasons for this, including the possibility that these organisms have membranes that function more appropriately at lower temperatures (see above), or the interaction between temperature and moisture (see below), another explanation involves the temperature sensitivity of photosynthesis and respiration. As mentioned above, respiration is closely tied to temperature and for most plants reaches a maximum in the 30-35 C range. The response of photosynthesis is different: it is generally less responsive to changes in temperature and, for C3 plants, it generally reaches a maximum at temperatures below 30 C, sometimes well below (Figure 7). The reason that photosynthesis is less responsive to temperature is partly due to the fact that some of the key chemistry is photochemical and photochemical reactions are not strongly dependent upon temperature. An additional factor is that carbon dioxide, a reagent in photosynthesis, must dissolve in water to make it to the site of photosynthesis (the chloroplast) and the solubility of carbon dioxide decreases as the temperature increases. Because of this, C4 plants, which have mechanisms to concentrate carbon dioxide, generally have higher temperatures for peak photosynthesis than C3 plants. When considering the effects of temperature on photosynthesis, respiration and growth, one can consider photosynthesis as 'making food' and respiration as 'eating food' . As temperature increases in the 25-35°C range, plant appetite continues to increase rapidly while the rate of food production levels off or declines. The net effect of this is that at higher temperatures there is increasingly less food to power new growth. Consequently, plant growth often tails off at temperatures lower than one might expect. Psychophiles, Cryophiles and Thermophiles A number of organisms, in particular certain bacteria but also some fungi and protists, are termed 'psychrophiles' or 'cryophiles' because they do best at low temperatures, sometimes at temperatures below freezing. While the basic pattern of increased activity with increased temperature holds, the range of activity is shifted to much lower temperatures: 0 to 10°C and sometimes -10 to 0°C. These organisms have modified membranes and, for the ones that operate below freezing, antifreeze compounds that allow them to operate at such low temperatures. Since a very common mechanism of food preservation is low/freezing temperatures, these organisms may pose problems for the food industry. A cryophilic fungus has turned out to be the culprit in the 'white-nose disease' of bats, a disease that has recently decimated populations of bats that overwinter in caves with temperatures in the 5-15°C range. The bat's behavior of lowering body temperature during the winter (in order to save energy) has provided these fungi with perfect conditions for growth. At the other end of the tolerance range are thermophiles, who operate well above the normal activity range of 0-35°C. As with psychrophiles, the vast majority of thermophiles are prokaryotes, most often archaea, but there are some thermophilic eukaryotes, all of them fungi. Several of these thermophilic fungi are important components of large-scale composting operations important to the production of commercial mushrooms where the combined metabolic heat generation of the compost can elevate the temperature of the mulch to 80°C. Fruit Ripening One additional process affected by temperature will be mentioned because of its commercial significance: fruit ripening. In addition to the influence of temperature on the growth of fruits, the temperature continues to affect fruits after growth ceases, in the developmental process we describe as ripening. This process brings about important changes in characteristics (aroma, color, taste, texture) that are of significance to both consumers and producers. This developmental process is often controlled in various ways by temperature, and temperature can have a significant impact on the commercial value of a variety of fruit crops by influencing the appearance of both desirable and undesirable traits. In a more general sense, the temperature can influence the ecologically significant characteristics of fruits that affect their role in seed dispersal by influencing their attractiveness to frugivores. Temperature as a Cue For many plants, and some fungi and protists, temperature provides an important cue that is used to coordinate growth and other activities with seasonal changes in conditions. Just as gravity organizes plant activity in space, the temperature can coordinate plant activity in time. In this situation, the temperature is not just a condition that the organism responds to, it is a signal that conveys information about what conditions will be like in the future, similar to the way that day length (photoperiod)can provide information about the coming seasons. However, since the noise in the temperature signal is substantial, using it to predict future conditions is more complicated: a return to warm conditions after cold ones could be a January thaw or it could be a real (spring) thing. For many plants, spring is sensed as a warm period after a measured period of cold. An example of this is seen in the germination patterns of many seeds. The seeds of most plants are shedin a dormant condition. Although some seeds don 't have specific germination requirements, they simply need a few weeks and they are able to germinate (this has been selected for in many crop species), many seeds require specific conditions or a series of specific conditions in order to germinate. Especially in temperate habitats, it is often a cold temperature treatment that will' break 'dormancy, i.e., allow the plant in the seed to resume growth (Figure 9). This pattern is beneficial because it would prevent seeds from germinating and thereby becoming susceptible to cold until after the harsh conditions of winter. Because the original horticultural practices developed to break seed dormancy involved layering seeds and keeping them moist and cool, such treatment is termed' stratification '. The key part of the treatment is the temperature treatment, not the layering. Contrary to the normal metabolic pattern, where activity is promoted by warmer temperatures (i.e., warmer temperatures produce more response than lower ones), in the stratification response activity is promoted by lower temperatures, with colder temperatures having greater effects than higher ones.Typically temperatures need to be below 50°F (10°C) to be effective and become more effective as the temperature decreases down to 0°C. Temperatures below 0°C, and temperature treatments when the seed is dried out, are not effective, indicating that metabolic activity is essential for the response. The process can be modeled in a manner similar to growing degree days, except in this case what is accumulated, termed' chill units ', requires temperatures below a certain threshold (typically 10°C), and more chill units are accumulated as the temperature decreases down to 0°C. When a seed accumulates enough chill units its dormancy is broken; at this point, the embryo' s behavior is typical of most organisms, and activity (growth) is promoted by warmer temperatures. Besides breaking the dormancy of the embryos in seeds, cold treatments are also a very important cue in breaking the dormancy of shoot apical meristems (buds). Home gardeners often bring shoots of flowering trees and shrubs (e.g., apple) indoors to 'force' them to flower early (Figure 10). This practice works as long as the shoot has been exposed to cooler temperatures for a long enough length of time prior to warming it up. Shoots often will not force in December but will in February. The exact amount of 'chill time' that a shoot needs before it will respond to warmer temperatures varies. This phenomenon is sometimes the reason why certain trees may not be able to be grown in southern latitudes:they never receive enough cool temperatures to cause them to emerge from dormancy. Accumulation of chill units is also a cue for some plants to flower, a process termed 'vernalization.' In some situations the cold treatment itself is the trigger for flowering; in other situations, the cold treatment simply flips a switch and allows the plant to flower in response to a second signal (e.g., photoperiod) that previously would not elicit any response. Temperature's effect on other conditions Temperature is also important because it interacts with a number of other conditions. In terrestrial habitats, probably the most significant interaction is between temperature and moisture. Temperature affects evaporation, and occasionally condensation, rates. Evaporation occurs when an individual water molecule is moving fast enough to escape the cohesive forces of its neighbors. Since the velocity of molecules is a function of temperature, the warmer it is, the more likely evaporation is to occur. The tendency of a substance to evaporate is reflected in a property called vapor pressure, which measures the amount of the substance (in this case water) present in the vapor state when the liquid and air are in equilibrium. Figure 11 shows the very strong effect temperature has on vapor pressure. Under certain circumstances, evaporation will be directly related to vapor pressure and consequently would roughly double with each 10oC rise in temperature. In environments where lost water is difficult to replace, temperature can be of great significance to desiccation rates and the survival of organisms. For plants and fungi, the combined factors of temperature and water availability are of utmost importance in determining species abundance and activity. Note that although the temperature has a major influence on evaporation through its effect on vapor pressure, other factors are also important including the humidity of the air, the surface area of contact between the air and the water, and the degree of mixing (convection) of the air above the hydrated surface. Finally, although temperature affects evaporation, evaporation, in turn, affects temperature. In the case of plant leaves, evaporation can cause leaves to be significantly (over 2o C) cooler than the air temperature. Temperature also affects the availability of certain compounds by affecting their solubility in water. While the solubility of many solids in water increases with higher temperatures, the opposite is true for gases, and in particular for carbon dioxide and oxygen. This is particularly significant for photosynthesis and, as described above, is part of the reason why the response of photosynthesis with increasing temperature is not comparable to that for respiration even though both involve a host of enzyme-mediated chemical reactions that generally are enhanced at higher temperatures. Another situation where the decreased solubility of gases at high temperatures can be a problem is flooded soils. The effect of flooding is more damaging at high temperatures than at low ones. A variety of factors contribute to this: (1) decreased solubility of oxygen at higher temperatures, (2) increased rates of soil respiration at higher temperatures as carried out by the sum of organisms present in the soil (plant roots, fungi, bacteria, protozoans, etc.); increased respiration means decreased oxygen (3) increased oxygen requirements for plant roots because of the higher metabolic rates associated with higher temperatures. Water and Terrestrial Habitats Along with temperature, moisture is a key environmental variable dictating the distribution of organisms on terrestrial habitats. The reasons for this should be clear: • water is an essential component of living tissues and a reagent in many essential reactions, including photosynthesis and ATP hydrolysis • in terrestrial habitats, water is nearly always lost to the atmosphere in the process of evaporation • for terrestrial autotrophs, who obtain carbon dioxide from the atmosphere, evaporation is all the more likely to occur since organisms must expose themselves to the atmosphere to acquire carbon • for plants and animals, water is the medium in whichmaterials move when transportedand for animals, water is the basis for excretion Tolerance to drying The vast majority of organisms maintain their moisture conditions at a particular level through the familiar process of homeostasis. Most plants (and most organisms in general) would be considered homiohydric, i.e., they maintain their water levels at a 'set point' . To do this requires that an organism adjust either water gain or water loss. To a limited extent, plants adjust water gain: when they get drier, the driving force for water absorption is increased and this can result inan increased flux (remember the flux equation!). However, plants have only a fairly limited ability to 'get drier, ' and when they start to desiccate their most significant adjustments involve reducing water loss rather than increasing water gain. When plants experience water deficits their response is to reduce water loss by: (1) reducing the permeability of the plant to water by closing stomates, and (2) reducing the surface area for loss, generally by shedding leaves. Again, remember the flux equation and how these changes relate to it. Leaf loss is especially obvious in seasonally dry habitats where woody species lose all their leaves and herbaceous species spend the dry season as bulbs or other underground parts, both groups producing and possessing leaves only when conditions are more mesic. These measures to reduce water loss come at the price of reducing a plant 's ability to feed itself. The very significant effect that moisture has on plant distributions reflects the fact that individual, population and species success involves balancing water loss and carbon gain. In some situations, a species may be successful by being able to acquire' its own'water source. Alfalfa and mesquite roots often penetrate deep enough to tap groundwater sources unavailable to other plants. However, a majority of plants in an area sharea common water source, the soil, i.e., the roots of many species are occupying the same volume of soil as other species, makingthe supply of water uniform for mostspecies living in an area. Consequently, conservation by one species or individual only leaveswaterthat can be taken by otherspecies. Species are successful by managing theiroverall growthand patterns of growth. This represents an area of diversification between different species. Homeohydric organisms are intolerant of desiccation and die if their water status drops below a certain level ; most plants cannot recover from a loss of 10-15% of their water. Probably the main reason for this in vascular plants is 'catastrophic xylem dysfunction' which is a consequence of cavitation and positive feedback loops related to cavitation. Recall that individual vessels and tracheids may cavitate if the water in them is pulled too forcefully, the result of water loss at a time when there is a restriction of water acquisition as the soil dries. Cavitation results in a loss in a part of the xylem conducting system and this makes cavitation more likely in the remaining conducting elements (see the flux equation); increased resistance to flow as a result of cavitation means that there has to be a greater pull (higher tensions) in order to acquire the same amount of water. Thus there is a positive feedback loop: cavitation makes more cavitation likely which will make more cavitation likely. Catastrophic xylem dysfunction (no ability to transport water) may result quickly after the first cavitation event, leaving the plant with no ability to rehydrate itself. There are a small number of organisms including a very few animals (tardigrades), some protists , and a few plants, that are poikilohydric: their water status is not strongly regulated but is allowed to assume the level dictated by the environment that they are in. Obviously, these organisms can only be successful (assuming that they live in an environment that dries out at least some of the time) if they are tolerant of desiccation, a phenomenon that is very rare in organisms, although they may produce parts like spores and seeds that are tolerant. Poikilohydric organisms can lose up to 90% of their water yet are still able to revive themselves when water again becomes available. The only plant group where desiccation tolerance is common is in non-vascular plants, many mosses and some liverworts, (ironically groups that are often considered to be restricted to moist environments); it is also present a few ferns and clubmosses and in a very few seed plants. While there are some mosses that are restricted to moist habitats, most are desiccation-tolerant and many are particularly prominent in arid situations, both arid habitats (deserts) and arid portions of more mesic habitats, e.g., growing on rocks that have no ability to store water. Some of these species do have features to lessen water loss, e.g., a drying response that involvescoiling of 'leaves' around the stem, lessening the surface area exposed to the atmosphere. Nonetheless, many mosses are capable of tolerating extreme desiccation and the whole organism, not just a select part, and can remain viable after undergoing repeated cycles of desiccation. They are inactive during dry periods but are able to quickly resume activity when moistened. Tolerance of flooding At the other extreme, terrestrial organisms can be affected by excesses of water. Generally this is an indirect effect of a lack of oxygen was discussed above when considering the interactions between temperature and oxygen. Water and Aquatic Environments Salinity One might assume that there are no problems associated with water in an aquatic environment since water is abundant. However, water does play an important role in dictating the organisms present in any particular aquatic environment, primarily because of the process of diffusion. Because water tends to diffuse from regions where it is purer to regions where it is less pure, living things are strongly affected by the purity of the water that they live in and this is primarily determined by the water 'ssalinity. All life has the ability to both accumulate and to generate solutes, and therefore the water in organisms is decidedly impure.Consequently, if organisms are placed in pure water, water diffuses into them. The influx of water has two potential results: one is chemical, the cell solutes become so dilute that normal functioning is impeded; the second is mechanical, the influx of water can cause the organism to swell and ultimately burst. However, if the organism is enclosed in a rigid container the influx of water pressurizes the organism and the flowof water ceases with only modest changes in volume. Another possibility that allows organisms to live in' fresh'(i.e., pure) water is to have mechanisms that allow water to be expelled from the organism at the same rate that it enters. The problems associated with the diffusion of water into organisms are eliminated if the purity of water is the same outside as it is inside the organism, and there are a number of organisms (many marine animals, some protists) that require such an environment where the purity of the cytosol is comparable to that of seawater. There also are habitats, termed saline ( 'salty' , although the salt need not be NaCl) that have a water purity even less than that of most organisms. Most forms of life are excluded from such saline environments because diffusion causes them to lose water and they cannot tolerate the decrease in the internal water content that results from water loss. The organisms that are able to tolerate such environments do so by having more than the normal concentration of solutes in their cytosol, generally adding unique solutes that are typically not found in living things. The problems of life in saline environments are not restricted to reduced water content. Additional problems stem from toxic concentrations of the solutes that make the habitat saline. Generally, this would be sodium and chloride ions but there are habitats where other solutes (e.g., potassium, calcium)are damaging. With the exception of sodium, which most plants don't require, these elements are essential for living things, but at high concentrations, they can interfere with normal cellular or organismal functioning and become toxic. Oxygen and Aquatic Environments Oxygen is of key importance in aquatic environments. Oxygen readily dissolves in water but its solubility is such that oxygen is generally less available than in terrestrial habitats. More significantly, its abundance varies much more in aquatic habitats than in terrestrial ones. When considering terrestrial environments, because of convectional mixing (winds) due to themuch lowerdensity of aircompared to water, and, to a lesser extent, because ofthe much more rapid rate of diffusion in gases, the oxygen levels of the air rarely change much. Processes (primarily biotic ones) may increase or decrease oxygen levels but rapid mixing with the huge reservoir of oxygen in the atmosphere as a whole, which is slightly less than 20% oxygen, rapidly returns the air in these areas to atmospheric values. In contrast, liquid water is much denser, its movement is much more sluggish and consequently, the possibility of localized areas with oxygen concentrations substantially altered from that of the habitat as a whole is much more likely. Under certain situations aquatic habitats will be saturated with oxygen, i.e., holding all the oxygen that can dissolve in water, an amount that is temperature-dependent and decreaseswith increasing temperature. As would be expected, water is saturated with oxygen when the air and water are in close contact (i.e., the surface of bodies of water) or in situations where photosynthetic rates are high, thus increasing oxygen levels (generally theseareas are also close to the surface). However, there are lots of aquatic situations where the amount of dissolved oxygen is not at saturation. Generally, this is due to the depletion of oxygen by living things and the lack of mixing with water that is in contact with the air, a situation found at the bottom of lakes, in slow-moving streams, and waterlogged soils. Impediments to mixing will make oxygen depletion more likely. Two of the most common impediments are density gradients and solid materials. Sphagnum bogs usually have oxygen-depleted water at very shallow depths, depths where oxygen levels are usually much higher. This is the result of the fact that the sphagnum mat hinders the movement of the water column. Although the oxygen-rich atmosphere is centimeters away, oxygen levels drop to nearly zero. A similar thing can happen in ponds that are covered with a thick 'pond scum' of algae. Anothersignificant hindrance to water movement is density gradients set up by temperature. Less dense water 'floats' on more dense water and this will reduce oxygen transfer from the atmosphere to the denser water. The density of water decreases as the temperature increases from 4 C; hence, in this range, warmer water is less dense than cooler water. A consequence of this is that the water is layered ( 'stratified' ) during the times of the year that it is being heated from above, during the summer in northern latitudes, all year round in the tropics. The wind may cause turbulence in the water column but the penetration of this turbulence is limited by the density differences. The greater the temperature differences between the top and bottom, the more resistant the lake is to mixing. Because of this stratification, the bottom layers of a lake may become depleted of oxygen because they do not mix with the oxygenated water atthe surface. In tropical areas, low oxygen levels at the bottom of lakes occur year-round, but in temperate areas, mixing, and as a result aeration of the bottom layers, becomes increasingly likely during the fall. This is because, unlike the heating of the summer, which reinforces the stratification by making the top warmer, cooling breaks down the stratification by making the surface denser. As long as the lake is in a location that cools enough, the lake will eventually become 'isothermal' , i.e., the same temperature throughout the water column. Being isothermal also makes the lake the same density from top to bottom and, as long as the wind blows hard enough (how hard depends on the depth of the lake), the lake will 'mix' , bringing aerated water from the bottom to the top. This is significant from a nutritional standpoint because organic material settles to the bottom of the lake and decomposes there. Minerals released by decomposition are only distributed throughout the water column when the lake is mixed. Further cooling of the lake once again results in stratification, as the density of water decreases(and the colder water floats on top)as the temperature drops from 4 to 0 C. If the lake freezes, the addition of an ice layer eliminates any wind-driven mixing whatsoever and oxygen levels at the bottom of the lake once again drop if respiration exceeds photosynthesis.Thisis usually the case(although some photosynthesis does take place in ice-covered lakes, it is relatively low because of decreased light penetration). In the spring (in the northern hemisphere) heating of the surface first eliminates the ice and then eliminates the stratification, making the lake uniform in temperature and density at 4 C, and again allowing for mixing by the wind. Further heating causes the lake to again becomestratified. Thus lakes in temperate habitats have an annual cycle that includes two brief periods in the fall and spring where mixing is very likely, so long as the wind blows and the lake is not too deep. This situation, termed spring and fall 'turnover' , is highly significant because it allows for mixing of the water column, bringing oxygenated water to the bottom of the lake (and also bringing minerals to the top of the lake (see below)). Light and Aquatic Environments As is the case in terrestrial environments, light plays an important role in dictating the distribution of photosynthetic organisms and it is even more important in aquatic environments because significant differences in oxygen concentrations can develop within the water column, depending upon the balance between photosynthesis and respiration. Light intensity is influenced by the depth and transparency of the water, the latter often being strongly influenced by the number of living things living in the water. Since aquatic photoautotrophs need light to survive, they need to be in the upper levels of the water, or, in the case of some flowering plants, float on the surface or even emerge from it. Phytoplankton (small photosynthetic organisms that 'float' in the water column) need to have features that prevent their settling. Features that are sometimes significant are large surface area to volume ratios (i.e., not spheres), oil or air bodies that decrease density, flagella and phototaxis (movement towards light (see cryptophytes). Some phytoplankton are known to migrate up and down diurnally, moving up to gain more light during the daylight hours. Currents and Aquatic Environments Currents are very significant in some aquatic environments and can have a strong influence on community structure. Currents are significant because they can mix portions of the water column, in particular, they can bring oxygen from the upper layers to the lower layers and nutrients from the lower layers to the upper layers. This is significant because oxygen may be limiting in the lower layers and nutrients may be limiting in the upper layers. Consequently, the current can substantially change the activities taking place. Nutrients and Aquatic Environments Nutrients are often limiting primary productivity and consequently total activity in aquatic situations. This is a result of the fact that most aquatic environments have two distinct parts: the upper layers where photosynthesis occurs and where inorganic nutrients are incorporated into biomass, and the bottom region, where there is typically little photosynthesis, but where biomass from the upper layers tends to settle, decomposition occurs , and nutrients are released. In such a system the activities of both the top and bottom can be limited by a lack of interaction between the two parts: the upper layers are limited by a lack of nutrients, hence little accumulation of biomolecules occurs; the bottom layer becomes limited by a lack of material to eat. Nutrients transported into aquatic systems can be very important. Nutrients can be carried into aquatic systems by runoff from the surrounding land, especially agricultural land where nutrients are added through fertilization. Nitrogen and phosphorus often play key roles in determining the amount of primary production occurring and the total amount of biological activity taking place. However, as was the case in terrestrial systems , there are circumstances where other nutrients can play key roles.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.26%3A_Interactions_Involving_Conditions.txt
Interactions between individual organisms Organisms interact with each other and these interactions can have significant consequences to the participants. Most students are familiar with the classification scheme below which organizes interactions into types based on the consequences of the interaction on the two participants: effect on the 'larger' organism (-) negative (0) neutral (+) positive effect on the 'smaller' organism (-) negative competition amensalism predation, herbivory (0) neutral amensalism 'neutralism' commensalism (+) positive parasitism commensalism mutualism There are multipleproblems with this scheme. It is not clear what level, organism or population, it is focused on or how effects might be measured. If considering at the individual level 'positive' might be monitored by organism size, growth rate, longevity or reproductive success. But if considering the population, level one might consider population density or population growth rate. Sometimes what is 'positive' and what is 'negative' may not be obvious. Some fungal endophytes substantially increase the growthof plants (positive effect) that they infect, yet at the same time reduce or eliminate the likelihoodof producing offspring (negative effect). Nitrogen-fixing bacteria infecting roots may benefit plants (faster growth, bigger plants) if soil nitrogen is low, but harm plants (slower growth, smaller plants) if nitrogen levels are high. Pollinator visits may benefit plants if they transport pollen to other members of the same species but not if their next visits are to different flower species. Perhaps the most significant biological context for the terms would be evolutionary (positive = enhanced reproductive success) but this may depend on circumstances that are difficult to evaluate. Predators would generally be thought to have a negative on prey populations, but in a number of situations, predators are thought to 'benefit' prey populations by preventing overpopulation (Figure 1). Another problem with the scheme is that it ignores the fact that the consequences of interactions may be very different at different levels of biological interaction. Seed predation (e.g., Clark's nutcracker eating pine seeds, Figure 2)) is clearly harmful to most individual pine organisms (i.e., the embryonic pine individual present in a seed) but apparently benefits the pine populations by allowing for dispersal. Another way to organize biotic interactions is not based upon arbitrary considerations of what 'benefits' or 'harms' the organisms/populations involved, instead, it is based upon the medium through which the interaction occurs: • trophic interactions—one organism eats another or part of another, obtaining material (carbohydrates, proteins, fats) that can be used both for ener gy (i.e., burned in cellular respiration) or partially broken down and reformed into molecules of the consumer • resources/ conditions interactions—Resources are materials ( e.g., oxygen ) that an organism either produces, making them available for other organisms or depletes/consumes, making them less available for other organisms . Conditions are physical parameters, e.g., pH, temperature, humidity, light intensity. Conditions influence organism behavior and organisms can change conditions and thereby affect other organisms. Resources and conditions are combined here because several can be considered both as a resource and a condition. Oxygen can be considered a resource because oxygen can be produced or consumed but it also is a condition that has physical consequences, e.g., oxygen concentrations affect the solubility of ions in the soil solution. Similarly, light is a resource that plants ' consume ' , reducing its availability to the shaded plants below, but it also is a physical condition that influences all organisms in a number of ways. • work interactions—one organism does work for another organism (work in the sense of physics, and chemistry, a process that requires the expenditure of energy, e.g., moving material from one place to another). TOPICS • Trophic interactions • Predation • Grazing • Parasitoids • Parasites • Leftovers • Interactions involving resources and conditions • Work interactions Trophic Interactions Although all trophic interactions are 'organism A eats organism B' , resulting in a transfer of material from A to B, the way the eating is done varies greatly and it may be the case that the most significant consequences of the interaction do not involve the transfer of material. Below are four categories of trophic interactions involving the organisms considered in this course. The categories are based on the consequences to the two 'players' of the trophic relationship: the organisms doing the eating ( 'eater' ) and the organism being eaten (the 'eatee' ). Although it is generally the case that the eatee is harmed because it loses material, and the eater benefits because it gains material, this is not necessarily the case and sometimes other components of the interaction are even more significant. Predation The eating event kills the 'eatee' (the organism being eaten) and the eater consumes multiple prey items during its life (Figure 3). In plants, this generally only occurs when the plantsare small when they are seeds ( 'seed predation' ), or the consumption of seedlings. The embryonic plants found in a seed are particularly nutritious per unit weight because, compared to larger plants, they have relatively less structural material (i.e., cell walls) and relatively high concentrations of minerals and vitamins. The eater benefits from the nutrition obtained (assuming that eatee does not contain toxins that the eater cannot handle) and the eatee is eliminated. This interaction has driven evolutionary changes involving chemical, physical and phenological (timing) changes in plants, and consequent changes in predators, for as long as seed plants have been around. In a number of instances, the interaction has developed into a mechanism of seed dispersal, utilizing an eater 's mobility and perhaps its caching behavior (see the reading on pines and the Clark' s Nutcracker). Seed predationalso was probably a driving force in the development of (fleshy) fruits as a means of seed dispersal:plantsdeveloped features that would reward the eatee in a way that did not involve (permanently) consuming the seed and killing its embryo. Seed predation also accounts for fruit structure that most definitely doesprotect the seeds inside (e.g., nuts), although seed predators have responded by developing structures (sharp teeth of saki monkeys or beaks of goldfinch, Figure 4) and behaviors that allow them to open seeds, or digestive systems that grind the seed coat or fruit coat away. Although most of the organisms that we have studied are photosynthetic autotrophs (plants, algae) and are the eatees, we have also considered some organisms that are the eaters (cellular and plasmodial slime molds, and some of the euglenoids and dinoflagellates). Some fungi are predators in the classic sense (i.e., they capture prey and kill them, http://www.mykoweb.com/articles/FungalSnares.html), and a number of fungi are predators in a less classical sense, being capable of killing their food with toxins or other processes. Grazing The eater (grazer) does not kill the eatee, but only eats part of it, and usually, the grazer eats parts of several individuals. Most familiar examples of herbivory (eating of plants) are grazing: cows and grass, deer and shrubs, J apanese beetles (Figure 5) and ornamental plants. While most grazing on plants is on their leaves, some organisms graze on other parts: pollen, flowers, ovaries, roots). Although p lants are the most common kind of organism grazed upon there are several other ' inanimate ' groups that are grazed: photosynthetic protists ( ' algae ' ), a few non-photosynthetic protists (plasmodial slime molds) and many fungi . Grazing is most likely to occur on organisms that have indeterminate growth. Most grazing on plants is on leaves and the eatee is affected both by the loss of photosynthetic area (and hence the ability to photosynthesize) and also because of the loss of nutrients (e.g., nitrogen and phosphorus) that are relatively hard to replace. Too much grazing can be fatal for the eatee but lesser amounts of grazing sometimes actually produce beneficial results; for instance, grazing of apical meristems can induce branching and produce a plant that actually produces more leaves, flowers and fruits. One particularly significant aspect of grazing is that it is a means of disease transmission between individuals , comparable to a mosquito (also a grazer) spreading malaria. Leafhoppers and aphids are both insects that have piercing mouthparts to acquire nutrients from phloem tissue in leaves and stems. If they move from an infected plant to another plant they can transmit pathogens (viruses, bacteria and others) in the process, and often this is the most significant aspect of their grazing (Figure 6). Parasitoids The distinctive feature here is that the reproduction of the eater is obligatelyand directlyassociated with the trophic event and that the eatee dies as a result of the association. While any heteterotroph must consume food in order to acquire the matter and energy needed to reproduce, in the case of parasitoids the connection is direct because a propagule (usually a fertilized egg) is deposited on the eatee. The vast majority of parasitoid interactions involve insects, one as the eater and another as the eatee. But occasionally plants are parasitoid prey, sometimes by organisms consumingseeds (e.g., granary weevils (Figure 7) and acorn weevils http://video.nationalgeographic.com/video/animals/bugs-animals/beetles/weevil_acorn/) and also some fungi, termed necrotrophic fungi, who infect their hosts (plants), kill them with toxins and then feed on the dead tissue, eventually producing fungal reproductive structures. Parasites As in grazing, the eater generally does not kill the eatee, but in contrast to grazing, the eater generally only feeds upon one host and thus is not typically a means of spreading disease from one eatee to another. Evolutionarily, one might argue that parasites (and perhaps some grazers) adopt a strategy of keeping their host alive in order to assure a food supply for a longer time. There are a number of fungi called biotrophic fungi, including the important plant pathogenspowdery mildews and rusts, that feed off of living plant tissue and would be considered parasites. They produce structures called haustoria that penetrate the cell wall and interact with the plant cell plasma membrane, providing them with access to materials (e.g., sugars, amino acids) present in the cytosol. Dodder (Figure 9) a non-photosynthetic flowering plant, also produces haustoria. These penetrate into the phloem tissue of their hosts and provide them with nutrition. The fungal component of mycorrhizae would be considered parasites, as would be the nitrogen-fixing bacteria that form galls in some plants. Indeed, mostgall-forming organisms (insects, fungi, mites) would be considered parasites. The gall is an abnormal growth induced by the presence of the parasite. The parasite is fed by its host and ultimately exits the gall. (As an example see www.wenatcheenaturalist.com/sagebrush-galls/ or www.fllt.org/inside-the-goldenrod-gall/ ). Most of these interactions are similar to parasitoids in that the reproduction of the eater is dependent on the interaction, however, the host is not killed. In most instances, the eatee suffers because of a loss of nutrients, and the eater benefits because it is provided with nutrition and often with protection as a result of the structure of the gall. Saprophytes, i.e., eating 'leftovers' All organisms are a source of food after they die and thereby represent an 'easily captured' prey item. Heterotrophs that consume material (plant, animal, fungal and others) that is already dead (i.e., they did not kill it) are termed saprophytes. Because plants are continually shedding leaves and roots (and in many cases stems), these discarded items are often abundant and provide food for a number of organisms. The nutrient quality of these discarded items is generally substantially below that of living tissues because the plant, in the process of senescence, recycles materials, retrieving much of the material present in the soon to be discarded item before it is actually shed. Leaf protein, nucleic acid and mineral concentrations all decline drastically before leaves are shed and the remaining material is much less digestible both because most of the molecules that remain(e.g., cellulose, lignin) are more difficult to degrade and because of the lack of nitrogen makes it hard to build up substantial populations of saprophytes. Organisms(especially larger ones. e.g., earthworms, insect larvae) feeding on dead organic material often obtain nutrition, perhaps most of their nutrition, from the consumption of much smaller organisms (e.g., bacteria, amoebae, fungi) that are present on the decaying material and not from theorganic material itself, i.e., they are really getting their nutrition from being predators, not saprophytes. Bacteria and fungi are the most significant saprophytes in the soil but other groups (cellular slime molds, plasmodial slime molds and heterotrophic forms of euglenoids) may also be saprophytic. In aquatic systems, a significant amount of organic material can be broken down to the point that it dissolves and ispresent as dissolved organic material, which some organisms are able to assimilate. Conditions/Resources Interactions All organisms change the resources and conditionsaround them. The extent to which this affects other organisms depends on: how big the organism is (big things have more of an effect than small ones), how plentiful they are (i.e., their population size) and precisely what changes they bring about. Any organism is a 'producer, ' i.e., it grows and produces a resource (i.e., biomass) that some other organisms can eat. Therefore all organisms must provide resources. Plants (andmore generally autotrophs) are particularlyimportant in a resource sense because, being the base of food chains, their activity represents how many trophic resources are available to entire communities. Also, except for autotrophs who are self-feeders, all other organisms, i.e, . heterotrophs, eat something and can influence other species by depleting that resource. But there are many other ways that organisms interact with each other besides affecting trophic resources. Here are some examples: The trees of a forest substantiallychange the conditions below them.Temperatures are moderated (cooler in the daytime, warmer at night). Wind is moderated. Rainfall/snowfall patterns are changed. For deciduous forests the annual deposit of leaves covers the ground surfaceand acts like insulation, keeping the soil warmer in the fall and cooler in the spring. In evergreen forests, leaves layer the ground but the fact that they do not come all at once alters the dynamics. Leaf litter affects soil chemistry. Thus different species can have different effects. The tipping over of a tree root system that occurs when trees are blown over changes the topography and exposes lower mineral layers. And some species (e.g., yellow birch) germinate best in mineral soil because the roots of seedlings are unable to penetrate a blanket of leaf litter. Oxygen consumption by organisms in terrestrial habitats generally has little impact because the oxygen levels in the air are high (~20% of the air is oxygen) and because winds keep the air well-mixed and localized depletions are unlikely. In contrast, oxygen depletion in the soil and in some aquatic situations can havevery significant consequences. In waterlogged soil, oxygen consumption by roots, fungi and a host of soil organisms, coupled with reduced oxygen movement in soils water-filled pores, can make the soil anaerobic. Similarly, unless there are processes promoting mixing of the water column, respiration by heterotrophs at the bottom of the lake significantly lowersthe oxygen levels, potentially affecting all organismsliving there. A globally significant example of organisms changing oxygen availability and consequently affecting other organisms involves Sphagnummossand areas known as bogs. Sphagnum mosscan develop high population densities and this, coupled with their pattern of growth, creates a dense mat of stems elongatingat the top but withan extensive layer of dead stem and leaf material below. The stems and leaves hold substantial quantities of waterand water is also held in the spaces between plants, producing what is essentially a giant sponge. This creates a habitat of stagnant water, where there islittle mixing of the surface layer of water with the water below. Consequently, at a very shallow depth, the water becomes anaerobic because of oxygen consumption by saprophytes feeding on the dead plant material. In addition, the chemistry of sphagnum cell walls causes the waterto becomeacidic. The acidic conditions, combined with lack of oxygen, greatly reduce the decomposition of plant material, thereby reducingthe supply of nutrients(remember that nutrients become available to plants because of decomposition), and cause peat (un-decomposed plant material) to accumulate. The soil conditions prevent a large number of species (e.g., trees) from existing in the area or causes them to be stunted. Instead, bogs have a characteristic group of species, often members of the blueberry family, that are tolerant of the soil conditions. One of the types of plants found in the nutrient-poor conditions of a bog are 'carnivorous' plants including pitcher plants, which nicely demonstrate the nutritional distinction between autotrophs and heterotrophs. Heterotrophs obtain both 'food' (a carbohydrate supply for cellular respiration) and nutrients (e.g., nitrogen) from the material they consume. Carnivorous plants obtain energy through photosynthesis just as most plants do, making food in photosynthesis and then eating it. The significance of their predation is that it provides carnivorous plants with non-carbohydrate nutrients which are otherwise hard to come by because of the habitats where they dwell. There are a wide variety of devices for capturing prey (generally insects), including pitchers, snap traps, flypaper, bladders and lobster traps ( https://earthsky.org/earth/lifeform-of-the-week-carnivorous-plants-are-out-for-blood ). Pitcher plants have a highly modified leaf whose petiole serves as a container for rainwater. The pitcher also possesses features that attract and capture insects who eventually drown there. The water develops a decomposition community of bacteria, fungi, water molds, amoebae, insect larvae and others. As a result of their activity, nutrients become available in a small enough form for the plant to absorb as they do in normal aerobic soil. In contrast, nutrients do not become available to the roots due to the waterlogged peat that pitcher plants are rooted in. Dense growth of algal (usually cyanobacteria but sometimes green algae) can 'seal' the top of ponds, creating a situation comparable to sphagnum bogs because the wind is not able to inducemixing of the oxygen-rich top layers of the water with the lower layers. Because no light can penetrate the dense algal layer on top, no photosynthesis is possible except at the surface. These factors, coupled with the magnitude of dead plant material that is created by the algal growth and the decomposition of this material by heterotrophs below, cause the lower water levels to become anaerobiceventually drastically altering the species present and limiting the rate of decomposition. Resources /conditions represent significant avenues whereby species can interact with each other. In particular , two species requiring the same resource can affect each other by making the resource less available for other organism/species. Plants interact with other plants by their consumption of light, nutrients and water. This is the classic explanation for an interaction described as 'competition' although there are other reasons besides resource depletion that might explain why the presence of one species might deter the growth of another species (or at the population level, the presence of one population lessens the population density of a second population). Globally, two of the most important biotic consequences involving resources are the addition of oxygen to the atmosphere by photosynthetic organisms and the addition of simple mineral forms of nutrients into the soil or aquatic systems as a result of the decomposition carried out by heterotrophs. Plants provide resources in other ways; their physical structure is important to many other other species : birds nest in trees ; many spiders use plant structures as a base for their webs; p arts of plants and pieces of lichens are often used as building materials for nests. Work Interactions A number of species interact with each other by providing services, i.e., doing work, for other species. For plants, the most significant of these results fromorganisms that provide mobility, mobility for male gametophytes in pollination and mobility for seeds. Animals transport seeds both 'passively' , when seeds or fruits stick to fur, and 'actively' when the plant attracts animals to a trophic reward (generally fruits, but sometimes seeds, Figure 14) with the mobile animal then transporting the seeds and depositing them (often by defecating) some distance away. For the most part, pollination is active with the plant advertising a trophic reward, which may be nectar (a sugar secretion) and/or may be pollen. In the case of pollinators, not only are some species capable of moving pollen but they can do it in a very directed way, transporting it to members of the same species of plant, thereby allowing cross-pollination and cross-fertilization to occur. This specificity (i.e., mobility to a specific, favorable location) occasionally is the case for seed transport, e.g., Clark's nutcrackers transport seeds to sites that are particularly favorable for the growth of the pines whose seeds they are transporting; certain ant dispersed species bring about movement of seeds to sites (ant nests) that are particularly favorable for seedling establishment (Figure 14). While the common interaction is a 'quid pro quo' with food provided by the plant 'in exchange for' work by the visitor, occasionally the plant is providing a non-food reward. Some orchids provide specific chemicals that serve as pheromones for the insects that acquire them. The Yucca plant provides not only food but also a shelter for larval yucca moths that develop from the eggs that the yucca moth deposits as it is pollinating the plant. Ficus trees provide food and nesting sites for pollinators. Two excellent sites that consider these interactions are: [Both these links come from an outstanding website ( 'Wayne' s Word') that is an excellent source of botanical information. Take some time to explore it.] There are a number of examples of 'cheating' by both the visitor and the plant. Some visitors can consume the food reward without picking up pollen and consequently without providing the plant with a service. Plants may attract visitors with visual displays but give them no rewards. 'Protection rackets' describe a relationship where the plant provides food and another species does work by protecting the plant from herbivores. This relationship is particularly well developed in some Acacia trees and shrubs where the plant not only provides food rewards but also provides nesting spots for colonies of ant defenders. Additionally, while the typical food reward (for pollination, seed dispersal and defense) is nectar, a compound that is cheap to produce, some Acacia species provide more complex food rewards, Beltian bodies, packets that are much more rewarding nutritionally because they contain lipids and proteins. These are much more expensive for the plant to make. An extension of this interaction is the three species interaction of plants, aphids and ants. Aphids are insect herbivores that tap into the plant 's phloem tissue using their stylet. Since phloem sap has abundant sucrose but scant amino acids, the aphid eats a lot of phloem sap to acquire the amino acids it needs and the excess sucrose is excreted as ' honeydew ', aka ' frass' (insect excrement). Ants have developed a relationship of defending the aphids from predators while acquiring the honeydew that the aphids produce. Nitrogen-fixing bacteria do chemical work, the reduction of nitrate to ammonia, for their host plants, in exchange for food and a protected habitat. In nodule forming plants the protected habitat are galls on the roots. The aquatic fern Azolla forms small cavities on the surfaces of leaves that the nitrogen-fixing cyanobacterium Anabaena colonize. This relationship is utilized by rice farmers who encourage the growth of Azolla, a small aquatic plant that lives on the surface of bodies of water. Nitrogen fixed by the cyanobacterium becomes available to the rice when the Azolla dies and is decomposed. A more 'one-sided' work interaction involvesinsects acquiring and utilizing chemicals that the plant synthesizes. Monarch butterflies acquire a poison from the milkweed plants that they eat. The plant gains nothing but the insect acquires a chemical that deters predation. A similar situation occurs with poison dart frogs. The frogs become poisonous because of the insects that they consume, with yet-to-be-determined plants eaten by the insects providing the specific chemicals. Plants can also be on the receiving end of defensive chemicals as is the case with some fungal endophytes who produce toxins that can affect herbivores. A number of species utilize the work performed by one species in order to produce a particular structure. One might consider the role of coral animals and lichen fungi to be providing services (structure) for the dinoflagellates and algae that live inside them. Plants provide structural services for other plants as well; vines utilize the structure of other plants and thereby avoid the costs associated with producing structural cells (sclerenchyma fibers) that are needed to produce a rigid stem that can withstand the forces of gravity and wind. There are a group of plants called 'hemiparasites' that utilize the root systems, the structure, of other plants. Their hosts supply them not with food (carbohydrates, which would be a trophic interaction and would require connecting to the phloem tissue) but with water and minerals, that move passively up the host's roots and into the stem of the hemiparasite. At least some of the benefits of mycorrhizal associations may involve a similar type of relationship, with the fungus providing structure to explore the soil to acquire water and nutrients, and the plant providing food for the fungus. In other mycorrhizal associations, there may be more specific actions involved, for example, the fungi may be producingenzymes that mobilize mineral elements and transfer them to their host. Eating a plant is generally considered positive for the herbivore (the ' eater ' ) and negative for the plant (the ' eatee ' ) but plants may be poisonous to the herbivore and plants may ' benefit ' in a number of ways (e.g., increased growth, increased seed production) in response to being eaten. Further Reading “The Microbial World: Biotrophic plant pathogens” by Jim Deacon	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.27%3A_Biotic_Interactions.txt
What is agriculture? It is an activity whereby an organism actively cultures/cultivates/cares for other organisms with the intent of somehow utilizing these organisms directly or indirectly. While we are focused on the agricultural interactions involving humans, other organisms, specifically numerous ant species, carry out agriculture, culturing fungi, aphids and other organisms. Agriculture generally involves the 'domestication' , a genetic modification of organisms, both plants and animals, allowing them to be better utilized. Agriculture involving humans and plants is certainly one of the most significant biotic interactions, an activity that influences vast expanses of land, roughly 12% of the earth's land surface. Although there is much less agricultural activity in aquatic/marine systems, there is some, and secondary effects from terrestrial activities, e.g. fertilizer run-off, also has an impact. Like all interactions, agriculture involves modifications of both partners. And while we will focus on the non-human component, generally flowering plants, it is important to keep in mind that agriculture has brought about tremendous changes in humans, with probably the most significant ones coming about as agriculture originated and humans altered their patterns of activity, movement and social interactions. It is significant to note that relative to the existence of humans, agriculture is a recent innovation, starting roughly 10, 00 years ago. For most of their 200, 000 year existence, humans were not involved with agriculture although they certainly did influence specific plants by their activities. It is also significant that agriculture apparently developed separately in multiple regions. Authorities now list eleven sites of agricultural origin, including the Middle East, Africa. the Far East and North, South and Central America. In each of these regions distinct species were utilized. The table below lists some of the earliest crops along with their region of origin: Table 1. crops site of domestication wheat, peas, lentils, flax, figs, chickpeas Middle East potato, tomato, pepper South America corn, squash, beans Mesoamerica banana, sugarcane, taro New Guinea rice, mung beans, soy beans China millet, sorghum, Africa eggplant, mungo bean, pigeon pea India The majority of crops, and certainly the crops associated with the origin of agriculture, were wild plants that humans had already discovered to have desirable features (most commonly features related to eating but sometimes the features were mechanical, e.g. cotton, or chemical, e.g. a waterproof latex from tree bark). The next step was the appreciation that the plant could yield more product if it were somehow cared for, e.g. planted, pruned, etc. For most crops, the practice of collecting and planting seeds was crucial to crop development. Through time, many plant species were genetically modified by humans through selection of seeds from plants with particularly desirable traits, e.g. large seeds. Genetic modification of agricultural organisms (Darwin called this 'artificial selection' ) was most rapid when dealing with annual plants that could be selected for yearly. This chapter examines the histories of several crops that reveal interesting biological features. TOPICS • How do crops come to be? • Wheat • Strawberry • Naval oranges • Banana • Corn • Hybrid seed • Generating variability Wheat The plant known as 'wheat' actually includes three distinct species in the Triticumgenus: einkhorn wheat, emmer wheat, and bread wheat. Each of these species has wild relatives that may be considered separate species or may be lumped with the domesticated form. These species are related evolutionarily in what is known as a polyploid series. Einkhorn has a diploid chromosome number of 14 and produces haploid gametes with seven chromosomes. Emmer wheat has 28 chromosomes, 14 of which came from Einkhorn wheat and 14 of which came from a related, but separate genus (Aegilops, although some workers have lumped Aegilopsand Triticum). Bread wheat has 42 chromosomes, 28 of which come from emmer wheat and 14 from another species of Aegilops. Polyploidy is common in plants and is an aspect in the history of multiple crops. It can come about several ways, the most common being a hybridization event where gametes of two separate species are combined. Viable gametes cannot be produced in the hybrid because meiosis is thwarted by the fact that there are no homologous chromosomes to pair, the chromosomes from one parent do not have 'matches' because the second parent was a different species with different chromosomes. Consequently, the hybrid is sterile; this ensures that the two parents are reproductively isolated, i.e. separate species. However, hybrid sterility can be overcome in several different ways. One is to produce functional gametes (i.e. cells that can fuse with other cells) without going through meiosis, i.e. to produce 'unreduced gametes' . If these 'unreduced gametes' find each other and fuse then a new species is created, one that has twice the chromosome number of its either of its parents. In the case of emmer wheat the new species has a diploid chromosome number of 28, 14 (seven pairs) coming from einkhorn wheat and 14 (seven pairs) coming from Aegilops. Another possibility is that the cells within the hybrid replicate their chromosomes (mitosis) but the cell does not divide, leaving a cell with double the number of chromosomes of its parents, and significantly, producing a cell that has a match for each chromosome. Such a cell (or derivatives of this cell) could go through meiosis because it does have pairs of chromosomes. In both of these situations a new 'polyploid' species is produced, for example emmer wheat. Polyploidy is also discussed in Chapter 31. Bread wheat was produced by the same polyploid mechanism following hybridization between emmer wheat and another species of Aegilops . Hence, bread wheat possesses three genomes (sets of chromosomes), one from einkhorn wheat and two from two different species of Aegilops. Each set consists of seven chromosomes, thus dipoid cells of bread wheat have 42 chromosomes, two copies of each of the three sets of chromosomes. The origin of bread wheat is quite recent, less than 10, 000 years ago, and after both einkhorn and emmer wheat had been domesticated. Strawberry The strawberries found in grocery stores have a very interesting heritage involving Chile, eastern North America and France. Strawberry is in the genus Fragaria and there are over 20 species occurring primarily in temperate regions of North America, Europe and the Far East. Most of these species have seen very limited agricultural utilization but are harvested in the wild. Although it has very limited commercial production, one European species, F. vesca, especially some clones with particularly large fruits, has been cultivated for over 500 years, primarily in parts of Turkey. A South American species with white fruits, F. chiloensis, , native to the west coast of North and South America was cultivated by native tribes in what is now Chile. In the early 1800 's six specimens of F. chiloensis were transported to France and propagated in several gardens alongside specimens of F. virginiana , a North American species. The two species hybridized, forming what is called ' garden strawberry ', Fragaria x ananassa (the ' x' in the name indicates that it is a hybrid). It is this hybrid that is now widely cultivated throughout the world, generally being propagated through cuttings. Navel oranges Another crop with a 'chance' origin is the navel orange. It occurred as a 'sport' , a mutant branch, on an orange tree growing in Brazil. Remember that branches originate from lateral buds, meristematic tissue left behind by the elongating shoot apical meristem. Occasionally, some of the lateral bud meristems possess mutations that cause them to produce a branch that grows abnormally or one that produces leaves that are unusual (a common manifestation is a branch that produces variegated leaves, leaves that are not uniformly green but are colored a variety of ways). In the case of the navel orange the branch was unusual because its flowers, which normally occur singly, occured as pairs, with a second flower produced very close to the 'normal' flower. The proximity of the two flowers is manifested in an altered fruit development, producing not two distinct fruits but rather a single fruit with another fruit inside it. This is what produces the navel for which the plant is named. If one peels and opens up a navel orange, the second fruit is very evident at navel end. This fruit does not possess a skin and is much smaller than the normal fruit , typically less than an inch in diameter. But, like the normal fruit, it is composed of wedge-shaped sections. A second abnormality of navel oranges is that the pollen is sterile and consequently cannot fertilize flowers. Because of this, the fruits produced by navel oranges are seedless. Navel oranges are perpetuated by cuttings, and all the navel oranges grown world-side are ultimately derived from to the original branch produced on the tree in Brazil. A cutting can be rooted to form a naval orange tree but are more commonly cuttings are grafted on to an existing root stock. A variety of species, generally close relatives, can be used as rootstocks and rootstocks can be selected for favorable characteristics, e.g. temperature, drought and pathogen tolerance. This allows horticulturalists to develop new varieties of rootstocks as pathogens evolve. Banana Unlike naval oranges which are propagated by grafting branches (called scions) on to a variety of rootstocks, bananas are propagated by cloning of whole plants, i.e. taking a cutting, usually a branch, and having it form roots. Cloning from cuttings is much less 'technological' than grafting and the utilization of cuttings as an agricultural technique goes back to the time when agriculture was developing. There are a large number of banana varieties and it is thought most appeared in the wild and were selected because of favorable features, in particular large fruits that lack seeds. Obviously a lack of seeds makes propagation by seed impossible, but cloning allows these favorable characteristics be perpetuated. Modern studies indicate that the many banana varieties are derived from two species and polyploid derivatives of these species. Most bananas grown commercially are triploid, with a genetic constitution of AAB meaning that they possess two chromosome sets of one type and one chromosome set from the other. Such a triploid may be the result of a tetraploid (AAAA, that produces gametes that are AA) hybridizing with a (normal) diploid (BB, that produces gametes that are B). The offspring of this cross are sterile because meiosis is impossible, but cloning allows the plant to be perpetuated. Moreover, the sterility brought about by hybridization has created a favorable feature — no seeds. Triploids may also arise by the the union of an unreduced gamete from a diploid species (the species is AA but produces gametes that are AA instead of A) combining with a normal gamete from another species, e.g. a diploid species BB producing haploid gametes, B. The offspring is triploid, AAB, and sterile. For most plant species the production of fruits is a consequence of the production of seeds, with the initiation of seed development triggering the initiation of fruit development. The production of fruits when seeds are not developing at all, or when seeds are initiated but soon aborted, is called parthenocarpy. It is generally considered to be evolutionarily unfavorable since the basic function of fruits is to promote seed dispersal and producing fruits without seeds is a waste of resources. Parthenocarpy can appear 'spontaneously' , but it generally will not be perpetuated, unless of course it is selected by early agriculturalists. More recently, parthenocarpy may be developed in breeding programs. An example is the seedless watermelon, which, like most bananas, is a sterile triploid, but it was produced by plant breeders crossing a tetraploid plant with a (normal) diploid plant. Seedless watermelons do have seeds but they are small and not fully developed. Seedless watermelons do require pollination to initiate the seeds but they soon abort. In some crops (e.g. some varieties of tomato) parthenocarpic varieties produce fruits even if pollination is lacking. Corn Corn 's origin as a crop has been a mystery because there had been no obvious ancestor, i.e. a species that looks like corn and could be considered to be something that primitive agriculturalists might manipulate to produce the entity that we know as corn. Research over the last 75 years has revealed that there is a close relative, called teosinte, but its proximity to corn is obscured by the fact that it ' looks ', i.e. has a morphology, that is substantially different from corn. Studies have revealed that corn and teosinte are actually the same species — they readily interbreed. The morphological difference between the two are actually the result of changes in only a few (less than 10) genes. It is now thought that selection on teosinte developed the variety (subspecies) that we now consider to be corn, a plant that unlike teosinte: does not branch, has much larger ' ears' (clusters of female flowers), and has seeds that are not enclosed in a rigid container but are relatively easily removed, allowing easier access to an edible structure. Corn was responsible for dramatic changes in agriculture, in particular the development of seed companies, commercial entities that provide seed to individual farmers. Up until early in the 20th century most farmers provided seeds for themselves by storing seed from the previous crop. When storing seed for the next year 's crop, most farmers, passively or actively, selected for increased yield by saving seed from plants that were disease resistant, pest resistant and generally higher yielding. Early in the 20th century agriculture changed drastically in a number of ways, one of them being that farmers started to purchase seed from companies because they could provide seed that was better than what farmers had on hand. This better seed was the result of agricultural research occurring both in' land grant colleges '(who were charged with improving agriculture) and also in private companies when it was realized that that money could be made by supplying seeds to farmers. Corn was instrumental to this process because it is amenable to producing what is known as ' hybrid seed'. Hybrid seed Hybrid seed is seed that is produced by crossing two inbreed lines, where each inbreed line consists of plants produced by multiple generations of breeding with close relatives. Genetic research had shown that while inbreeding produced plants that grew and yielded poorly, a hybrid plant, produced by the crossing of two inbreed lines, was particular vigorous ( 'hybrid vigor' ), more vigorous than either of the parental types before they were inbreed. 'Hybrid vigor' opened the door to seed companies, making them profitable for two reasons: (1) hybrid seed must be purchased anew each year because the seed from the hybrid crop is NOT particularly vigorous; it isn't a hybrid—both parents are essential the same, (2) developing hybrid seed was an activity that farmers growing crops for food probably would not want to take part in: they were interested in crops that could be grown in a season and sold to make a profit. Corn is particularly amenable to producing hybrid seed because it has separate male and female flowers that are found on different parts of the plant. Corn tassels are clusters of male flowers. These can be removed and the pollen they produce can be used to fertilize specific plants. With corn, controlling who breeds with whom, which is essential to the production of hybrid seed, is relatively easy. The success of hybrid corn seed has spurred research into producing hybrid seed in a wide variety of plants including many that do not have separate male and female flowers. Seed producers have utilized a variety of techniques that make hybrid seed production possible (see chapter 31) Hybrid seed has several favorable features in addition to producing vigorous plants. The plants in a hybrid crop are more uniform than those produced from open pollinated seeds. Uniformity in size and time of maturation may greatly enhance harvesting. Hybrid crops also allow favorable traits developed in parental lines to be combined. Generating variability Whether or not one is utilizing hybrids, crop development requires variability followed by selection of plants with favorable features. Open pollinated crops generate variability both through naturally occurring mutations and also by chance shuffling of genes in the sexual process. Although there had been suspicions on the existence of sex in plants and the roles of pollen and pollination, the observations of Rudolf Cameraius late in the 17th century revealed the role of pollen and made possible the generation of variability by the intentional crossing of two related species. Often these efforts were stimulated by the botanical explorations and the collection of 'new' plants, e.g. the production of commercial strawberries described above. This allowed closely related plants to be grown together and crossed. Early in the 20th century workers discovered that they could generate variability with treatments that induce mutations: specific toxic chemicals or harsh radiation. And most recently modern molecular techniques allow for the most precise modifications of plant characteristics through the introduction, or occasionally removal, of specific genes. Although the later process is the only one described as 'genetic modification' , one should appreciate that crops have been genetically modified once they started to be cultivated. One should also appreciate that modern techniques are by far the most specific, meaning that the modifications are the most targeted, with the least amount of disruption of non-target genes and features (see chapter 31).	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.28%3A_Agriculture.txt
Ralph Waldo Emerson defined a weed as 'a plant whose virtues have not yet been discovered' , but in fact a number of weeds were known to have 'virtues' and were spread by humans intentionally. Dyer's woad is a significant pest in the western U.S. but was brought to North America intentionally for its use a source of blue dye (hence the common name). Many weedy plants, e.g. purple loosestrife (Figure 1), were intentionally introduced by gardeners who found them attractive. A large number of weed organisms of all types are similarly the result of intentional introduction in new habitats (honeybees, earthworms, gypsy moth, starlings and many more). Is there a better definition of weed? Ecologist consider organisms to be 'weedy' if they have a suite of characteristics (high reproductive potential, extensive dispersal abilities, rapid growth rate, ability to reproduce even under adverse conditions) that would make them likely to appear and survive in disturbed habitats. Disturbed habitats, sometimes called ruderal habitats, are areas that have once been populated but some disturbance, e.g. fire, has eliminated what once lived there. Significant for terrestrial habitats, they generally are sites with developed soils, as opposed to sites that were never vegetated and have no soil. So although ecological weeds are considered 'pioneer species' , they are not pioneering on to previous uninhabited land our very young soil. Ecological weeds can colonize and quickly dominate a disturbed site but may not persist because they often are unable to compete with other species that eventually arrive at the site. But 'weed' is not used just by ecologists and its definition is both utilitarian and subjective: 'A plant that interferes with the management objectives at a particular location. It is a plant growing where it is not wanted. Under certain situations, the plant may not be totally undesirable.' This definition focus on plants but undesirable organisms come from the entire spectrum of life, including the non-plant organisms considered in this book: cyanobacteria, green algae, red algae, diatoms, dinoflagellates and fungi. Weeds are 'pests' , organisms that are undesirable for reasons that are specific to a particular situation and, as noted above, their undesirable nature depends upon situation. • honeybees are pests when they nest in houses • earthworms are desirable in agricultural situations but are weeds in native habitats where they can alter conditions and disrupt the native community • dandelions are weeds in lawns, where some consider them unsightly, but are useful to pollinators and to foragers who eat their leaves and flowers • sandbur is highly undesirable on beaches because of its sharp fruits that are painful to step on and stick to clothing • dyer's woad clearly is (was) useful as a source of dye but if one is managing land for other purposes then it is a weed • weeping willow trees are desirable as ornamentals but their roots can clog drainage systems • the nitrogen fixing bacterium Rhizobium is desirable if it invades plant roots in habitats where nitrogen is relatively scarce. When nitrogen is abundant Rhizobium actually decrease plant growth because they are being fed by the plant The last example highlights the fact that there is some overlap between 'weeds' and 'disease' , something that will be considered in the next chapter. TOPICS • Features of weeds • Controlling weeds Features of weeds As mentioned above, weedy plants typically grow fast and reproduce both rapidly and abundantly. But given the flexible and utilitarian definition of weed a key feature of weeds is that they must have characteristics that someone might consider undesirable. Here are some examples: • dandelions interrupt the smooth continuous texture of a lawn giving what some consider a an undesirable look. • sandbur produces fruits that are very painful to step on or get caught in a stocking • burdock, beggar's tickseed, stickseed and many others produce fruits that stick on clothing • box-elder trees produce an unappealing form that readily sheds branches. Its abundant fruits clog gutters • poison ivy, wild parsnip, giant hogweed, St. Johnswort are toxic to many human The foremost undesirable feature of agricultural weeds is that their presence in cropland deters the growth of whatever crops are being grown, an interaction that generally would be labelled competition, a concept that is easy to cite but is often much more difficult to pin down. The basic idea is that if two species utilize the same resources (water, light, nutrients) then the presence of of a competitor can reduce the availability of these resources and thereby diminish the growth of the crop. The phenomenon of decreased crop growth when in the presence of weeds is well established, but the exact mechanism is elusive and certainly may vary between different weeds. Note that the best competitor for any particular crop plant is another individual of the same type because it requires the same resources and acquires them in the same manner. Thus intraspecific competition (between individuals of the same species) may be hard to separate from interspecific competition (crop vs. weed). Keeping track of resources is often challenging and other interactions might account for the pattern. C ompetition could be due to factors such as allelopathy (the weed produces chemicals that deter the growth of the crop) or perhaps because the weed attracts insect pests/disease organisms that may affect the crop. For these reasons competition is often defined without the specific requirement of resource depletion. Most agricultural weeds are plants that deter the growth of crop species for undetermined reasons. What might make a particular plant likely to be an agricultural weed? Here there is large overlap with characteristics of ecological weeds: • weeds seeds germinate readily with few or no specific germination requirements • weeds grow quickly and since resource acquisition is strongly tied to plant size, growing quickly allows weeds to be very effective competitors • weeds readily reproduce, allowing for their perpetuation on a site and producing a substantial 'seed bank' of seeds in the soil. Although most weed seeds germinate readily, not all do, and some seeds remain viable for tens of years, meaning that ungerminated weed seeds remain in the soil for prolonged time periods While the above apply to annual weeds, there are also perennial weeds which reproduce readily from fragmented roots which may be produced by tilling. Why till? because most crops are annuals and they would have a very hard time competing against already established plants. But note that tilling 'plays into the weed' s strength': it is a form of disturbance which is generally something that weeds require. The characteristics listed above also would be desirable features of a crop plant: germinate readily, grow quickly, reproduce abundantly. Indeed, several crops are thought to have been domesticated from weeds (e.g. wheat, sunflower, barley, carrot). Another feature that is commonly associated with weeds is that they are non-native, i.e. they were introduced into an area where they previously had not be present, generally because of human activity (both intentional and unintentional). While some would consider any non-native to be a weed, most would require that the introduced species must be invasive, i.e. spreading from where it was introduced. Many introduced species are invasive and this is generally attributed to the fact that 'natural controls' (herbivores, disease) are not simultaneously introduced with the weed. While this certainly explains the invasive nature of some introductions, other factors come into play. Dyer 's woad was introduced in the eastern U.S. and showed only a modest invasive nature as it spread westward and was restricted to repeatedly disturbed sites like the sides of roads. Arriving in California and Utah in contaminated alfalfa seed its behavior changed substantially, becoming much more invasive and entering habitats that are much less disturbed, replacing native plants. Part of this behavior is probably due to the fact that woad' s native habitat is much more similar to the arid west than to the more mesic eastern and central part of the country. An interesting invasive pattern is shown by black locust, a tree native to central and southeastern U.S. but not to the northeast. After it was intentionally introduced to the northeast it has become invasive as it has in several other parts of North America. What had limited its spread previously is unknown. Again appreciating that what a weed is is subjective, black locust might be considered a weed in the northeast but not in the areas where it is native. Another interesting pattern is seen in Phragmites australis , common reed. Apparently a variety of this species was native to North America and was present when European's arrived. This native variety of the species is not invasive and does not form large monotypic stands. Ecologists noted that the behavior of the plant changed drastically in the 20th century, with the plant becoming much more invasive. What actually happened was that a European variety of the same species had been introduced and this was the plant was exhibiting the invasive behavior. The two varieties (non-invasive North American ; invasive European) are very closely related (same species) and very difficult to distinguish. Apparently minor genetic changes can be responsible for invasive behavior. However, lots of weeds are 'natives' (ragweed, giant ragweed, sunflower, Jerusalem artichoke, milkweed, New England Aster, goldenrod) and most of these have not invaded new habitats but have continued to occur in the disturbed habitats found in any particular region. Weed control In most situations weeds cannot be permanently eliminated but their populations may be controlled using three approaches: (1) chemical control, using pesticides (herbicides) to kill the weed (2) biological control, using biological agents (pathogens, herbivores) to reduce weed populations and (3) cultural control, modifying how the land is maintained in order to reduce weed populations. Chemical control Chemical control is a recent innovation, only becoming a significant control agent in the last eighty years. The basic idea is simple: find some chemical that kills weeds. The difficulty is that most chemicals that kill weeds are non-selective, i.e. they don't just kill weeds, they kill all or most plants, including those whose growth you are trying to promote. A wide variety of herbicides have been developed but the three below are widely used and show a degree of selectivity and therefore can be used in some situations without damaging the plants/crops one is trying to grow. 2, 4 D (2, 4, dichlorophenoxyacetic acid) is the oldest widely used herbicide. Its discovery as a useful product, a weed killer, was the result of 'basic' research, i.e. research that was not focused on utility (developing a weed killer) but rather research that simply involved developing an understand of the natural world. In this case, workers were studying the effects of auxin, the first chemically identified plant hormone, originally studied by Darwin one hundred years earlier. The only naturally occurring auxin is indoleacetic acid, but early in the 1940 's workers discovered a number of chemicals, with structures similar to indoleacetic acid, that could produce similar effects on plant growth and development. One of these artificial auxins was 2, 4 D. It was up to Dr. Franklin D. Jones to do some ' applied ' science, i.e. apply basic research to a practical problem. Dr. Jones was looking for something to kill the poison ivy that was plaguing his children. He tried 2, 4 D and found it was very effective in killing poison ivy. Significantly, 2, 4 D is selective: it kills most broadleaf plants (dicots) but spares ' narrow-leaved' plants, grasses and similar species. Because this selectivity matches what one might look for eliminating lawn weeds and weeds of cereal grains (e.g. corn, wheat), 2-4 D has proved to be highly useful. Roundup (glyphosate) was developed in the 1970 's and is the most widely used herbicide both in agricultural situations and in home/garden situations. It is not at all selective, basically killing whatever plants to which it is applied. It is also a systemic herbicide, meaning that if it is applied to the leaves it can be transported to the roots and rhizomes and can kill them too. Selectivity was developed because resistance to Roundup, using genes from bacteria, has been genetically engineered (i.e. gene transfer) into several crop species, first soybeans (' Roundup Ready Soybeans), and later to corn and cotton. Fields with these specific crops can be treated with Roundup to kill all other plants. Atrazine is the second most used herbicide in the U.S., but mostly in agricultural situations and less in residential situations. It is selective, killing most broadleaf species and many weedy grasses, but being tolerated by several crop species: corn, sorghum, and sugar cane (all are grasses). Additionally, an atrazine resistant (GMO) canola variety has been developed as well. Concerns about herbicides abound and include: human health concerns, ecological concerns and concerns about the development of herbicide resistant 'superweeds' . Both Roundup and Atrazine have been used extensively enough that there are new varieties of weeds that are unaffected by these chemicals, comparable to the evolution of antibiotic resistant bacteria. Biological control Biological control involves the use of other organisms to deter the growth of weeds. In general, this type of control is developed for introduced, invasive species of weeds and a search is made for herbivores or pathogens (see Chapter 30 on disease) that are native to where the introduction came from but are not present in the region that they have invaded. Care must be taken to avoid introducing species that might be harmful to existing native species. This is more likely if the biocontrol agents selected are 'specialists' in their feeding habits. Purple loosestrife is an example of an invasive weed that has been controlled (not eliminated) by introductions of insect herbivores, beetles and weevils that specialize on purple loosestrife. These species are common in purple loosestrife's native habitat (Europe and Asia) but were not introduced to North America when purple loosestrife was. Cultural control Cultural control By definition weeds are always a problem, at least a problem for someone. Although weeds can be an 'issue' in native habitats, the vast majority of weed problems involve humans (gardeners, farmers) trying to raise specific plants, i.e. trying the 'culture' plants that are somehow desirable. The cultural practices that are followed can influence the magnitude of the weed problem. The choice of crops, the timing of planting, the seeding density, the distance between rows, the number of sequential seasons that a crop is planted, all are cultural practices that may influence the severity of weed problems. Because most crops are annuals, they need to be planted each year and planting involves disturbance, thereby encouraging weed growth. Indeed, some early 19th century farmers considered early versions of the plough to be 'poisoning the soil' and promoting weed growth. Appreciating that farmers are in a catch-22 condition, they need disturbance but disturbance promotes weed problems, there are cultural practices that can lessen the problem such as the timing of the ploughing and how intensive the ploughing is. A modern technique is called 'no-till' farming utilizes minimal tilling, thereby giving weeds less area to utilize and that area that is available is seeded with a crop that may out-compete the weeds. Perennial non-woody crops such as alfalfa, asparagus, strawberries, raspberries require different cultural practices that might include items like mulching, mowing, tilling or the intentional planting of understory plants that might suppress weedy growth. This is also true for woody perennial crops like grapes and apples. Cultural practices vary widely depending on the crop and its characteristics. For instance flooding is an effective means of weed control but can only be utilized if crops, e.g. rice, tolerate the flooding. Fire can be used for annual crops and for woody (tree) crops if it is a low intensity surface fire. Most weed management strategies utilize ' Integrated Pest Management ' , an approach that incorporates chemical, biological and cultural approaches to manage not only weeds but also insect pests and pathogens.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.29%3A_Weeds_and_weed_control.txt
As any farmer will tell you there are many threats to growing plants. Some of these have been covered in earlier chapters: extremes in temperature and moisture (Chapter 26); and interactions with other plants, i.e. weeds (Chapter 29). A large number of additional threats come from trophic interactions with a vast diversity of grazers, parasites and and predators. Certainly the most familiar of these are insects but other invertebrates (mites, nematodes, mollusks) and vertebrates can be significant obstacles to growing plants. Moreover, a large number of fungi, bacteria (Figure 1) , protists and viruses are also be important threats. TOPICS • Grazing herbivores • Absorbing herbivores • Plant defenses • Boundary • Chemicals • Phenology • A sampling of plant disease • Phytoplasmas and defining disease • Late blight of potato—the disease triangle • Wheat rust disease—complex pathogen life cycles • Corn smut disease—Mexican truffles • Dutch elm disease —overreaction can kill you • Rice blast disease—changing strategies • Fire blight of apple—bacterial phytopathogens • Crown gall disease—making a disease a tool • Viral diseases—tobacco mosiac virus, cauliflower mosaic virus, ring spot disease of papaya Grazing herbivores Most animal herbivores, e.g. woodchucks and adult japanese beetles, are considered grazers, eating parts of the plant and using their mobility to get to other plants. However, a substantial number of insect herbivores have feeding stages (generally larvae, e.g. leaf min e rs, emerald ash borers , larval potato beetles) that are immobile to the extent of getting to new host plants. These might better be considered parasites because they feed solely on one host plant. Most non-animal herbivores (fungi, bacteria) are basically immobile and are considered parasites although some are capable of grow ing from one host to another and many are transported from one plant to another by wind, rain and insects. Most grazers on plants are ingesters (see Chapter 27), they remove and consume part of the plant, shred it to some extent and then digest the pieces in an internal tube, and ultimately excrete undigestible to their environment. Grazers, although they can severely reduce crop yields, rarely completely kill the plant it is eating both because they tend to specialize on only part of the plant (most commonly leaves) and because the plant is capable of replacing the organs/parts of organs that have been lost. The plant material acquired by grazers is generally not very nutrient dense but varies substantially depending upon the part of the plant eaten. Nutritional quality is largely influenced by how many living cells are present (dead cells are basically all cell walls and are indigestible for most herbivores). Most herbivores specialize on one of the tissues listed below, but there are few generalists that feed on multiple tissues, e.g. browsers like moose and deer often eat stems, leaves and meristems. • primary growth of stems and roots — although stems and roots in primary growth have more living cells than those with secondary growth, they still are nutrient poor. Most of those cells that are living are not very metabolically active and consequently they are poorer in nutrients when compared to cells that are more metabolically active (e.g. leaf mesophyll cells). • woody stems and roots, heartwood: Heartwood has no living cells and has increased levels of secondary chemicals. It generally has the lowest nutritional quality of any plant tissue, but there are heartwood specialists • woody stems and roots, sap wood: Sapwood has some living cells (the rays) and these may be 'loaded' with starch and other nutrients, depending on the season. Hence sapwood is considerable more nutritious than heartwood but still is largely composed of cell wall material. • woody stems and roots, vascular cambium — this meristematic tissue is nutrient rich and has relatively less cell wall material compared to mature cells. Moreover, it is more extensive that apical meristems, i.e. there is more material available to eat. • the bark tissue of woody stems is nutrient poor with few living cells and an abundance of secondary chemicals. The portion of cells that are living decreases as the stem/root ages and hence bark of younger stems is more nutritious than the bark of older stems • stems and roots that have been modified as storage structures — rhizomes, corms, bulbs, stolons. They are composed of living cells that are storing carbohydrates, usually in the form of starch. They are rich in digestible carbohydrates but may be deficient in amino acids (proteins) and other nutrients • phloem feeders: These organisms (including aphids, leaf hoppers, mealy bugs and white flies , all significant agriculture pests) are not consuming any cells, but instead tap into the phloem transport system and acquire the materials that are being transported through it. Phloem sap has very high concentrations of sucrose along with much smaller concentrations of amino acids and some minerals. Because the ratio of carbohydrates to amino acids in phloem sap is so high most phloem feeders excrete 'honeydew' , essentially phloem sap — still rich in carbohydrates but with most of the amino acids removed. Honeydew is utilized by several other organisms, in particular some ant species and the sooty mold fungus. • xylem feeders: Xylem sap has very few nutrients, almost no carbohydrates but with some of mineral ions. Also, while phloem feeders acquire sap passively because it is under pressure inside the phloem cells, xylem sap is under tension and requires 'sucking' (developing greater tensions than already present) in order for it to flow into xylem feeders. Nonetheless, there are some insects (larval cicadas, larval spittlebugs) which feed on xylem. Absorbing herbivores In contrast to grazers, most non-animal plant herbivores are absorbers (see Chapter 27), absorbing nutrients from 'their environment' , with 'their environment' being the interior of a plant. Most of these organisms are bacteria and fungi, but some, like water molds, are protistsand a few are animals (e.g. nematodes, the larval stages of some insects). Most of these organisms are considered parasites and are generally considered to be plant pathogens. They invade plant tissues and then acquire materials in one of three ways: (1) the parasite feeds on materials that 'leak' from host cells.(2) the parasite kills host cells, causing cellular materials to become available. Organisms that feed this was are described as being necrotrophic (feeding off dead material). (3) the parasite and hostform a structure called an haustorium, a fusion of both the host cell membrane and the parasite cell membrane. (Note that the development of the haustorium generally requires breakdown of the cell walls of both the host and parasite.) Materials are transferred from host to parasite through the haustorium and both host and parasite stay alive. Organisms that feed this way are described as being biotrophic (i.e. feeding off living material). Some biotrophs are relatively benign herbivores (they benefit from keeping their host alive), and consequently many acquire relatively small amounts of resources from their hosts. But many biotrophs (e.g. rusts, smuts, downy mildew, powdery mildew) can be devastating to farmers as infestations often can reduce plant yields to next to nothing. Plant defenses An effective boundary: Except for large grazing animals, organisms need to get inside plant tissues in order to feed on the plant. The boundary makes this difficult by producing a surface that is hard to penetrate and inhospitable for life (see Chapter 3). For above ground primary growth, the boundary consists of epidermal cells that are tightly bound to each other, making it difficult to penetrate between cells. Additionally, above ground primary growth is coated with a cuticle that is difficult to pierce and hard to live on because it is hydrophobic. Below ground, mature primary roots have an endodermis that serves many of the same functions as the epidermis + cuticle does above ground. However, the youngest parts of roots have not developed an endodermis. This makes water acquisition easier but it also makes it easier for pathogens to enter. Pathogens/herbivores gain entry both by utilizing stomatal openings and also by having mouthparts that can penetrate the cuticle/epidermis, or having a needle-like or saw – like ovipositer (egg-laying organ) or, in the case of some fungi, producing an appressorium, a specialized cell type that is able to fuse with the epidermis and produce a structure that can penetrate it. Pathogens and herbivores also gain entry through wounds and openings in the epidermis as the result of growth processes, e.g. branch roots, the shedding of leaves and branches. Chemistry: All plants produce diverse chemicals that influence herbivory and pathogens. Some are feeding deterrent chemicals that are poisonous or may advertise that poisons are present within the plant. At the same time, some chemicals produced by plants clearly attract certain herbivores. The assumption is that these chemicals had once served as feeding deterrents but that the herbivore has developed means to detoxify the poison and is now using the chemical to identify a host that relatively few competitors will be able to utilize. For example most insect herbivores will not eat milkweed but several insects (monarch butterfly larvae, the milkweed beetle and milkweed bugs) choose to feed on milkweed. Some even utilize the plant's poisons as their own, making them less likely to be consumed. Plants also produce chemicals because they recognize that they are under attack. The production of these 'induced' chemicals imply that the plant has an ability to sense the presence of the pathogen and the chemicals produced may: (1) kill the invader (phytoalexins) , (2) trigger defensive responses in neighboring plants and/or attract predators that may control the herbivore, or (3) elicit an 'hypersensitive response' , causing the invaded tissue to rapidly die. Note that the hypersensitive response may be effective in deterring biotrophic pathogens but actually benefits necrotrophic pathogens. Phenology: Plants (and farmers) may be able to avoid herbivores/predators by adjusting the timing of seed germination, growth and flower / fruit production. Poinsettias, phytoplamas and the nature of plant disease Poinsettia 's did not always look as most of them do now. The plant in the wild and the plant that was originally propagated as an ornamental plant was much taller plant and produced relatively few ' flowers ' (the structures that look like a flower are actually a cluster of flowers surrounded by colorful, usually red, bracts). Early in the 20th century a plant with a novel form appeared, one that was much shorter, branched much more frequently, and produced more flowers. This form could be propagated by cuttings and the assumption was that the original plant was a mutant, a ' sport ', like the original naval orange. Sports generally cannot be perpetuated by seed because the mutations making them distinctive are often recessive. But they often can be perpetuated by cuttings because cuttings are essentially continued growth of the original plant. There are other phenomena besides mutations that might account for an altered growth pattern that can be perpetuated by cuttings. Two possibilities are viruses and phytoplasmas (small bacteria lacking cell walls that live only in plant cells). Note that these three possibilities for the abnormal plant (mutation, viral infection phytoplasma infection) all could be described as ' plant disease' but that what is unusual is that the diseased plant is desirable not undesirable. It turns out that almost all the poinsettia produced today are diseased! And the culprit turns out to be a phytoplasma. So what is plant disease? In the poinsettia discussion it was associated with 'abnormal plants' A difficulty with this definition is that it is 'normal' for biological entities to be 'abnormal' . That is, if you look at a population (group of organisms) they aren 't all alike, they vary, some are ' outside the norm '. Additionally, ' normal ' is not readily defined. It can be defined statistically as a central tendency, e.g. abnormal is one more than one standard deviation from the mean. Although not perfect, the ' abnormal ' definition works with plants partly because the plants under consideration are typically those of economic importance and ' normal' is a type of plant that provides the most economic return. Additionally, most crops have been bred to be uniform. Thus a diseased plant is recognized by abnormal structure or functioning. Common symptoms of diseased plants included stunted or deformed growth and yellowed (chlorotic) or dead (necrotic) leaves. But occasionally one might find a diseased plant that is 'bigger than normal' , that branches more than normal, or that has leaves that persist on the plant longe r than normal. In an arbitrary manner plant disease excludes insect herbivores even though have similarities with 'true' plant pathogens. Since this book is dealing with inanimate life we will not consider insect herbivores except as introduced above and as covered in the next chapter dealing developing new plants. Late Blight of Potato and the ' disease triangle ' The causes of abnormal functioning, i.e. diseased plants, are legion, including: weather conditions, nutritional (soil) factors, genetic changes and a wide spectrum of disorders resulting from interactions with a variety of other organisms — bacteria, fungi, water molds, nematodes, insects and with biotic entities like viruses. With respect to these biotic causes of plant disease, plant pathologists describe what is called the 'disease triangle' where disease results from a combination of environmental conditions, host susceptibility, and disease-causing organism 's virulence. Disease is a consequence of a susceptible plant encountering a competent (i.e. virulent) pathogen under environmental conditions that favor the invasion and spread of the pathogen. A classic example of the disease triangle is late blight of potato, caused by the water mold Phytophthora. Potato is native to South America but was brought to Europe in the 17th century as a food crop. The disease organism, which also affects tomatoes, apparently originated in Mexico in the early 1800' s. The disease requires cool, moist conditions, a susceptible potato host and a virulent pathogen. The pathogen spread throughout North America in the early 19th century and made it to Europe probably as a result of importation of diseased potatoes to Belgium in 1845. It quickly spread throughout Europe, and in particular to Ireland, where potatoes were the primary food source and were grown extensively in monocultures. The cool moist conditions typical of Ireland were well-suited to the growth and reproduction of the pathogen. Moreover, the potatoes grown were genetically uniform and also highly susceptible to the blight. The result was devastating, over a million Irish died of starvation and another million emigrated, mostly to the United States. The severity of the blight varied over the next twenty years, primarily due fluctuations in environmental conditions. Note that crop failure not only eliminates food, it also eliminates 'seed potatoes' (potatoes saved to be planted the following year). Thus, even if favorable conditions might yield a relatively high crop (yield per acre), food shortages persist because fewer acres may have been planted. Late blight of potato continues to be a problem, with outbreaks tied to environmental conditions. There are partially resistant varieties but these are only temporary because the pathogen evolves to overcome the plant's resistance. The pathogen is an obligate biotrophic parasite, meaning it can only survive on a living host. It survives from year to year on potato tubers or potato plants left in the field. It spreads readily by spores (usually asexual) that require moisture to stay alive and are dispersed by wind and by raindrops. Pathogen growth and spread can be extremely fast if weather conditions are appropriate. The spores germinate quickly and enter susceptible plants through stomata, wounds, and directly through the cuticle. Once inside the leaf they produce hyphae that grow between cells and produce haustoria that penetrate the cell wall and interact with the host cell membrane and allow nutrients to pass to the fungus. The disease requires a match between the host and the pathogen. P. infestans infects potato and also tomato, which is a close relative of potato. But many other close relatives are not suitable hosts. And there are other species of Phytophthora that affect other plant species but do not infect potatoes, e.g. P. quercina causes sudden oak death syndrome Wheat rust — complex parasite life cycles There are many different rust diseases that affect a variety of hosts, some do not utilize two different hosts , but all are host specific meaning that they can affect only a group of closely related plants: a variety, a species or several species from a single genus. The life cycle for wheat rust was introduced in Chapter 12 and a figure from that chapter is reproduced below. Note that five different types of spores are produced that differ from each other by their ploidy level (diploid, dikaryon or haploid), what type of plant they are produced on, and what type of plant they can grow on (if any) and how they function. teliospores are dikaryon spores and the only stage of the life cycle that grows, albeit very temporarily, independent of a host. It also is the only stage that can overwinter. basidiospores are haploid spores produced after the teliospore germinates and undergoes karyogamy to produce a diploid cell which then undergoes meiosis to produce haploid basidiospores. These spores are dispersed in the air and only germinate and grow on barberry plants. pynciospores are haploid spores produced from hyphae produced in a structure emerging from the upper surface of barberry leaves. Also in this structure are haploid receptive hyphae which can receive pynciospores, fuse with them (plasmogamy) to form dikaryon hyphae. These grow to the lower surface of the leaf and form a structure called an aecium that produces dikaryon aeciospores that are dispersed by the wind and infect wheat plants. Mycelial dikaryotic growth from the aeciospores can cause significant damage to the host wheat plant and also produces urideospores, produced in and orange structures called uremia. The uridospores spread Puccinia graminis to other wheat plants, facilitating disease spread through wheat crops. As the wheat plant starts to senesce, both from the pathogen and from its natural, monocarpic cycle, the dikaryotic hyphae in the wheat plant produce teliospores , spores that can survive the winter and completing the life cycle. Because wheat is an extremely important crop and because the disease spreads rapidly and evolves quickly, wheat rust is probably the most significant agricultural disease. Resistance to the disease involves genetics of both the fungus and the plant. Resistant plants have an ability to recognize invasion by the fungus and to respond to it. Recognition of the fungus is the result of the plant perceiving a chemical produced by the fungus is present. An avirulent fungus can become virulent by becoming unrecognizable, typically by not producing a specific chemical that that the avirulent (and thereby recognizable) fungi had been making. Hence virulence in the pathogen is typically recessive (inability to make something that the wild type does make). Plant resistance requires a dominant gene that gives the plant the ability to recognize and respond to the presence of the virus. Corn smut — Mexican truffles Corn smut produces large, distinctive galls that are edible and highly desirable in Mexico. In other parts of the world the disease is very unwelcome, substantially reducing crop yields. Like the rusts, smut diseases are basidiomycetes and like the rusts the fungus is generally found in the dikaryon state, with cells possessing two haploid nuclei. Basidiomycetes only produce only a single diploid cell that immediately undergoes meiosis to form haploid spores. These germinate and grow into haploid hyphae that in smuts can produce new cells by budding (like yeast) and like yeast can be grown on an artificial medium, meaning that this stage is NOT biotrophic but acts like a saprophyte. However, when haploid hyphae of two different mating types find each other and fuse and form a dikaryotic hyphae, it is now biotrophic, only able to survive on living cells of spe cific plants, in this case, corn and teosinte (a close relative of corn). Hence, to be a successful pathogen the haploid hyphae need to find each other on living corn (or teosinte) material. Additionally, the dikaryon hyphae only invade active tissues, most commonly the flowers, where they induce abnormal growth, galls, with greatly enlarged cells surrounded by hyphae. They do not form typical haustoria but do form structures that allow the transfer of materials from the plant to the fungus. As the galls mature they change color from silky white to black and also change textures, becoming softer. Although the galls look 'fungal' (if such a thing is possible!) they are actually mostly plant tissue. Inside the galls some fungal cells undergo karyogamy (fusion of the two haploid nuclei) to form a diploid cell and complete the sexual cycle. Corn smut is the most significant smut disease but there are other smut fungi that infect other agricultural grasses (sugarcane, barley, oats) as well as smuts that attack wild grasses and sedges. Rice blast disease — changing pathogen strategies Rice blast is a devastating fungal disease that affects several cereals but is most significant in affecting rice. It is an ascomycete and the dikaryon stage is brief in time and extent. The pathogen is technically described as a hemibiotroph because initially it behaves like a biotroph, surviving with living plant cells, but eventually becomes a necrotroph, killing cells and obtaining nutrients from them. Haploid spores land on rice leaves, developing fruits, and other plant parts and are able to penetrate the cuticle by generating substantial pressures hydrostatically within a specialized cell called an appressorium. Once inside the fungus is able to spread by entering individual plant cells through plasmodesmata. After a certain amount of time that depends upon the tissue that has been invaded, the fungus shifts to a necrotrophic lifestyle, killing the host cells. Dutch elm disease — overreacting can be deadly Dutch elm disease is caused by an ascomycete fungus that has a symbiotic relationship with a a bark beetle, a type of beetle that feeds on the vascular cambium and tissues (secondary xylem and phloem) that the vascular cambium produces. The fungus is transported from infected trees to new trees by the beetle and benefits not only by the transport but also by being placed inside the plant in the tissues that the fungus feeds on. The fungus feeds only on dying cells. but, unfortunately for the tree, its presence triggers the production of gums. Presumably such a response could help stop the spread of the fungus by making it more difficult to move. However, in elm trees the substances that are produced plug the vessels and trachieds of the host, making them unable to transport water up the plant. Like a number of human diseases, the damage of a pathogen stems mostly from the host response and less so from the actual activity of the pathogen. Dutch elm disease is one of many 'wilt diseases' caused by both fungi and bacteria that result in reduced water transport and wilting. In most of these the blocking of xylem tissue is the result of the plant response to the pathogen. Fire blight and bacterial phytopathogens The majority of plant pathogens are fungal, but some, like late blight of potato, are oomycetes and some, like the phytoplasmas of poinsettias are bacteria. While phytoplasmas are unusual because they are obligate intracellular parasites, most bacterial diseases do not enter into the cell but they do produce 'effector' molecules that they are able to transfer into living cells and effect specific results such as hormonal responses that bring about tumors, exudation of materials, or cell death. Most bacterial plant pathogens are not easily classified as biotroph/necrotroph although clearly phytoplasmas are biotrophs, as is the gall-forming Agrobacterium (see below).Fire blight is interesting in this respect. It is caused by Erwinia amylovorathat affects members of the rose family, in particular apples and pears, sometimes with catastrophic results. The bacteria can live as a harmless epiphyte living on sugars exuded by the stigmas of flowers and the nectaries at the base of flowers. From these locations E.amylovoracan be spread by pollinators throughout a plant and throughout an entire orchard. At some point it is triggered to become a much less benign associate and it becomes necrogenic, killing host cells as a consequence of the effector molecules it produces. Crown gall disease — a disease used as a tool against disease Many plant diseases alter the growth pattern of plants, often producing characteristic structures called galls. The abnormal growth that is manifested in a gall usually is a consequence of changes in the amounts of plant growth regulators, aka hormones. This can be the result of the pathogen producing these chemicals (in fact one plant hormone, gibberellic acid, was first discovered as a result of it production by a fungal disease). But altered levels of plant growth substances can also be a consequence of the pathogen causing its host to produce more or less of a particular substance. The most common way this happens is that the pathogen alters gene expression in its host. Agrobacterium tumifaciens does this by actually altering the genes present in host cells via a process called transformation, a type of horizontal gene transfer. Among other genes that are transferred is one that codes for the production of the plant growth substance cytokinin which plays a role in the cell proliferation required for gall formation. The bacterium lives saprophytically in the soil but is able to recognize wounded plants when it contacts them and is transformed into a virulent form that makes its way into the plant. A . tumifacien s is a significant pathogen on several crop species, in particular perennial ones like walnut, apricot and plum. A. tumifaciens notable for its very broad range of hosts which is one of the reasons why it has proved useful in the genetic engineering of plants as it can be used to transfer specific genes from one organism to another (Chapter 31). Tobacco mosaic virus, cauliflower mosaic virus, and ring spot disease of papaya Plants are affected by a large number of viruses that can cause very significant crop losses. Tobacco mosaic virus (TMV) is not one of the most damaging viral pathogens but it is notable because of its role in the understanding of viruses and its use in bioengineering. TMV was the first virus to be isolated and purified and this allowed for the recognition that infectious agents need not be cellular in order for them to cause disease. Viruses are composed of both protein and genetic material (either DNA or RNA) and upon entry into a cell they insert genetic material that codes for the production of viral protein and genetic material. A critical part of the inserted viral genome is a region called a promoter that 'promotes' the expression of the genes downstream from it, thereby ensuring their expression. Genetic engineers have utilized this region of the genome of several viruses in order to insert desirable genes from one organism into another organism. In particular the cauliflower mosaic virus (CaMV) has proved to particular useful in producing 'genetically modified' organisms. One crop where the CaMV promoter was very useful was in the development of strains of papaya that are resistant to the ring spot disease of papaya, a disease that is caused by yet another virus that threatened to eliminate the papaya as a commercial crop.	textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.30%3A_Threats_to_agriculture-_insects_and_pathogens.txt

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