chapter
stringlengths 1.97k
1.53M
| path
stringlengths 47
241
|
|---|---|
Ancient agriculture required plant propagation, making new plants. Plants don ' t live forever and many crops are annuals or are harvested less than a year after planting. Although the earliest agricultural efforts may not have involved intentionally propagating plants, fundamental to the development of agriculture was the acknowledgment that making new plants is an essential part of the process. The techniques used to propagate plant crops vary depending upon the crop. For most familiar crops it required storing some seed (i.e. not eating it) and planting it at some point in the future. For crops such as cereal grains and most legumes , where the seed is the part that is harvested and eaten, development of the ' store and plant ' technology was relatively straightforward and rapid. However crops such as tomato, squash and eggplant , where a fleshy fruit is harvested and the seeds are small and inconspicuous, required more technology: a recognition that seeds were present in the fruit and a method for processing of some of the fruit to obtain seeds for planting. Perennial plants do not require propagation each year, they could be maintained without propagation. But eventually they required some means of making new plants, especially if the agriculturalists are moving to a new area. For reasons discussed below, propagation of perennial plants often did not involve seeds but instead, asexual, means of propagation.
For most of its existence agriculture did not involve attempts to produce novel plants, plants with characteristics that distinguished them from their parents. However, the hope from the earliest onset of agriculture was that one might be able to improve the characteristics of the crop, producing crops that yielded more, tasted better, stored better, were easier to harvest, and were more tolerant of hardships, in particular, more tolerant of disease..Primitive farmers were happy when they found desirable novelties and also were able, knowingly or unknowingly, to gradually change the crops they grew. But they did not have the understanding and technology to intentionally create something novel. This has become possible over the last 100 years. Although an understanding of aspects of asexual reproduction was important for some crops, it was the recognition of the sexual process in pl ants, in particular the functioning of flowers and pollination , that has been critical to the development of the technologies of crop improvement (Figure 2). All of the major crops have been, and continue to be, intentionally modified. And this is one of the many factors that has changed, and made more complex, the business of agriculture. Where it was once basically controlled by a farmer who served both as a producer and salesman, it is now a vastly more complex system that depends on farmers, seed producers, researchers, fertilizer producers, equipment manufacturers, agricultural scientists, the government, and vast array of 'middle-men' .
TOPICS
• Asexual reproduction—propagation by cuttings
• Sexual reproduction by seeds and the importance of breeding system
• Hybrid seeds
• The green revolution
• Creating novel plants
• grafting
• generating variability
• genetic engineering
Asexual reproduction
Most woody plants do not 'breed true' , meaning that if you plant a seed from your favorite apple tree, or from a 'wild' tree growing in the woods, it is highly unlikely that the seed will grow into a tree comparable to the parent. In fact, the apples that you might harvest will probably be less than desirable. Similar patterns would be found for grapes and olives, two ancient crops that have long been propagated not from seed but instead asexually. The easiest technique is 'rooting' , cutting a stem and placing it in moist soil in hopes that it will sprout roots (see the discussion adventitious roots in Chapter 8). A similar procedure can be done with roots, inducing them to produce new shoots. Since the middle of the 20th century an artificial plant hormone has been used to promote adventitious growth in shoots/roots that might not do so otherwise.
Obviously, asexual propagation does not produce novel material, it o nly perpetuates existing ones. It is important in a large number of vegetable crops including banana, pineapple, potato, sweet potatoes, cassava and many more. It also is the most common means of propagating of most ornamental flowering plants started in the greenhouse (e.g. geranium, begonia). For some of these plants (e.g. banana, naval oranges and some ornamental flowers) asexual reproduction is essential because the plant is a sterile hybrid and cannot produce viable seeds. For other species, e.g. potato (Figure 3), pineapple (Figure 4) and many others asexual reproduction is simply an easier means of propagation, eliminating the seedling stage which is sometimes more sensitive to conditions than cuttings are. A disadvantage of asexual propagation is that the clones are genetically uniform and thus crops are more susceptible to widespread failure (e.g. in late blight of potato). Another problem is that viral diseases are transmitted in cuttings but not through seeds.
Sexual propagation —seeds and the significance of breeding system
Propagation by seeds is probably the most familiar process to most of us. For annual species grown as crops, propagation only requires the discipline to store seeds for the next season. Unlike asexual reproduction, sexual reproduction can result in variation. Variation has positive and negative effects on farming. On the one hand it allows for crop improvement and the production of novel plants (see below). On the other hand crop uniformity is generally helpful to agriculture because it makes cultural practices (e.g. planting and harvesting) more easily handled. Significant to crop variability is the breeding system of the crop. If the crop has a closed breeding system (Chapter 17) as the result of being apomictic or from having a bisexual flower and being self fertile, then offspring are likely to be the same as their parents and a crop may show little variation. Additionally, if a novel plant does appear, a closed breeding system makes it easier for a farmer to perpetuate plants with that specific feature. For instance, an important characteristic for cereal grains is to have 'non-shattering' heads, meaning inflorescences that do not shed their seeds, holding them on the plant and making harvesting easier. With a closed breeding system, seeds from non-shattering heads are likely to pass that feature on to their offspring since they may have no sexual process at all (apomixis) or are most likely to breed with themselves. In contrast, plants with a more open breeding system are more likely to be variable, with offspring that don 't all look alike and don' t necessarily look like their parent. And when a plant with favorable characteristics is found, it is more difficult to perpetuate these features through time. In fact, it is likely that these features will disappear quickly, from being 'washed out' by breeding with individuals that do not possess the feature. It is also significant that population size and reproductive isolation influence variability. A population of plants with an open breeding system may be very uniform if the population is small and reproductively isolated from other populations of the same plant, as can be the case for crop species.
Hybrid seed
Even before an understanding of the basis of genetics was developed the phenomenon of 'inbreeding depression' , had been noted: the decline in vigor in populations that are continually inbreeding. The degree to which this happens varies among species. It is probably not surprising that inbreeding depression is not a generally a problem for species with closed breeding systems. But for plants with open breeding systems, inbreeding can cause substantial reductions in crop yield. This was recognized by farmers and was part of the reason that seed companies, who took steps to avoid this problem, developed a clientele. Early in the 20th century plant breeders realized that although inbreed lines show reduced vigor, a 'hybrid cross' between two inbreed lines, produced plants that were more vigorous than either of the parental lines before they had been inbreed. Central to the production of hybrid seed is the need to control who breeds with whom. The technique requires that multiple generations bred only with close relatives, something that is easily accomplished by having populations isolated from each other. The next step is more difficult: ensuring that the inbreed lines NOT breed within the population but instead breed with individuals of another inbreed line. This was first done with corn, a plant with separate male and female flowers that are located in different parts of the plant. Crossing of inbreed lines can be accomplished by removing the male flowers (detasseling) from one inbreed line, thereby making these plants solely female and ensuring that if any seed is produced the male parent has come from a separate plant, usually from a second inbreed line that was planted nearby. Hybrid corn was first developed in the 1930's and became the dominant seed source by 1950, with yields increasing dramatically.
Large scale production of pure hybrid seed is nearly impossible in plants with perfect flowers (both male and female structures in the same flower). However, botanists discovered that it is possible to make plants with perfect flowers become unisexual. In the late 18th century workers noticed that not all pollen was viable and the ability to produce viable pollen sometimes often showed maternal inheritance. Later work indicated that there were cytoplasmic (i.e. non-nuclear) factors, inherited maternally (in plastids), that influence the production of viable pollen. Thus, geneticists were able to produce plants that were 'male sterile' , not able to produce viable pollen. Having plants that were unisexual (female) made the crosses that were needed to produce hybrid seed much more feasible. Hybrid seed production was further enhanced when 'restorer genes' were found that would restore the ability to make viable pollen. This allowed breeders to two cross two lines, one of which was unisexual, yet have the resulting hybrid produce flowers that are fully functional. Because of cytoplasmic male sterility the number of plants for which hybrid seed could be produced increased dramatically. Another means to the same end is the use of 'chemical hybridizing agents' , chemicals that make plants male (usually) sterile.
A negative consequence of planting hybrid seed is that seed cannot be stored year to year. Although the hybrid plant is vigorous, offspring of the hybrid plants are much less vigorous and also more variable. Growers utilizing hybrid seed need to purchase seed each year or switch to using open pollinated seeds instead of hybrid seed.
The Green Revolution
In the late 1960 's several scientists warned of an inevitable global famine, based in part on the assumption that crop yields could not be improved. Fortunately agricultural research, with a series of innovations that became known as the ' green revolution ' was able to drastically increase yield (Figure 6) and the global famine did not occur, although local famines continue to be a problem, usually the result of politics and war. Central to the green revolution were the efforts of Norman Borlaug, both as an agricultural researcher who developed high yielding varieties and as administrator who worked extensively to have new agricultural practices accepted by countries including Mexico, India and Pakistan. Central to the green revolution was hybrid seed and the development of new high yielding varieties of wheat and rice. Surprisingly, these varieties were actually dwarf plants. This had one direct effect: the problem of ' lodging' (plants being knocked over, usually as the result of wind) was lessened because the plants were shorter. But the new varieties also had a number of other features that helped to increase yield: increased seed production per plant, enhanced disease resistance (especially against rusts) and greater tolerance of drought or excessive rain. Also significant was that the new varieties would respond with increased yield to increased levels of fertilization. As a result of the new varieties and the new agricultural practices, crop yields more than doubled.
How can crops be improved? And who does the work of crop development?
Crop development requires careful observations and recognition of individuals with favorable traits. By the end of the 19th century the importance of generating variability was increasingly recognized as being significant to crop development. However, in general, farmers desire crop uniformity because it makes growing and harvesting easier and their focus is on growing crops not developing crops. During the 19th century, seeds were increasingly provided by the sources other than the farmer storing seeds or exchanging seeds with neighbors, and crop improvement was increasingly out of farmers'hands. During the latter half of the 19th century the federal government provided seed to anyone who asked for it. And, at the end of the century, land grant universities were charged with improving agriculture and this included developing improved varieties of crops. During this time period, private commercial seed companies became increasingly important as both a source of seeds and as a venue for improving crop quality.
Creating new plants using asexual methods of propagation
Although asexual reproduction is cloning, simply perpetuating what already exists, it has often been important in crop innovation. Novel plants are sometimes produced spontaneously by mutations of the seed or in branches of existing plants, and asexual reproduction of these mutants allows them to become new crops. This is what happened with navel oranges (Chapter 28), McIntosh apples (and many other apple varieties), poinsettia (Chapter 30), and a large number of ornamental plants. Cloning is also important as a means of perpetuating plants (generally hybrids) that have been created naturally (without human intervention) or artificially (with human intervention) that are unable to reproduce sexually.
Related to asexual reproduction is grafting, cutting a branch or bud off one plant and attaching it to a different plant, producing a novel organism, a chimera. There are a variety of reasons why this practice might be desirable, but one obvious one is in order to combine the favorable traits of two individuals into one individual, e.g. a good root system with a good shoot system. This is well represented by wine grape propagation. Stems from a European species are grafted on to root stocks from a North American species. The North American species produces inferior grapes for making wine but its root system can withstand attack from the insect pest Phylloxera. The root system of the European species is highly susceptible to Phylloxera but produces grapes of superior quality for wine. Phylloxera was mistakenly introduced from North America to Europe in the early 1800's and devastated European wine production. It was revived when workers were able to plant grapes composed of European shoots grafted on to North American rootstocks. Most fruit trees (apple, peach, plum) are similarly constructed with rootstocks that are vigorous and disease resistant grafted to shoots that produce desirable fruits.
Creating novel plants using the sexual process
Crossing with relatives
The relatives might be ancestral varieties that the crop originated from or species closely related to the crop. Technically, a crop species should should not hybridize with other species (i.e. it is an isolated gene pool, see Chapter 17) but sporadic seed production does occur. Although successful crosses may be infrequent, as long as there are some viable offspring, these can be back-crossed to the original crop (i.e. cross the hybrid plants with plants from the parental population) with significant introduction of novel traits (i.e. variability) that may include desirable features. Occasionally, workers are successful crossing with more distant relatives (different genera, even different families). Part of this surprising possibility may be poor taxonomy (i.e. they actually are more closely related than depicted in the taxonomy) but apparently sometimes crosses can happen between plants that are not that closely related.
Polyploidy
For a cross to be successful the parents need to have the same chromosome number and the chromosomes of the two parents need to be similar enough that they can pair during meiosis. When hybrids between different species are produced they are generally sterile because of the inability to pair chromosomes during meiosis. Although the hybrid is sterile it is often possible to propagate it asexually , i.e. to clone the hybrid, . A number of ornamental plants are perpetuated this way. It also is what has occurred with banana, the plant that is cultivated is a sterile hybrid, unable to produce seed but thiis one of the features that make the commercial banana desirable! Another 'solution' to the problem of hybrid sterility is polyploidy, increasing the chromosome number. This sometimes happens without human involvement (see discussion of the evolution of wheat in Chapter 28) but in the last 100 years workers have developed techniques to promote polyploidy following hybridization, thereby creating a new species with characteristics of both parental lines.
Treatment with mutagens
A common means of generating variability, and perhaps producing favorable traits that can be selected for, is to treat the seeds with a chemical mutagen or radiation. Although most of the treated seeds do not survive or have unfavorable features, usually some seeds survive that may have desirable features. These plants can be crossed with existing varieties in hopes of introducing favorable features to the crop. The technique is also used with asexual propagation. The original ruby red grapefruit appeared as a sport on a normal grapefruit tree. Irradiation of branches of the original ruby red has produced the even redder varieties Rio Red and Star Ruby.
Genetically modified organisms
A much more focused technique of combining traits from different organisms is the production of 'GMO' s, genetically modified organisms; the phrase should be non-sensical to any trained biologist because all organisms are genetically modified, that is what evolution is about. But if we focus only on agricultural organisms the term has come to distinguish 'normal' agricultural organisms, all of which have a long and substantial history of genetic modification by humans from 'abnormal' agricultural organisms, ones produced using the relatively recent techniques of molecular biology that allow for much more focused genetic modification, with genes manipulated in various ways including: turned on, turned off, duplicated, removed and, in particular, moved from one organism to another. One famous example is 'golden rice' , rice to which additional genes, genes that would cause the rice produce beta-carotene, a vitamin D precursor, into the endosperm of the seed. A second example is 'Bt' corn, which has a gene derived from the bacterium B acillus thuringiensis , that produces a protein that is toxic to some insects, in particular the corn borer moth. Consequently 'Bt-corn' can avoid predation by corn borers. Interestingly, the bacterial toxins had been used by organic farmers, being mass produced by culturing B. thuringiensis , extracting the toxins and then spraying them on corn plants. A final example is 'Roundup ready' soybeans. Roundup is a commonly used herbicide that is effective because it blocks an important synthetic pathway. Plant molecular biologists were able to introduce genes into several crops, including soybean and cotton, that greatly reduced the the toxicity of roundup to these crops, making them 'roundup ready' . The advantage of modern molecular techniques is specificity: plants are modified in very specific ways. In contrast, developing new crops by hybridization or by chemical or radiational means will have multiple effects — yet the breeder is only paying attention to a small number of characters they are hoping to modify.
GMO 's have been vigorously opposed by a variety of groups for a variety of reasons. This opposition has decreased substantially in the last five years, partly because many of the problems that were cited have not appeared even though GMO plants have been in wide use over the last fifteen years. Any large-scale production of crops with novel characteristics will have possible risks but the GMO' s are probably one of the more benign techniques to generate variability. Consequently the production and use of GMO s is likely to increase in the coming years. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/01%3A_Chapters/1.31%3A_Propagating_plants_and_developing_new_plants.txt |
• 2.1: A Diversity of Organisms
• 2.2: Acetabularia, an unusual unicellular green algae
• 2.3: Agaricus bisporus, the commercial mushroom
• 2.4: Alfalfa
• 2.5: Bracket Fungi
If you are observant and spend much time hiking in the woods you are sure to encounter a bracket (shelf) fungus, fruiting bodies of wood decay fungi that are found both on standing and fallen trees and form a hard outgrowth with a spore producing surface facing downward.
• 2.6: Calupera - A Large Coenocytic Green Algae
Caulerpa is a large green algae that appears to be multicellular because it is organized into different parts, seemingly leaves, stems and roots. But it is actually just a single large cell. And since an individual organism might be two meters in extent, Caulerpa produces the largest cells on earth, except for maybe some plasmodial slime molds. They are mostly found in shallow waters in warmer oceans but a few occur in fresh water.
• 2.7: Chlamydomonas, a small unicellular green alga
• 2.8: Chytrids - Tiny Fungi
Chytrids (Chytridomycota) are a group of fungi that are rarely directly encountered, primarily because they are small and they generally eat things that are small.
• 2.9: Clubmosses - Lycopodium
Club mosses are representatives of the Lycopodiophyta, plants that are very important in the fossil record and in the history of plant life but are not particularly diverse or common now. World-wide there are around 1000 species in the group. As is the case with many of the ferns the common names for club mosses have been much more stable than the scientific names, several of which have been changed in the last thirty years.
• 2.10: Coccolithophores, photosynthetic unicellular algae
Coccolithophores are some of the most important organisms that you have never heard of !! They are very small marine organisms who have a very significant impact on earth's geology and ecology. They are distinctive because they have a coating that consists of a number of ornate calcium carbonate plates.
• 2.11: Coltsoot - Tussilago farfara
Tussilago farafara is a common herbaceous plant throughout much of North America, occurring in disturbed habitats, usually in relatively moist sites. It is one of the first flowers to be found in the spring, often on roadsides
• 2.12: Corn
• 2.13: Corralorhiza - A Plant that Eats Fungi
Corralorhiza is a representative of the orchid family. The orchids are one of the largest families of flowering plants, a group with over 25, 000 species. Although the genus Corralorhiza is restricted to North America, with roughly a dozen species, most members of the family are found in the tropics. Probably the most commonly seen orchid in the northeastern US is the pink lady slipper but there are another 10-15 species of orchids that relatively easy to find.
• 2.14: Cryptomonads - Unicellular Photosynthetic Algae
As the name implies, cryptophytes (crypto = hidden) are unicellular algae that are often hidden. This is a consequence of their relatively small size (10-30 um), the fact that they often occur in deeper waters, and the fact that they are often difficult to collect in an intact condition. However, they are significant contributors to aquatic food chains, both marine and fresh water, and have interesting features that relate to their evolution.
• 2.15: Dandelion
Dandelion is an extremely common plant through temperate North America and Europe. It is widely recognized as a weed, a word that generally means that it is an undesirable plant, undesirable because it grows in places where people are trying to grow something else, and, at least to some people, undesirable because of its looks — perhaps not so much the bright yellow flowers, but more likely because of the fruit heads and the rosettes of leaves in an otherwise uniform carpet of grass.
• 2.16: Diatoms - Unicellular Photosynthetic Algae
The diatoms are a phylum of unicellular photosynthetic algae and are a group significant for their unique structure and ecology.
• 2.17: Dictyostelium - A Cellular Slime Mold
Dictyostelium is a 'cellular slime mold', a very unfamiliar (to most) organism that has proved to be useful as a 'model organism' to study significant biological processes, in particular, development. It has a multicellular stage that develops not as a result of a cell dividing repeatedly producing daughter cells all stuck together. Instead multicellularity is the result of the aggregation of many individual cells.
• 2.18: Ephedra - Jointfir
Ephedra (the common name is also ephedra, and it is also called jointfir) is a representative of a small, diverse group of seed plants that unfortunately has no common name. They are simply called 'the gnetophytes' after the name for the phylum, Gnetophyta.
• 2.19: Euglena- a unicellular algae
Euglena is a genus of unicellular, freshwater organisms that are very common in ponds and small bodies of water, especially if they are rich in nutrients and consequently high in algae (aka 'pond scum' ). Euglena itself is sometimes photosynthetic and is a component of the green sludge in such ponds. But at other times it is non-photosynthetic and is a component of the diverse group of organisms that are eating the green sludge or perhaps eating the other things that eat the green sludge.
• 2.20: Ginkgo
Gingko (Ginkgo biloba) is a commonly planted tree that many have probably seen but may not have distinguished from other trees. In spite of the fact that its form is very similar to most trees it has a number of distinct features. In particular, most trees are flowering plants (angiosperms) or conifers, ginkgo is neither!
• 2.21: Glomeromycota- important mycorrhizal fungi
The Glomeromycota are a very common, yet rarely seen, group of fungi. They are ubiquitous partners with angiosperms, forming associations called mycorrhizae, more specifically 'endomycorrhizae', also called vesicular/arbuscular (VA) mycorrhizae. Most plants (more than 80%) are mycorrhizal and most of these form endomycorrhizae with a fungal associate in the Glomeromycota.
• 2.22: Gonyaulax - A Dinoflagellate
Gonyaulax is representative of a n important group of unicellular organisms, the Pyrrophyta (sometimes called Dinophyta). The common name for the group is the dinoflagellates. Like the Euglenophyta, the group contains both photosynthetic and non-photosynthetic forms. Gonyaulax and several other dinoflagellates are notable for their association with two familiar phenomena: ocean bioluminescence and red tides, although most dinoflagellates are not.
• 2.23: Halobacterium
Halobacterium is one of several organisms that can color high salt environments red, like the hypersaline pools in Owens Lake, California. Halobacteriumis significant not just for its tolerance of extreme salinity but also because it is a member of the Archaea and because it has some peculiar metabolic abilities.
• 2.24: Hemlock
• 2.25: Horsetails, the genus Equisetum
• 2.26: Juniper
• 2.27: Kelp - Laminaria, a brown algae
• 2.28: Lungwort Lichen (Lobaria pumonaria)
• 2.29: Marchantia - Thalloid Liverwort
• 2.30: Marsilea - The 4-leaf Clover Fern
• 2.31: Molds - Ubiquitous Fungi
• 2.32: Nostoc - The Smallest Multicellular Organism
• 2.33: Oedogonium- a filamentous green algae
Oedogonium is representative of a number of organisms in a very diverse group, the green algae. In this book we consider several members of the green algae that illustrate a range in form and structure.
• 2.34: Physarum - A Plasmodial Slime Mold
• 2.35: Phytophthora
• 2.36: Pinus - Pine Trees
• 2.37: Polytrichium - Hairy Cap Moss
• 2.38: Populus
• 2.39: Potatoes- Solanum tuberosum
• 2.40: Porphyra- an edible red algae
• 2.41: Redwoods- the tallest and largest trees
• 2.42: Rhizobium- nitrogen fixing bacteria
• 2.43: Rhizopus
• 2.44: Rice
• 2.45: Rust fungi (order Pucciniales, formerly Uredinales)
• 2.46: Sagebrush
• 2.47: Sarracenia, a carnivorous plant
• 2.48: Seaweed, Fucus- a brown algae
• 2.49: Sensitive fern
• 2.50: Soybeans (and other beans)
Soybean, Glycine max, is an important annual crop throughout much of the temperate regions of the world but especially in the United States, which leads the world in soybean production, followed by Brazil and Argentina. Much of the U.S. production is exported. Soybean is particular notable because of the many ways it is used. It is eaten fresh and dry. The seeds can be processed to yield soy oil or to make soy milk (produced by grinding soy seeds in water, producing an emulsion of protein & oil.
• 2.51: Sphagnum-peat moss
The genus Sphagnum is by far the most important non-vascular plant group on earth. The 120 species in the genus are primarily found in cool, moist habitats, mostly in the Northern Hemisphere but some do occur in the southern part of the Southern Hemisphere. The genus is important because it can dominate large areas and change conditions at these sites, making them less hospitable for some species and more hospitable for others.
• 2.52: Sunflower - Helianthus annuus
The sunflower is a familiar plant that has the distinction of being the only widely used crop species that originated in North America. Although Native Americans domesticated the plant and selected for plants with single heads and larger seeds, its initial use after being introduced into Europe was primarily as an ornamental plant in gardens. It first became popular as a crop plant in Russia, largely as a consequence of edicts from the Eastern Orthodox Church concerning diet restrictions during
• 2.53: Tar Spot Fungus
The fungus Rhytisma lives inside tree leaves and produces large black spots on the leaves late in the growing season (August and September) as the leaves start to senesce. The most common species in the northeastern U.S. occur on maples but there are other species that occur on other tree species. The black spots form when the fungus produces large black masses of hyphae ( 'stroma' ) that break through the epidermis of the leaf.
• 2.54: Thermus aquaticus
T. aquaticusis the organism that makes PCR (polymerase chain reaction) possible. It is an 'thermophile' , capable of living in high temperatures, specifically at temperatures over 70 C (150 F). It was discovered in 1969, at a time when biologists assumed thatno living thing could surviveat temperatures over 55 C. WhileThermuscan 'only' withstand temperatures up to 80 C, other organisms can live at temperatures even closer to the boiling point of water.
• 2.55: Wheat
Wheat should be familiar to everyone although perhaps only as a food and not very much as an organism. Wheat is one of the oldest crop species, originating in Turkey probably close to 10, 000 years ago, although some researchers place its origin even older. As described below what we call 'wheat' is at least three different entities, differing in chromosome number, evolutionary history and also features related to harvesting and baking.
• 2.56: Wood Ferns
The wood ferns (genus Dryopteris) are a group of over 400 species and are commonly seen throughout temperate areas, especially in forests. Many are planted as ornamental plants and they are commonly used in landscaping and gardens. The group is known for hydridization, polyploidy and subsequent speciation which accounts for the large number of species (see discussion of speciation through polyploidy in Chapter 28).
• 2.57: Yeast
Brewer's (aka baker's yeast or commercial yeast), is the organism that is used to make bread rise and produce wine from the fruits of grape. It also is extremely important as a 'model organism' in biology. It was the first eukaryote to have its entire genome sequenced and studies using S. cervisiae have been highly significant in developing our understanding of meiosis, mitosis and cancer.
Thumbnail: Forest mushrooms. (Unsplash License; Adam Nieścioruk via Unsplash)
02: Organisms
The following section contains descriptions of over 50 groups of organisms that represent some of the diversity of the inanimate world. Some, like corn, are already familiar, while others are probably unfamiliar. But all have interesting aspects to their biology, and most are significant to human endeavors. For each group there is information concerning the following areas, matching the five sections of the book:
• taxonomy and phylogeny
• structure
• reproduction
• matter and energy acquisition
• interactions, including interactions significant to humans
The taxonomic level (e.g. species, genus, family) of the groups that are being characterized varies. For most of the descriptions I give a genus name but the description usually characterizes a bigger group, often an entire phylum. You should appreciate that almost all taxonomic entities have aberrant forms that may not fit into the description given. For example, I use the genus Rhizopus to represent the bread molds, a phylum of fungi. Not all members of this group are exactly like Rhizopus but the description does characterize many of the members of this group.
Note that this book is NOT organized by groups but rather by important features that organisms possess: structure, modes of reproduction, means of matter and energy acquisition, and interactions with other organisms and with the physical environment. Because of this, much of the information for any particular group may not come into focus until reading the 'textbook' part of the book.
Acetabularia, an unusual unicellular green algae
Agaricus bisporus, the commercial mushroom
Alfalfa
Bracket Fungi
Calupera, a large coenocytic green algae.
Chlamydomonas, a small unicellular green alga
Chytrids, tiny fungi
Clubmosses: Lycopodium
Coccolithophores, photosynthetic unicellular algae
Coltsoot: Tussilago farfara
Corn
Corralorhiza, a plant that eats fungi
Cryptomonads, unicellular photosynthetic algae
Dandelion
Diatoms, unicellular photosynthetic algae
Dictyostelium: a cellular slime mold
Ephedra: jointfir
Euglena: a unicellular algae
Ginkgo
Glomeromycota: important mycorrhizal fungi
Gonyaulax: a dinoflagellate
Halobacterium
Hemlock
Horsetails, the genus Equisetum
Juniper
Kelp: Laminaria, a brown algae
Lungwort lichen (Lobaria pumonaria)
Marchantia: thalloid liverwort
Marsilea: the 4-leaf clover fern
Molds: ubiquitous fungi
Nostoc: the smallest multicellular organism
Oedogonium: a filamentous green algae
Physarum: a plasmodial slime mold
Phytophthora
Pinus: pine trees
Polytrichium: hairy cap moss
Populus
Potatoes: Solanum tuberosum
Porphyra: an edible red algae
Redwoods: the tallest and largest trees
Rhizobium: nitrogen fixing bacteria
Rhizopus
Rice
Rust fungi (order Pucciniales, formerly Uredinales)
Sagebrush
Sarracenia, a carnivorous plant
Seaweed, Fucus: a brown algae
Sensitive fern
Soybeans (and other beans)
Sphagnum-peat moss
Sunflower: Helianthus annuus
Tar Spot Fungus
Thermus aquaticus
Wheat
Wood ferns
Yeast | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.01%3A_A_Diversity_of_Organisms.txt |
Acetabularia is a member of a very diverse group, the green algae. Other members of the same group that we will consider are Oedogonium, Chlamydomonas and Cladophora , all of which are quite different in form and structure.
Taxonomy and Phylogeny
The green algae are generally put in their own phylum, Chlorophyta, but this phylum is placed variously depending upon the perceptions of the observer. Some workers still consider them to be one of the protist phyla. Workers who reject the protist kingdom often put green algae in the 'Archaeplastid supergroup' . However, since some of the green algae are closely linked to plants, some workers combine plants and some or all of the green algae into a 'Viriplantae' group. ( See the reading on Chlamydomonas for more details on their classification. )
Structure
Acetabulariahas an unusual structure by being large, unicellular and possessing features that might be considered organs— 'roots, stems and leaves' . The single cell isattached to the substrate by root-like cellular extensions. These extensions connect to an elongatestalk which ends in an umbrella-like cap that is often 1 cmor more across. The single nucleus of this remarkable organism is found at the base of the stem.
Reproduction
Sexual reproduction in Acetabularia is initiated when the single (diploid) nucleus goes through multiple mitotic divisions; these nuclei subsequently undergo meiosis and migrate to the cap where they are released in cysts that break open to release mobile gametes. These gametes find each other and fuse to form a zygote which attaches to a substrate and grows into the mature form. Asexual reproduction is also possible if mobile (diploid) zoospores are released and behave like zygotes, attaching to a substrate and developing into the mature form.
Matter and energy
Acetabularia is a typical photoautotroph, using the energy of sunlight to synthesize carbohydrates from carbon dioxide and then using the carbohydrates as an energy source in cellular respiration and as building materials to synthesize a variety of biomolecules.
Interactions
Acetabularia is generally found in warm, marine waters. Since it attaches to substrates and requires light for photosynthesis it is generally found in shallow waters, to depths that depend on water clarity. Acetabularia is eaten by sea urchins and fish.
2.03: Agaricus bisporus the commercial mushroom
Agaricus bisporus, is the most familiar mushroom for most of us — it is the commercial mushroom sold in grocery stores and put on pizza. It comes in various forms: button versions, brown versions and large portobello versions — all of which are varieties of the same species. Its popularity is not so much a consequence of flavor as it is a consequence of its suitability for commercial production. Agaricus does grow wild, typically in fields or lawns but all of the Agaricus mushrooms sold in stores are grown on a controlled medium and in a controlled environment, often in caves or underground structures not so much for the darkness but because of constant temperatures and high humidities.
Phylogeny
Agaricus , and nearly all of the fungi that would be described as mushrooms, i.e. that produce stalked structures with a cap, are club fungi = basidiomycete fungi (Phylum Basidiomycota). Most mushrooms have 'gills' on the underside of the cap where spores are produced and Agaricus shows this feature. Historically all mushrooms with gills were put in a taxonomic entity (usually an order, the Agaricales) but recent molecular analysis has demonstrated that gills are not a sound feature on which to base a phylogenetic classification. Although there still is an order Agaricales, named for Agaricus, it does not contain all gilled mushrooms and it does include a number of fungi that do not possess gills.
Structure
Like nearly all fungi and nearly all club fungi, the bulk of a mushroom's structure is a network of unicellular, branching filaments (hypae) that permeate, in the case of Agaricus, the soil, or the compost that the mushroom is grown on/in (typically manure with other material added to it). In club fungi the filaments are cellular, meaning that there are individual cells, delineated by the presence of cross-walls (septa). The septa are not complete but usually have a pore in the middle that allows cytoplasm to move from one cell to another. The fruiting body of Agaricus is a consequence of drastic change in the behavior of hyphae. Instead of growing in a diffuse manner and spreading throughout their environment, they grow close to each other and intertwine, forming a solid structure that emerges from the substrate it is growing in and produces the familiar mushroom structure
Sex and reproduction
Agaricus completes its sexual cycle by producing basidiospores on the margins of the gills of the mushroom. Like almost all fungi in the Basidiomycete group, the organism exists primarily in a 'dikaryon' state where each cell has two nuclei, one from each parent after two haploid hyphae fuse. Only in certain parts of the fruiting body do the two nuclei fuse to form a diploid cell that then undergoes meiosis to produce haploid, 'sexual' spores. However, for a mushroom farmer, reproduction of Agaricus is totally asexual. They do not sow spores, instead they use pieces of mycelium (the name given to cluster of hyphae), induce it to grow and then stimulate it to produce fruiting bodies. Some of the mycelium remains and can be used to continue the process. The mycelium is probably capable of living thousands of years.
Matter and energy
Agaricus is a typical heterotroph that fee ds upon biomass produced by other living organisms. They secrete enzymes into their environment that break down organic matter into simple forms that can be absorbed into the hyphae and then they re-assemble these materials to make new fungal biomass. Fungi are considered 'decomposers' , but what is not often appreciated is that their nutrition is the same as predators, herbivores and omnivores (including humans). All are heterotrophs and obtain nutrition by breaking down (decomposing) organic material produced by other organisms. As a result of their activities they make more of themselves (i.e. they could be considered a 'producer' ) but because they break down much more material than they produce they are net 'decomposers' .
In commercial operations, the mycelia are feed 'conditioned' compost. You may have heard that mushrooms eat horse droppings — this isn 't exactly true. To feed commercial mushrooms farmers take compost containing horse droppings and other materials (e.g. straw) and allow it to ferment for a week or two. During this time the compost is ' eaten ' by bacteria, other fungi and microscopic animals. These organisms break down the compost, putting it in a form more acceptable to the commercial fungus. They also build up their populations, and the commercial fungus feeds on these ' primary decomposer ' populations. So the commercial fungus doesn' t eat horse droppings, it eats things that themselves eat horse droppings, along with the remnants of horse droppings left behind after the 'first' eating.
Interactions
Like most organisms, interactions between Agaricus and other organisms and the physical environment are extremely important to its success . This is reflected in the links below that describe how mushrooms are commercially grown . As described above, Agaricus is known as a 'secondary decomposer' — it feeds on material after it has been eaten by 'primary decomposers' ; this is similar to the interaction of cows with the microorganisms in their stomachs. Cows cannot digest grass, they need the microbes to act on the grass (in one of their stomachs) and produce something that they can utilize. Agaricus is also very strongly affected by (i.e. interacts with) physical conditions, in particular temperature, humidity and the concentration of carbon dioxide, both to allow the mycelium to grow rapidly and to initiate the production of fruiting bodies.
Further Reading | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.02%3A_Acetabularia_an_unusual_unicellular_green_algae.txt |
Alfalfa (Medicago sativa), is an important perennialherbaceous crop. Most people are familiar with annual crops (planted in the spring and harvested in the fall), and with woody perennial crops (grapes, apples, cherries) but there also are perennial crops that are non-woody. While a few produce food for humans (sugar cane, asparagus, rhubarb, groundnuts) most herbaceous perennial crops are 'forage' crops producing food (usually called 'hay' ) for domesticated animals, especially horses and cattle. While many think of hay as being annual and perennial grasses, there are a number of dicot flowering plants, including alfalfa and clover, both perennials, that are very important sources of 'hay' . Humans do eat alfalfa plants, but only in the form of alfalfa 'sprouts' , young germinated seeds.
Phylogeny
Alfalfa is in the pea family. It is a flowering plant (angiosperm) and is a dicot (eudicot) in one of the largest and most important plant family, the pea family, which includes numerous important crops and many ecologically important species.
Structure
Alfalfa growth produces a typical stem with trifoliate leaves and branches that originate in the axils of these leaves. However, this growth only lasts a year in most of the (temperate) habitats where the plant grows, habitats where winter cold kills most of the above ground plant. Alfalfa 's existence as a perennial depends upon what is known as a ' crown', which is a section of the stem close to the ground surface. This structure produces adventitious buds that provide for growth after most of the above ground portion of the plant dies in the winter. Under agricultural conditions the crown also allows the plant to re-sprout after nearly all of the above ground portion of the plant has been harvested. Harvesting often occurs up to six times over the growing season.
Sex and reproduction
Alfalfa is a typical flowering plant that has bisexual flowers that require pollination in order to set seed. Flowers are 'irregular' , meaning that they are not radial symmetrical like a rose or buttercup. Irregular flowers are typical of the pea family. The anthers and pistil are under tension between a pair of petals that form the 'keel' of the flower. To effect pollination an insect must land on the keel in such a way to triggers a rapid movement of the stamens to 'slap' the underside of the visitor. (see the “Alfalfa Pollen Explosion” video). Honeybees are poor pollinators of alfalfa, they visit to obtain nectar but don 't trigger the movement of the stamens, perhaps because they don' t like being slapped by the anthers. If successfully pollinated, corkscrew fruits develop with small seeds.
Matter and energy
Alfalfa is a photosynthetic autotroph which uses the C 3 photosynthetic pathway. Like many of the pea family alfalfa houses Rhizobium bacteria in nodules on its roots. The Rhizobium bacteria provide a source of nitrogen to the plant, but also represent a sizable drain on photosynthate because substantial amounts are needed to 'feed' the bacteria.
Interactions
Alfalfa originated in the Middle East, probably Iran, and has been cultivated by humans for over 2500 years to provide food for livestock. Because of human introductions it is now found world-wide, primarily in temperate habitats. It is only slightly invasive and outside of habitats that are under cultivation can be found on roadsides and other disturbed habitats. It is drought tolerant and does well on sites that are quite dry. Consequently alfalfa is grown extensively in the western US. Its root system commonly goes down three meters into the soil to acquire water and occasionally goes down 15 m (over 50 feet!!!!). Interestingly, it produces chemicals that deter the germination of its own seeds, necessitating that fields alternate from alfalfa to another crop before being reseeded in alfalfa.
Because honeybees are poor pollinators, farmers growing alfalfa for seed (as opposed to growing it for hay when pollination doesn't matter) rely on other pollinators. These other pollinators need to be managed to produce generate the high pollinator population densities needed to effect pollination. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.04%3A_Alfalfa.txt |
Two examples of bracket fungi: Fomes and Ganoderma
If you are observant and spend much time hiking in the woods you are sure to encounter a bracket (shelf) fungus, fruiting bodies of wood decay fungi that are found both on standing and fallen trees and form a hard outgrowth with a spore producing surface facing downward. Unlike most mushrooms (gill fungi) that produce spores on linear rows (gills), these fungi produce spores in a tissue perforated with numerous cylindric pores, generally from 0.2 to 2mm in diameter, through which the spores are shed. Fungi producing such structures are called polypore fungi, and while there are a few polypore fungi that do produce a 'mushroom' shaped fruiting body, the majority of polypore fungi are bracket fungi, growing off trees trunks and branches like a shelf or a 'bracket'.
Phylogeny
Both these genera discussed here ( Fomes and Ganoderma ), and all fungi considered bracket fungi, are Basidiomycetes (club fungi) in the Kingdom Fungi. When fungal taxonomy was based on morphology (form), all woody polypore fungi were lumped together, i.e. there was a taxonomic entity that included all woody polypore fungi. M ore recent analysis has revealed that woody polypores come from multiple lines, i.e. that a grouping of bracket fungi or of 'polypore fungi' is artificial, not phylogenetic.
Structure
Both of these fungi are typical fungi, producing colonial filaments of cells (hyphae) that branch and fuse to form a feeding structure called a mycelium. This branched dendritic form penetrates the heartwood of trees to obtain nutrition. As a result of certain stimuli the hyphae will grow in a very different way (highly condensed and intertwined) and in a different place (outside the tree stem) to produce a fruiting body, where special cells associated with sexual reproduction, are produced. The fruiting body of both these genera is described as being 'trimictic', meaning that it is composed of three different types of hyphae: generative hyphae, the ones that produce spores; skeletal hyphae, with very thick-walled hyphae and little branching; and binding hyphae, hyphae with extensive branching.
Sex and reproduction
Both of these fungi undergo the normal sexual process shown by basidiomycete fungi ( 'club-fungi' ). Haploid spores of two different mating types need to germinate on a tree and find each other to form a dikaryotic mycelium that feeds on the tree and grows. At some point a fruiting body is produced in which special cells undergo karyogamy to produce a diploid cell that immediately undergoes meiosis to form haploid basidiospores that are dispersed through the air to other trees.
Matter and energy
These fungi are typical heterotrophs that feed upon biomass produced by other living organisms. They are called 'heart rot fungi' feeding on the heartwood, the central cylinder of tree trunks that contains no living cells. Sapwood, the outer part of a wood, contains some living cells, although a majority of the cells are dead at maturity. The living cells of the sapwood provide the tissue with greater resistance to fungal invasion, hence most wood eating fungi are able to infect heartwood but not sapwood.
Both of these fungi are described as 'white-rot' fungi, a name that describes the feeding preferences of the fungus. Wood has three main components: cellulose and hemicellulose (both polysaccharides) and lignin ( a complex polymer of phenolic subunits). Wood rot fungi often specialize, i.e. they have dietary preferences, for either carbohydrates or lignin. These species leave behind the material that they don 't ' choose' to eat, either lignin, which is generally brown in color, or cellulose, which is white. Brown-rot fungi leave behind the lignin, white-rot fungi leave behind the cellulose. Since using wood for paper or to make ethanol requires removing lignin, there is an interest in developing technologies that utilize white-rot fungi to do this.
Interactions
Since they kill no living tissues these fungi will not directly kill trees but they may decrease the mechanical strength of trunks and cause them to break more easily (however, some argue that hollow cylinders are stronger under some circumstances than solid cylinders, in which case the action of these fungi might be considered beneficial). The fungi need some sort of damage to the tree to allow them to enter the heartwood, this damage can come from a variety of agents–shedding of branches, damage from abrasion by the falling of neighboring trees or branches, feeding by wood eating herbivores such as beaver and porcupine, abrasion by deer and moose 'rubbing' the tree with their antlers or by bears stretching their claws, boys playing with hatchets.
The fungal hyphae are sometimes food for insects (larvae) that may in turn be food for other insects or for woodpeckers.
Both these fungi have interesting interactions with humans–read more about these below.
Further Reading
• “Ganoderma applanatum, the artist's conk” by Thomas J. Volk
• “Fomes fomentarius, the tinder polypore” by Thomas J. Volk
2.06: Calupera a large coenocytic green algae.
Caulerpa, another example of green algal diversity
Caulerpa is a large green algae that appears to be multicellular because it is organized into different parts, seemingly leaves, stems and roots. But it is actually just a single large cell. And since an individual organism might be two meters in extent, Caulerpa produces the largest cells on earth, except for maybe some plasmodial slime molds. They are mostly found in shallow waters in warmer oceans but a few occur in fresh water.
Phylogeny and Taxonomy
Caulerpa is in the green algal phylum, in a group generally considered to be a class labelled the Ulvophyceae, a group not considered to be closely related to land plants although other green algae are.
Structure
Caulerpa is siphonaceous (coenocytic) meaning that the cells are multinucleate and specifically in this case there is only a single cell per organism. They typically have a horizontally running structure off of which come extensions to attach it to the substrate ( 'roots' ) and extensions to increase photosynthetic area. Depending on species, these may be blade-like, feather-like or spherical.
Sex and Reproduction
Most commonly Caulerpa reproduces asexually by fragmentation but it is also capable of sexual reproduction, although the details are not completely known. The algae sometimes concentrate their protoplasm in the tips of blades/leaves where it becomes cellular and is released as uninucleate gametes while the rest of the plant senesces and dies. The released gametes are capable of fusing with each other. At this point the knowledge of the life cycle falters. Meiosis must occur at some point but it is not known if it occurs right after syngamy, right before the production of gametes or perhaps that there are both haploid and diploid plants that look alike (cf. Ulva, see chapter 13).
Matter and Energy
Caulerpa is a typical photosynthetic autotroph, acquiring carbon as bicarbonate ion (HCO3) which is produced when carbon dioxide reacts with water to form carbonic acid which then ionizes. This is used to produce hexose sugars that are used both for material needs (to make cell walls, cell membranes, amino acids, etc) and also for energetic needs when the hexose are oxidized in oxidative phosphorylation. Caulerpa acquires 14 other elements obtained by absorbing small ions from the water.
Interactions
Caulerpa oxygenates the environment it is in and serves as a food source for a number of animals. However, it does produce toxins. Like the toxins associated with red tides and produced both by dinoflagellates and cyanobacteria, some toxins affect certain herbivores while others herbivores are unaffected but may accumulate the toxin, thereby allowing it to affect consumers of the herbivore. Caulerpa is native to warm waters around New Zealand and Australia but is invasive in parts of the Mediterranean and off southern California, where it is sometimes causes a variety of problems. It's spread to new areas may be partially due to its use in aquaria and their disposal in nearby waters. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.05%3A_Bracket_Fungi.txt |
Chlamydomonas, a unicellular green algae
Chlamydomonas is a unicellular organism in a group (the green algae). It is included here not because one is like to encounter it (except in laboratories and botany classes) but because it represents on of the many form found in the green algae and also because it is a 'model organism' , one that has proven to be useful in the study of biology. Chlamydomonas is certainly not a typical green algae but one could say that about any member of the group that includes filamentous forms (Oedogonium), sheet forming forms (Ulva), siphonaceous forms (Caulerpa and Cladophora), and multicellular forms (Chara) and even unicellular forms that are 1000 times bigger (Acetabularia) than Chlamydomonas.
Taxonomy and Phylogeny
The green algae (= Chlorophyta) are a group of eukaryotes that have some characteristics in common with plants (they are photosynthetic, possess both chlorophyll a and b, most store carbohydrate as starch and have cellulose cell walls. But they also differ from plants in several ways: most are not multicellular, being either unicellular, siphonaceous or filamentous; they do not retain embryos inside the previous generation as all plants do; few grow on land as almost all plants do. Because land plants are thought to have originatedfrom ancestral 'green-algal like organisms' putting green algae and plants in separate kingdoms, as done in the 'five-Kingdom' classification, with a Protist Kingdom that includes green algae and a separate Plant Kingdom, is very artificial. One remedy is to put green algae in the plant kingdomand some observers do this. Another alternative is to simply throw out the Kingdom level of taxonomy and this is what many modern treatmentsdo. If this were done then one might split the green algae into two phyla, one that includes land plants (Streptophyta) and one that doesn't (Chlorophyta).
Structure
Chlamydomonas is a small (<10 um) unicellular , mobile organism. It is roughly spherical in shape with two anterior flagellae that it uses to 'swim' in a breast-stroke-like manner. Unlike many green algae, the cell wall is not made of cellulose (as it is in land plants) but instead of a glycoprotein.
Reproduction
Chlamydomonas reproduces asexually when haploid cells divide (often multiple times) and form 2, 4, 8 or more daughter cells, which are then released. Sexual reproduction occurs when special cells (gametes) are produced that are capable of attaching to one another, first by their flagellae, and later by their anterior ends, thereby achieving protoplast fusion and forming a zygote. This develops into a zygospore ( dormant, resistant cell) in which meiosis occurs. Eventually zygospore germination occurs, releasing haploid mobile cells.
Matter and energy
Chlamydomonas is a typical photoautotroph, using the energy of sunlight to synthesize carbohydrates from carbon dioxide and water and then using the carbohydrates as a both an energy source in cellular respiration and also as building materials to synthesize a variety of biomolecules. However it can live in the dark if supplied with acetate — (why this is significant is considered when we discuss matter and energy). In addition to the accumulation of carbon , Chlamydomonas accumulates 14 mineral elements which it obtains from its habitat.
Interactions
Although the genus Chlamydomonasis found primarily in fresh and salt water habitats, it also can be found in soil (upper regions that get enough sunlight) and in snow (specifically C. nivalis, the organisms that causes 'watermelon snow' , producing a red pigment that is thought to protect it from high light intensities. Significant to the algae's success is the fact that the organism is mobile and phototactic, using a pigment similar to the rhodopsin of human eyes to direct its movement. As phytoplankton, Chlamydomonasis eaten by small heterotrophs, e.g. Daphnia.
Further Reading
• “Chlamydomonas” by M.D. Guiry
• “Reasons to Rejoice in Green Algae: Essay” by Lynne Quarmby, discusses reasons to study different organisms
• “Watermelon Snow: A Strange Phenomenon Caused by Algal Cells of The Chlorophyta” by W.P. Armstrong
• waynesword.palomar.edu/plaug98.htm
2.08: Chytrids tiny fungi
Chytrids (Chytridomycota) are a group of fungi that are rarely directly encountered, primarily because they are small and they generally eat things that are small.
Taxonomy and Phylogeny
Chytrids are a distinct group within the fungi and like all fungi they possess a cell wall made of chitin and store carbohydrates in the cytosol in the form of glycogen. The chytrid group is distinguished from other fungi by the fact that they produce flagellated zoospores, and flagellated cells are not present in any other fungal groups (an exception is a very small group that has only recently been separated from the chytrids). Chytrids are sometimes described as the most primitive group of fungi, but a more appropriate description might be that they are the group that diverged first along the line that produced four other fungal groups: bread molds (Zygomycota), endomycorhizal fungi (Glomeromycota), club fungi (Basidiomycota) and cup fungi (Ascomycota).
Structure
Many chytrids are unicellular: a single cell grows from a zoospore and eventually develops into a single celled sporangium that produces more zoospores (see the 'holocarpic' example in the accompanying image). In some species the sporangium develops entirely within a host cell, sometimes producing root-like rhizoids (see the 'endobiotic' example). Other species penetrate the host cell and develop rhizoids inside it but produce a sporangium that is attached and outside of the host cell ( 'epibiotic' in the accompanying image). Some chytrids are coenocytic, producing cells with multiple nuclei and sometimes producing short coenoctyic hyphae, cylindrical structures with multiple nuclei ( 'eucarpic polycentric' in the accompanying image ).
Sex and r eproduction
Some chytrids reproduces solely by asexual means via zoospores. Other species do reproduce sexually, producing gametes capable of fusing (syngamy) and cells capable of undergoing meiosis. A few species exhibit an alternation between a haploid and a diploid generation, as found in plants.
Matter and energy
Chytrids are heterotroph s , like all fungi and like humans. Like humans they sometimes consume dead materials (i.e. are saprophytes) but also may consume living materials, in which case the chytrids may act as a parasite or predator. An interesting aspect of chytrids is that many consume small things: spores, pollen, unicellular algae and protozoans or single cells of multicellular organisms.
Interactions
Chytrid ability to consume pollen is significant because of the copious amounts of pollen, especially conifer pollen, that is produced in some habitats.
They are an interesting group because, although aquatic, their small size allows them to be successful in the soil in the films of water that surround soil particles.
Some chytrids are significant because of diseases that they cause, most notably chytridiomycosis a skin disease of amphibians that is thought to have been significant in causing global declines in frog and toad populations, including some extinctions.
Chytrids also cause diseases in plants.
Further Reading
• “The Chytridiomycota” by David Malloch, New Brunswick Museum | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.07%3A_Chlamydomonas_a_small_unicellular_green_alga.txt |
Club mosses are representatives of the Lycopodiophyta, plants that are very important in the fossil record and in the history of plant life but are not particularly diverse or common now. World-wide there are around 1000 species in the group. As is the case with many of the ferns the common names for club mosses have been much more stable than the scientific names, several of which have been changed in the last thirty years. Several species are frequently encountered in the common understory forests of the Adirondacks of New York and in forests in New England. All members of the group that exist today are small plants, typically less than 10 cm in height. But in the past members of the group were much larger and formed forests. The group originated over 400 million years ago in the Paleozoic and the phylum is the oldest group of vascular plants that still has members today. Tree forms up to 35 m in height were common at the end of the Paleozoic, roughly 300 million years ago, and were important in forming deposits that are sources of coal and oil. All the tree forms disappeared at the end of the Paleozoic.
Taxonomy and Phylogeny
The club mosses form a distinct group that is generally recognized at the phylum level (Lycopodiophyta). They are one the groups of 'fern allies' , groups unified by having vascular tissue but lacking seeds. The other groups are the ferns, horse tails and wisk ferns(some people lump these three groups together into one phylum). Although ferns and club mosses can be linked by what they do not have (seeds) this is not a good criterion for forming a group and for this reason, and many others, ferns and club mosses are NOT thought to be phylogenetically close, so the 'fern allies' are not grouped together. The Lycopodiophyta includes three groups, club mosses, spikemosses and quillworts.
Structure
As the name implies, clubmosssporophytes (the spore producing form)look like mosses but they are generally bigger, reflecting the fact that they have vascular tissue, and they often have 'clubs' or strobili, structures where spores are produced. The plants have the typical plant structure of an elongating axis that bears flaps of tissue, 'leaves' that possess on a single strand of vascular tissue. Club moss leaves are called 'microphylls' to distinguish them from true leaves ( 'megaphylls' ) that have more extensive venation. On some club moss and spike moss species the leaves are overlapping and resemble those of cedar, which gives some species a common name of ground cedar. Most species produce above and/or below ground stems that run horizontally and send up vertically oriented branches.The gamete producing plant is often small, often only a few mm in size, rarely over a cm in size, and has an amorphous structure that produce small egg-producing archegonia and sperm producing antheridia.
Reproduction
Like all plants, club mosses exhibit alternation of generations. The group has a relatively large sporophyte and hard-to-find gametophyte that is small, uncommon and subterranean. The gametophyte depends upon an association with fungi to obtain carbohydrates. Gametophytes are bisexual and the flagellated sperm swims to the to the structures, the arechegonia, that produce eggs, . Other groups within the Lycopodiophyta ( Selaginella = spikemosses, Isoetes = quillworts) are heterosporous and some members, both living and fossil, produce structures approaching seeds, having megaspores are retained on the sporophyte and also a female gametophyte that develops endosporically.
Matter and energy
The clubmoss sporophyte is a typical photoautotroph, using the energy of sunlight to synthesize carbohydrates from carbon dioxide and then using t he carbohydrates as an energy source in cellular respiration and as building materials to synthesize a variety of biomolecules. The gametophyte is a heterotroph , a parasite on fungi (mycotroph), that obtains matter and energy from a fungus that it associates with.
Interactions
Although club mosses are common in northern hardwood forests, they are not particularly important. They are not obviously eaten by common herbivores, perhaps because of their chemistry, which contains alkaloids. Historically, the spores were used as an early form of photography 'flash powder' as they can ignite explosively. The spores were also used as a type of lubricating body powder. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.09%3A_Clubmosses-_Lycopodium.txt |
Coccolithophores are some of the most important organisms that you have never heard of !! They are very small marine organisms who have a very significant impact on earth's geology and ecology. They are distinctive because they have a coating that consists of a number of ornate calcium carbonate plates.
Phylogeny and taxonomy
Coccolithophores are closely related to a group of organisms (Haptophytes) that lack the plates. These two groups, together with some other organisms, have been classified a number of different ways. In a five-kingdom classification they are considered to be in the phylum Haptophyta in the kingdom Protista. The coccolithophores are sometimes considered members of the 'golden algae' group and some treatments lump 'golden algae' (haptophytes including coccolithophores and other groups), brown algae and diatoms together in a group called 'Stramenopiles' , largely on the basis of pigments. Other workers feel that the pigmentation similarity is an artifact of two independent secondary symbiotic events.
Structure
The distinguishing feature of haptophytes is a flagellum-like structure called a haptonema that is distinct from a flagellum due to a different microtubule structure. Most members of this group also have two flagella. Within the Haptophyta, the coccolithophores are distinguished by having an outside boundary of overlapping calcium carbonate plates / shields, called coccoliths. Because they are made of calcium carbonate, coccoliths represent a 'sink' for carbon dioxide: the carbon to form them is derived from dissolved carbonate ions, which are (generally) derived from dissolved carbon dioxide, which (generally) is derived from respiring organisms, either aquatic or terrestrial. What happens to the coccoliths when the organism dies depends on conditions. Under certain conditions they dissolve back into solution, under other conditions they sink to the ocean floor and can form deposits hundreds of meters thick. Such deposits form the dramatic 'white cliffs of Dover' and the Alabaster Coast of Normandy.
Reproduction
The primary means of reproduction is asexual cell division. Since both haploid and diploid forms are found the assumption is that they can undergo the sexual cycle but neither syngamy nor meiosis has been observed. It is believed that some members show a heteromorphic alternation of generations with a diploid, planktonic flagellate stage and a haploid, filamentous stage.
Matter and Energy
Most members of the group are photosynthetic and autotrophic but some members lack pigments and are heterotrophs; and many of the photosynthetic forms appear capable of absorbing organic material as well as synthesizing it. They are significant in being tolerant of low nutrient conditions and are found in the open oceans where nutrient supplies are very low.
Interactions
Coccoliths are tremendously important in a number of ways:
• they are the main photosynthetic forms of the open ocean and make a significant contribution to the oxygen production that most forms of life require
• they can remove carbon from ocean waters by forming coccoliths that can sink to the ocean floor and form geological deposits
• their optical properties can change water albedo and thereby ocean temperatures
• they produce sulfur compounds (dimethylsulfide, DMS) that can influence cloud formation and acid rain
• they serve as a food source for a number of other organisms
• they can form toxic algal blooms
Further Reading
• “Emiliania huxleyi” by Tobey Tyrrell
• “Emiliana” on Microbe Wiki | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.10%3A_Coccolithophores_photosynthetic_unicellular_algae.txt |
Tussilago farafara is a common herbaceous plant throughout much of North America, occurring in disturbed habitats, usually in relatively moist sites. It is one of the first flowers to be found in the spring, often on roadsides
Taxonomy and phylogeny
Coltsfoot is a flowering seed plant (an angiosperm) in the Aster family (Asteraceae), one of the largest families of flowering plants. The group is usually easy to recognize when flowering because the 'flower' is actually an inflorescence, a cluster of flowers. The flowers are often of two types: flowers with elongate petals radiating outward and flowers with short petals that are vertical. Coltsfoot and many familiar members of the family (sunflowers, asters, daisy) have both types of flowers but other members of the family (dandelion, chicory) may only have one of the two types of flowers.
Structure
Coltsfoot is a perennial that spreads extensively by underground stems (rhizomes) that produce shoots that live for two years. The first year the shoots are vegetative and produce a cluster of large leaves with grayish hairs, especially on the lower side. In the fall, flower buds develop at the base of the leaves and the leaves senesce and fall off. The following spring the flower buds (which are actually branch shoots) develop. These branches bear no true leaves, only rudimentary scales, but produce a dandelion-like inflorescence ( 'flower' ). The flowering shoots emerge very early in the spring and elongate to produce a gray stem roughly 10 cm long with a yellow 'flower' at its end that is the same size and color as dandelion but unlike a dandelion it has both flower types, like an aster. The 'flower' develops into a head of fruits, looking again very similar to a dandelion and, like dandelions, the tip of the flowering stalk arches over as the fruit develops and then returns to an erect position after the fruits are mature and ready to be dispersed.
Sex and Reproduction
As a typical angiosperm, Coltsfoot reproduces sexually and produces seeds in the ovaries of flowers. The seed contains an embryo that develops from a zygote formed by the union of a male gamete derived from pollen and a female gamete produced in the female gametophytes (embryo sacs) that are present in the ovules of the flower. The center flowers of a head do not have ovules while the outer flowers possess both male and female parts. The plants are self-incompatible and need pollen from another plant in order to set seed. Pollen transfer is accomplished by bees and beetles attracted to the flowers by nectar rewards and scent.
Matter and energy
Coltsfoot is a typical photosynthetic autotroph. Carbohydrates, synthesized in the spring are stored in the rhizomes to provide both matter and energy in the spring when there are no leaves and no photosynthesis. This is an excellent example of plant growth that is accompanied by no increase (actually a decrease) in plant weight. The rhizomes are depleted of carbohydrates, and therefore lose weight, in order to power the growth of the developing flowers.
Interactions
Native to Europe, coltsfoot has established itself in North America. While it generally is found in disturbed ( 'weedy' ) habitats, it occasionally invades 'natural' habitats as well. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.11%3A_Coltsoot_-_Tussilago_farfara.txt |
Corn (Zea mays), or maize, is an annual grass crop species that survives only because of its cultivation by humans. Its ancestry tells some interesting tales. For most crop species a wild ‘relative’ is readily apparent. This is not the case for maize but the answer may actually depend on what one means by ‘apparent’. There is no plant that bears strong resemblance to corn, especially in terms of its ‘ear’, a cluster of female flowers and later fruits. Its closest relative, called teosinte, differs in several ways from corn. Significantly, it differs in ways that make it an unlikely ‘proto-crop’, one that humans might manipulate by selective harvesting and planting in order to make it more desirable. However the genetic differences between teosinte and corn turn out to be quite small, differences in developmental genes that can greatly alter the ‘looks’ of a plant and, significantly, alter features that make it a desirable crop. Thus there is an ancestor of corn (a species of teosinte) that grows wild in Mexico, it just doesn’t look much like corn and has features, in particular a small number of fruits that are encased in a very rigid structure, that aren’t very suitable for harvesting.
Unisexual flowers of corn: female flowers (above) are clustered on a branch called an ear. There are typically 1 to 3 ears per corn plant, occurring (as they always do!) in the axils of leaves, male flowers are also clustered on special stems, these occur at the top of the plant in structures called tassels.
Whether this plant was actually utilized agriculturally and favorable characteristics (more fruits that are easier to open) were selected for, or a more suitable version appeared ‘ on its own ’ , without human intervention, is not known. Regardless once a version of corn appeared, probably 9000 years ago, it was rapidly transformed by early farmers selecting for favorable traits, in particular larger ears. Less than 2000 years ago modern versions of the crop appeared in the area that is now part of Mexico and rapidly spread throughout most of the Americas. It is an unusual grass in a number of ways: there are separate male and female flowers (most plants and most grasses have bisexual flowers) and it produces seeds that do not fall off the plant as those of most grass es do.
Phylogeny
Corn is a flowering plant in the monocot group, a phylogenetic entity that includes orchids, palms, lilies and grasses. The grasses are put together in the Poaceae family, a large family that includes staple crops (wheat, rice) and is extremely important ecologically, often dominating regions.
Structure
To people who think grasses always look like those in their lawns, corn looks quite different: it is large, both in terms of height and in the width of leaves. Initially the ‘ stem ’ is actually just the round basal parts (the sheaths) of individual leaves, with the oldest leaves on the outside and newer leaves being produced inside. As is the pattern in grasses and many other monocots (see the discussion of banana ‘ stems ’ in Chapter 8 ), the shoot apical meristem stays at the very base of the plant, near the ground. The ‘ stem ’ is produced by the sheaths of multiple leaves. Eventually a true stem emerges from the interior as the shoot apical meristem is elevated, ‘ telescoping ’ up the space formed by the sheaths of several leaves. The stem elongation ends when the shoot apical meristem transforms into a flowering meristem, producing a clusters of male flowers (the tassel) at the top of the stem. As is typical of all plants, branches form in the axils of leaves; what is unusual is that these branches produce very little stem, only a short axis with multiple female flowers. The base of this flowering branch produces multiple leaves that grow over the flowers to form the ear of corn. Emerging from the tip of the ear are the strands of ‘ silk ’ : the stigma and style of each individual flower enclosed in the ear.
Sex and reproduction
Corn reproduces sexually and is difficult to propagate vegetatively. Because it has separate male and female flowers it is very easy to control breeding and corn was the first crop for which hybrid seed was produced. Hybrid seed is produced by crossing two different inbreed lines and results in F1 plants that are particularly vigorous (see Chapter 28 and Chapter 31).
Matter and energy
Corn is a photosynthetic autotroph which uses the C4 photosynthetic pathway. Like most C4 plants , it has a particularly high rate of photosynthesis, has a high water use efficiency (carbon dioxide fixed compared to water loss) and will benefit less from rising carbon dioxide levels than C3 plants (Chapter 20).
Interactions
Corn is obligately tied to human agriculture and could not survive were it not for our efforts. It has been developed for a wide number of uses including animal feed (fodder, silage), fuel (ethanol), home heating (corn/pellet stoves), and a wide variety of food products. It is now grown world wide and is second only to rice in terms of world-wide production. It is affected by many pests/diseases including smut and rust fungi, army worms (moth larvae), aphids and viruses.
Corn carbohydrate chemistry
The bulk of a corn kernel (which is technically the fruit of the plant) is amylose starch, a carbohydrate with a very simple structure, consisting of a string of 6-carbon glucose molecules attached end to end, i.e. at two points. Some forms of starch (amylopectin starch) are not solely linear chains but are branched by because some glucose molecules are attached to three other glucose molecules rather than two.
The starch in corn kernels is formed from sucrose that is synthesized in photosynthesizing leaves and transported to the developing fruit in the phloem tissue. Sucrose is a disaccharide formed by combining one glucose with fructose, another 6-carbon sugar. After the sucrose is transported to the developing corn kernels the sucrose is broken down to a glucose and a fructose. The glucose is used to make starch directly; the fructose is converted into glucose and then is also used to make starch.
Corn kernels are sweeter earlier in their development, before the kernel is mature, because more sugar (sucrose, glucose and fructose) is present. As the fruit matures most of the sugars are converted into starch and mature kernels are usually not at all sweet. However, corn plants exhibit variation in the amount of starch produced, thereby producing variation in the degree of sweetness in mature kernels.Native Americans were aware of this when they introduced corn to Europeans. By the early 20th century agricultural research had developed substantially sweeter varieties of corn and isolated the cause of the sweetness, which is alack of (or lesser amounts of) one or several enzymes that are responsible for synthesizing starch from sucrose. Mature corn kernels of sweet varieties of sweet corn are ‘shrunken’ because they lack the starch that normally makes them plump. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.12%3A_Corn.txt |
Corralorhiza is a representative of the orchid family. The orchids are one of the largest families of flowering plants, a group with over 25, 000 species. Although the genus Corralorhiza is restricted to North America, with roughly a dozen species, most members of the family are found in the tropics. Probably the most commonly seen orchid in the northeastern US is the pink lady slipper but there are another 10-15 species of orchids that relatively easy to find, although they never are abundant and many occur in restricted habitats, e.g. bogs. Corralorhiza is an unusual angiosperm because it is non-photosynthetic, a characteristic that is very rare within plants in general but does occur occasionally in several plant groups.
Taxonomy and Phylogeny
The orchid family is distinctive in a number of ways and its members are generally quite easy to recognize when in flower. They are in the monocot group, which is usually considered a class (remember that families are grouped into orders, orders into classes, and classes into phyla). Monocots area monophyletic group that is thought to have diverged early (perhaps 130 million years ago) from the rest of the angiosperms. The remaining angiosperms (i.e. all flowering plants except monocots) do NOT form a phylogenic entity and hence modern treatments do not divide angiosperms into two groups (monocots and dicots) but into several groups, the two largest being monocots and 'eudicots', a group that includes most, but not all, of the old dicot members. Monocots have a number of features that distinguish them from other flowering plants: a single cotyledon in the seed, lack of secondary growth, flower parts typically in 3's, and stems with scattered vascular bundles.
Structure
Orchids are herbaceous perennial plants that have several distinct growth forms. Many orchids are epiphytes, plants growing on the trunks of other plants, and may have features including 'aerial roots' and 'pseudobulbs' which allow them to be successful under these conditions. Corralorhiza orchids do not have a typical orchid structure because they are non-photosynthetic and have very reduced/no leaves while most orchids have very visible leaves that may be stiff, oval and overlapping or sometimes may be grass-like. Many orchids produce rhizomes (horizontal stems running below ground), corms (short, fattened vertical stems) or tubers (enlarged stems that are not oriented vertically).
Reproduction
Most orchids exhibit sexual reproduction that is possible because of elaborate pollination mechanisms that most commonly involve bees or wasps. The flowers of orchids are unusual because pollen is not dispersed as individual grains but rather in large packets ( 'pollinia' ) that represent the the entire anther of an individual stamen and contain thousands of pollen grains. Seeds of orchids are extremely small, often less than 0.5 mm, sometimes less than 0.1 mm (less than 100 microns). This small size is possible because there is no endosperm, the embryo is much smaller than in most seeds and the seed coat is very thin. Because of the lack of endosperm, the germinating seeds of most orchids must quickly associate with a fungus in order for the fungus to provide the seed with the nourishment needed in order for the orchid to become established. Note that although plant/fungus associations are very common (e.g. in mycorrhizae), the relationship found in in the germinating orchid seeds reverses the normal flow of carbohydrates: in a typical plant/fungus association plants transfer carbohydrates to fungi, but in germinating orchid seeds the flow of carbohydrates is from the fungus to the plant. Once the orchid produces a photosynthetic structure the flow of carbohydrates is reversed; however, this never happens in Corralorhiza because it never produces a photosynthetic structure.
Matter and energy
Corralorhiza is a very unusual angiosperm because it is a heterotroph, a parasitic heterotroph, surviving on biomolecules that it does not produce but instead are acquired from a host organism (a fungus) that it associates with. Unlike most orchids that rely on 'mycotrophy' (fungus-eating) just during the seedling establishment phase (see above), Corralorhiza plants never become photosynthetic and never produce their own carbohydrates. Their mineral nutrition is also supplied by their host because they produce no roots to explore the soil to acquire nutrients. There are several other unrelated flowering plants with a similar lifestyle, including Indian pipes (Monotropa uniflora) and Snow flower (Sarcodes spp.). There also are flowering plants that parasitize the roots of other flowering plants: beech drops (Epifagus virginiana), witch flower (Striga spp.), and also those that parasitize the stems of other flowering plants: dodder (Cuscuta), mistletoe (Phoradendron, Viscum).
Interactions
Corralorhiza , and orchids as a group, have two interactions that have already been noted: with fungi during seed germination and with bees and wasp s in many elaborate pollination mechanisms. In spite of the fact that there are lots of species, the group is not particularly significant ecologically (i.e. it does not dictate the activities of communities/ecosystems). Orchids have limited economic importance, being rarely used as food, although the spice vanilla comes from an orchid s. Orchids have become important to the florist industry (e.g. as corsages) and also as house plants.
2.14: Cryptomonads unicellular photosynthetic algae
As the name implies, cryptophytes (crypto = hidden) are unicellular algae that are often hidden. This is a consequence of their relatively small size (10-30 um), the fact that they often occur in deeper waters, and the fact that they are often difficult to collect in an intact condition. However, they are significant contributors to aquatic food chains, both marine and fresh water, and have interesting features that relate to their evolution.
Taxonomy and phylogeny
While consistent structural features unify the cryptomonad group, their placement relative to other living things is problematical. Although they have similar pigmentation (chlorophylls a and c and phycobillins) with the dinoflagellates, this may be the result of ancestral forms of both groups separately ingesting the same eukaryotic algae (a red algae) in a secondary endosymbiosis manner.
Structure
Cryptomonads have a distinctive structure. They are unicellular and have two flagella with an anterior groove. Their chloroplasts have four membranes, reflecting secondary endosymbiosis, i.e., that a eukaryote ingest ed another eukaryote, in this case one with a chloroplast (see Diatoms). Because of pigmentation, the second endosymbiotic event is thought to have involved a red algae being ingested by a unicellular heterotroph. This pattern is also thought to be the case for dinoflagellates and diatoms. Cryptomonads possess unusual structures called ejectisomes that can be discharged when the alga is disturbed, triggering movement that may deter a herbivore. Reflecting their secondary endosymbiotic origin, they have DNA in four locations: a nucleus, the mitochondrion, the chloroplast and in a structure called a nucleomorph, thought to be a remnant of the nucleus present in the cell of the second endosymbiotic event. They have no cell wall but do have a proteinaceous layer just inside the plasma membrane similar to the pellicle found in dinoflagellates. As might be expected for an organism lacking a cell wall, they possess contractile vacuoles to maintain water levels.
Sex and reproduction
There is some evidence for sexual reproduction in at least one species but primarily they reproduce asexually by mitosis.
Matter and energy
Almost all cryptomonads possess photosynthetic pigments and are photosynthetic autotrophs, acquiring carbon and 16 other elements in inorganic form from their environment. However, cryptomonads do require B vitamins, reflecting their heterotrophic ancestry. And a few species lack photosynthetic pigments and are heterotrophs, obtaining food by phagocytosis (invagination of the cell membrane to engulf a food particle). Some photosynthetic forms are also capable of phagocytosis, indicating mixotrophy (being both an autotroph and heterotroph ).
Interactions
Because red light penetrates deeper in the water column and because cryptomonads possess phycobiliproteins pigments that can utilize red light, cryptomonads can photosynthesize at greater depths than other algae, and cryptomonads are often found at greater depths than other algae. Although they are not a particularly diverse group, they appear to be quite important in several habitats, typically cooler ones, both marine and fresh water, serving as the base of food chains. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.13%3A_Corralorhiza_a_plant_that_eats_fungi.txt |
Dandelion is an extremely common plant through temperate North America and Europe. Its common name, dandelion, comes from the French 'dent de lion' (tooth of a lion) referring to the shape of the leaves. It is widely recognized as a weed, a word that generally means that it is an undesirable plant (more details in Chapter 29), undesirable because it grows in places where people are trying to grow something else (e.g. in lawns or in crop fields), and, at least to some people, undesirable because of its looks — perhaps not so much the bright yellow flowers, but more likely because of the fruit heads and the rosettes of leaves in an otherwise uniform carpet of grass. In an ecological sense dandelions are weeds because of their ability to disperse, and their association with 'disturbed' habitats. In order to persist in a habitat that continually gets disturbed, a plant needs to be tough: able to survive, grow and reproduce even when factors that might kill other plants occur. Weeds typically disperse readily, grow quickly and are able to reproduce in spite of a variety of adversities. At the same time, most ecological weeds are poor competitors and, if disturbances do not occur, weeds will be replaced by species that are better competitors. Consider the distribution of dandelions in the Adirondack Park: they are rarely found in 'undisturbed' situations but are found where human activity 'disturbs' the area—next to campsites and along the margins of trails, places where competitors of dandelions aren't able to become established because of the trampling by people. In a comparable situation, dandelion can thrive in agricultural fields because it can tolerate treatments such as tilling the soil because of the ability of roots to regenerate whole plants.
Phylogeny and taxonomy
Dandelion is an angiosperm, the group whose members produce flowers and seeds (Kingdom Planta, Phylum Magnoliophyta or Anthophyta). Dandelions are in one of the largest families within the angiosperms, the aster / sunflower family (Asteraceae), a group that is usually easy to recognize because the flowers occur in dense clusters (inflorescences) that themselves look like a single flower.
Structure
Dandelion has a typical plant structure: a root-shoot axis with leaves produced on the shoot. It is an herbaceous perennial plant that forms rosettes, very short stems with leaves occurring in a circular pattern. As is true in all flowering plants, in the axils of each leaf is an axillary bud. In many plants these axillary buds develop into branches but in dandelion these branch shoots only develop into inflorescences, which, after developing fruits will fall off the plant. Dandelion produces an enlarged storage root (little material can be stored in the very short stem). This root is very capable of producing adventitious shoots; consequently, if one attempts to pull the plant up but fails to obtain all of the root, parenchyma cells in the remaining root develop into shoot apical meristems that grow to the soil surface and again produce a rosette of leaves. One sometimes sees clusters of dandelion rosettes, resulting from a broken root that has produced multiple new shoots.
Sex and reproduction
Dandelions reproduce by producing seeds, but the seeds are produced by apomixis, i.e. without the sexual process. Dandelion does produce flowers and these appear normal and develop ovules. However normal meiosis does not occur in these ovules and no haploid cells are produced; consequently haploid female gametophytes (= embryo sacs) are not produced and no egg os produced. Hence, there is no possibility of syngamy. However, seeds do develop, but the embryo found in the seed is not derived from a fertilized egg but instead from a diploid cell that is present in the ovule. Because there is no sex in Taraxacum officinale it is not a 'real' species, i.e. an 'interbreeding group' — there are multiple clones that collectively are considered a species.
Dandelion seeds are actually one-seeded fruits with the fruit and seed wall fused to each other (as it is in sunflower and in all members of the sunflower family). The top of the fruit develops into a parachute-like structure that helps disperse the seed. It has a stalk 1-2 cm long extending from the top of the fruit. The stalk ends with arms that radiate outwards. The arms have feathery branches emerging from them. Although the structure acts like a parachute by keeping the seed aloft for a longer time than would be the case otherwise, the mechanism of action is very different because the structure does not 'capture air' as a parachute does but it allows air to flow through it in such a way that that a vortex of low pressure forms above the dandelion fruit and this is what retards the rate of descent.
Matter and energy
Dandelion is a typical photosynthetic autotroph. It acquires carbon dioxide from the air and 14 mineral elements from the soil in order to grow. Energy from the growth process comes from cellular respiration where the plant oxidizes the carbohydrates formed in photosynthesis in order to acquire energy as ATP.
Interactions
As mentioned above, dandelion interferes with certain human endeavors: gardening, farming, manicured lawns. But dandelion does have some positive interactions with humans — its greens are edible, delicious in fact, if eaten when young. The flowers are not only pretty but are also edible and can also be used to color foods, e.g. dandelion pancakes.
Dandelions can be used to make wine, however the dandelions are only being used as coloring/flavoring agent — the sugars that the yeast ferment must be provided from cane sugar, honey, grape juice, etc. Dandelions flowers do produce nectar and pollen and these are resources for a number of insects, including honeybees. This is surprising since pollination is not required to produce seeds hence the production of resources (pollen and nectar) are serving no benefit to the plant. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.15%3A_Dandelion.txt |
Diatoms
The diatoms are a phylum of unicellular photosynthetic algae and are a group significant for their unique structure and ecology.
Taxonomy and phylogeny
The diatoms represent a distinct group but the placement of the diatom group is problematic both in terms of level (phylum or class) and in terms of phylogeny (i.e. who are they grouped with). They may be placed in the 'miscellaneous' kingdom, the Protist Kingdom, which is practical but not phylogenetically accurate. They have affinities to several other groups, in particular the brown algae. In a number of taxonomic schemes they are placed in a group called 'heterokonts', sometimes in a 'Chromista' kingdom and sometimes in a Ochrophyta phylum. The groups that are sometimes associated with them include the 'golden-brown' algae, the brown algae, and some non-photosynthetic forms, in particular the water molds (Oomycota). It is now thought that the group originated from an endosymbiotic association of a red algae (a eukaryote) with another eukaryote and that the chloroplasts of diatoms and related groups represent derivatives of the red algae.
Since the red algae themselves (like all eukaryotes) are thought to have originated from an endosymbiotic event (this is considered to be the primary endiosymbiotic event), the endosymbiosis that that produced diatoms is considered to be a 'secondary endosymbiosis'. Evidence for this can be found in the membrane system of the chloroplasts. The chloroplasts of red algae, green algae and plants have two membranes, one thought to be derived from a prokaryotic symbiont, a cyanobacterium (= blue-green algae), and one derived from the host that engulfed it (the phagosomal membrane (the membrane that surrounds the particle being engulfed). The chloroplasts of diatoms (and groups thought to be related to them) have four membranes. The two 'extra' membranes represent the outer membrane of the engulfed red algae plus the phagosomal membrane of the second endosymbiotic event. Diatoms, and the heterokont/chromista/ochrophyte group as a whole, are thought to be of relatively recent origin, obviously after the origin of red algae and also well after the origin of plants. The coloration of the diatoms, and of the photosynthetic members of the heterokont/chromista/ochrophyte group as a whole, is brown or yellow-brown (ocher is a yellow/brown color) and comes from the presence of a different pigment, chlorophyll c, in addition to chlorophyll a.
Structure
Diatoms are unicellular, and like most (but not all!) unicellular organisms, they are small, generally 20-100 um in size, and only visible to the naked eye as dust. They have a cell wall with a unique (in biological terms) composition, being composed of silica dioxide, a very common occurring mineral (quartz is silica dioxide, thus glass and (most) sand has the same composition). The cell walls of most organisms are usually polysaccharide in nature (i.e., carbon based). Thus most cell walls would be considered 'organic' if one defines organic on the basis of carbon (as most chemists do); but if one considers 'organic' to mean relating to living things then silica dioxide sometimes is organic, but only rarely, as only a few other groups of organisms utilize the material in their structure (see horsetails). Another distinctive feature of the cell wall of diatoms is that it is composed of two distinct parts ( 'frustules' ), a 'top' half that is slightly larger and whose sides overlap the 'bottom' half, much as the top of a shoe boxfits over the bottom. The frustule is 'sculptured' with minute pores that give it a very decorative look. Diatoms come in two basic forms: radially symmetrical forms(image at top of first page) and bilaterally symmetrical forms, like the image at the start of this section. When the diatom dies the two halves separate and the top and bottom, being composed of a very stable material resistant to decomposition, settle to the bottom of the body of water that the diatom was living in and become part of the sediment. Most diatoms exist as separate individual cells but a few are colonial, resulting from the failure of newly produced cells to separate from their parent cell.
Reproduction
Diatoms generally reproduce asexually by mitosis. The two frustules separate, each with a nucleus and cytoplasm. Each daughter constructs a new frustule and the new frustule is always the bottom (smaller one). This means that one daughter cell (the coming from the 'top' ) is the same size as the original and the other is slightly smaller. Thus, through time, the size of a population of diatoms gets smaller. For most diatoms, when they shrink to 1/3rd of the maximal size, sexual reproduction is triggered and , in the process , the maximum size is produced.
Sexual reproduction requires the normally diploid nucleus to undergo meiosis. In centric diatoms meiosis results in two types of gametes. A single cell that undergoes meiosis will either produce one or two larger, unflagel l ated gametes (eggs) or it will produce 4-128 smaller flagellated cells (sperm). Meiosis results in four daughter nuclei — cells that produce eggs typically lose two or three of the daughter nuclei and thus produce one or two eggs, while cells that produce sperm have meiosis followed by zero to five rounds of mitosis, producing 4 to 128 sperm. Sperm swim to fertilize eggs which are sometimes released from their parent cell. Upon syngamy a structure called an auxospore is produced that expands to produce the maximum size d cell. For most pennate diatoms sexual reproduction does not involve motile sperm. Two cells fuse to one another and undergo coordinated meiosis and the movement of haploid nuclei, allowing one or two auxospores to be produced per pair of cells.
Matter and energy
Diatoms are photosynthetic and are typical autotrophs, using the sun's energy to reduce carbon and accumulate carbohydratesand using the energy obtained from the oxidation of carbohydrates(i.e. respiration) to carry out a variety of life functions including the acquisition and accumulation of otherelementsnecessary for life. Although, like all life, they require N, P, S, K, Ca, Mg, Fe, Mn, Cu, Zn, Mo, Ni, B, Cl, they also require at least two other elements, silica and selenium, that many organisms (in particular, most plants) do not require.
• A few diatoms are heterotrophic and obtain reduced carbon and other materials by eating other organisms.
• Diatoms generally store reduced carbon, at least for long-term storage, as lipids rather than carbohydrates as plants do. This is significant to their distribution because lipids provide buoyancy and may allow the organisms to stay in the upper levels of a body of water that receives more sunlight.
• It is maybe significant that the silica cell walls of diatoms require considerabl y less energy to construct than the carbohydrate based cell walls of most other organisms with walls, in particular other unicellular algae. Some have argued that this is the reason that diatoms sometimes dominant the phytoplankton community.
Interactions
Here are a select few of the many interactions involving diatoms:
• global ecology–It is estimated that diatoms account for over 40% of the ocean's production of oxygen and reduced carbon. Therefore the group has a very substantial influence on important biogeochemical cycles, in particular for oxygen and carbon, but also for mineral nutrients and for silica.
• base of aquatic food chains-diatoms are a key component of phytoplankton communities which serve as 'food' for heterotrophs in these environments. When you are eating salmon, trout or tuna you are consuming at least some organic material that was formed by diatoms and transferred through a number of trophic levels before become part of the fish that was your meal
• competition with other phytoplankton –diatoms interact with a number of other unicellular algae in a competitive way (i.e. diatoms negatively affect the population sizes and growth rates of other algae). In at least some instances silicon plays an important role in this interaction, if silica is abundant diatoms are able to outcompete other algae, if silica is scarce diatoms are outcompeted.
• developing communities –colonial diatoms commonly form a film on both biotic (other algae, snail shells) or abiotic (rocks, boat hulls) surfaces. Mucilage secreted by the diatoms holds the colony together , and a variety of other organisms, bacteria, other algae, nematodes, etc. live in the film.
• economic interactions with humans –diatoms are important to human endeavors in a number of ways, besides their importance to global ecology:
• diatoms occasionally cause toxic bloomshttp://www.mbari.org/staff/conn/botany/diatoms/jennifer/toxin.htm
• the frustules of diatoms, preserved in sediments and rocks derived from sediments, is called 'diatomaceous earth' and has a number of industrial applications: as a porous filter (e.g. in aquaria), as an abrasive (e.g. in toothpaste), as a mechanical insecticide, as an absorbent, as a stabilizer mixed with nitroglycerin forming dynamite. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.16%3A_Diatoms_unicellular_photosynthetic_algae.txt |
Dictyostelium is a 'cellular slime mold', a very unfamiliar (to most) organism that has proved to be useful as a 'model organism' to study significant biological processes, in particular, development. It has a multicellular stage that develops not as a result of a cell dividing repeatedly producing daughter cells all stuck together. Instead multicellularity is the result of the aggregation of many individual cells. In addition to its use as a model organism, studying Dictyostelium offers an excellent opportunity to see life from a different perspective, appreciating that although all life is fundamentally the same it sometimes operates in very different manners.
Phylogeny and taxonomy
Since they are heterotrophic, mobile and (generally) unicellular they used to be considered 'protozoa'; other early treatments put them with fungi because they produce fruiting bodies and spores. Like a number of other 'misfit' groups, the cellular slime molds have been placed in the Protist kingdom, a heterogenous assemblage of eukaryotes that do not readily group with animals, plants or fungi. While certain aspects of their life-cycle are unique, their amoeboid like stages aligns them with amoebae, that look similar but are always single celled and never coalescing into a multicellular entity. Another relatively close group are the plasmodial slime molds (see Physarum) and some put these three groups (amoebae, cellular slime molds, plasmodial slime molds) together in a group called the Amoebozoa, and the Amoebozoa, along with Choanoflagellates, Fungi and Animals can be united in a group called the Unikonts.
Structure
Dictyostelium is eukaryotic and typically exists as 'amoeboid' cells that are small (typically~ 5 um in length), without a cell wall and capable of ingesting material by phagocytosis. Their normal food is bacteria. Peculiar to the group is the developmental ability of individual cells to come together to form a multicellular entity. Consequently Dictyostelium also exists as a multicellular form produced when cells aggregate into a 'slug' ~ 1 mm long. The slug is briefly mobile and then transforms into an immobile vertical structure up to one cm tall with a round spore producing capsule at its top.
Reproduction
The individual amoeboid cells reproduce asexually by mitosis, but this is only part of the life cycle. The multicellular entity also reproduces asexually: slug—>fruiting body—>spores——>more amoebae—> more slugs. Dictyosteliumis capable of a sexual process but does so only rarely, when two amoeboid cells fuse to form a single diploid cell, forminga structure called a macrocyst. Inside the macrocyst meiosis occurs, followed by mitosis and eventually haploid amoeboid cells are released.
Matter and Energy
Dictyosteliumis a predatory heterotroph, capturing (by phagocytosis) other living organisms (primarily bacteria) and using their biomolecules both as a source of energy (oxidizing them in cellular respiration) and also reconfiguring them into biomolecules of Dictyostelium.
Interactions
One of the interesting interactions involving Dictyostelium is its 'farming' behavior, an ability to produce spores that contain the bacteria that it feeds upon. The dispersal of such spores makes it more likely that Dictyostelium will have something to eat after dispersal (see link 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=475
Further Reading
• “Starving to be Social: The Odd Life of Dictyostelium Slime Molds” by Alex Wild
• “Dictyostelium discoideum” by Mary E. Sunderland
• “Dictiostelida” in Microbe Wiki | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.17%3A_Dictyostelium_-_A_Cellular_Slime_Mold.txt |
Ephedra (the common name is also ephedra, and it is also called jointfir) is a representative of a small, diverse group of seed plants that unfortunately has no common name. They are simply called 'the gnetophytes' after the name for the phylum, Gnetophyta. There are three genera in the group, Ephedra and Gnetum, both with less than 100 species, and Welwitchia, which only has a single species. Welwitchia has a very limited distribution (the Nambib desert of South Africa) while Gnetum is found world-wide in tropical areas and Ephedra is found world-wide in shrub lands (generally hot and dry habitats).
Taxonomy and Phylogeny
The gnetophytes are generally put in their own phylum, one of four phyla of seed plants without flowers (the others being conifers, cycads and ginkgo). Collectively, these four groups are grouped as 'gymnosperms' which some workers consider a phylogenetic entity while others do not, primarily because of difficulties relating their relationships with extinct seed plants and with flowering plants. While gnetophytes have some features (see below) in common with angiosperms (and distinct from other gymnosperms) most feel that there is not enough evidence to group gnetophytes and angiosperms together in a phylogenetic entity. The Angiosperm Phylogeny Group has the pine group as the gnetophytes closest relative.
Structure
Ephedra is a leafless shrub with multiple stems and branches that are typically 2 to 5 mm thick and green. The leaves are small, scale-like and often quickly fall off the plant. Plants produce male cones that produce microspores that develop into pollen , and female cones that produce megaspores that are retained inside the cones and develop into female gametophytes inside structure called ovules. Unlike other gymnosperms, Ephedra plants possess vessels in their xylem tissue, a feature that is found in many, but not all, angiosperms.
Reproduction
Like all seed plants, Ephedra produces female gametophytes inside ovules. The zygote is ormed when the egg, produced by the female gametophyte, is fertilized by a sperm nucleus produced by the male gametophyte (pollen). This zygote develops into a new sporophyte embryo that is packaged inside a seed, a mature (fully developed)ovule. Double fertilization, where there are two sperm nuclei, one fusing with the egg and a second fusing with a second nucleus of the female gametophyte, is a feature once thought to be found only in flowering plants, but it also occurs in at least some members of the genus Ephedra, although the details, in particular the lack of development of an endosperm, distinguish what happens in Ephedra from what happens in angiosperms. The female cones of some species become 'fruits' when the integuments thicken and become colorful. Technically fruits (if defined as ripened ovaries) are only present in angiosperms but if defined as 'structures to promote the dispersal of seeds' fruits evolved independently in: angiosperms, some conifers (e.g. juniper, yew), some gnetophytes (Ephedra) and ginkgo.
Matter and energy
Ephedra is a typical photoautotroph, using the energy of sunlight to synthesize carbohydrates from carbon dioxide and then using the carbohydrates as an energy source in cellular respiration and also as building materials to synthesize a variety of biomolecules.
Interactions
Ephedra can be a dominant species over a fairly large area, e.g. parts of southern Utah and Nevada. It is eaten by both vertebrate and invertebrate herbivores. At least some species of Ephedra are pollinated by insects, another connection with angiosperms. However insect pollination may be an ancestral feature and therefore is probably not a good feature to associate angiosperms with gnetophytes. Female cones of Ephedra produce a 'pollination drop' at their tip which serves both to capture wind blown pollen and to attract insects that may happen to be dispersing pollen. Some interpret these observations to reveal the evolution of nectar from a fluid that encouraged the capture of wind-blown pollen. But other workers cite evidence that insect pollination is the ancestral condition in the group and that the pollination drops that capture wind-blown pollen are derived rather than ancestral.
Ephedra is a source of both ephedrine and pseudoephedrine (a steroisomer of ephedrine), alkaloids that have been used in diet pills, as a coffee-substitute and as a cold medicine. It has the effect of decreasing nasal and bronchial congestion. These alkaloids can also be converted into methamphetamines which is why a number of common cold medications are no longer sold over the counter.
Further Reading
• “Gnetophytes” on Plant Life | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.18%3A_Ephedra_-_Jointfir.txt |
Euglena is a genus of unicellular, freshwater organisms that are very common in ponds and small bodies of water, especially if they are rich in nutrients and consequently high in algae (aka 'pond scum' ). As noted below, Euglena itself is sometimes photosynthetic and is a component of the green sludge in such ponds. But at other times it is non-photosynthetic and is a component of the diverse group of organisms that are eating the green sludge or perhaps eating the other things that eat the green sludge.
Taxonomy and Phylogeny
Euglena are in a small group (less than 1000 species), that in the past was claimed by both zoologists (because they are mobile and some are heterotrophic) and by botanists (because some members photosynthesize). Accordingly, the group has sometimes called 'Euglenozoa' by zoologists ( 'zoa' refers to animals) and has been called 'Euglenophyta' by botanists ( 'phyta' refers to plants). In the past the group has been put in the Protist Kingdom. Recent phylogenetic studies have them diverging very early from other eukaryotes and consequently putting them in a very small group that contains very unfamiliar unicellular organisms. Some close relatives of Euglena include the causal organism for sleeping sickness and for Chagas disease. Complicating their taxonomy is the fact that some in the group are clearly composite organisms, being the product of secondary endosymbiosis when a green algal was consumed but not digested by a flagellate.
Structure
Euglena is a unicellular organism with a complex internal structure that includes a contractile vacuole that can expel water and a red 'eyespot' . Photosynthetic forms contain a chloroplast. They possess two flagellae, one long, one short, which can allow the organisms to move. Euglena are also able to move by means of changing its shape (see video links). Outside the cell membrane is a flexible, protein-based structure called a pellicle. Although not generally considered a cell wall, it has similar functions in providing some rigidity and strength that the membrane cannot provide. However the pellicle is much more flexible than most cell walls and allows for the change in form that is often seen in Euglena motion.
Reproduction
Euglena reproduces asexually when cells divide.No sexual reproduction has been found within the group.
Matter and energy
Sometimes Euglena are a typical photoautotroph s , using the energy of sunlight to synthesize carbohydrates from carbon dioxide and then using the carbohydrates as an energy source in cellular respiration and as building materials to synthesize a variety of biomolecules. Euglenoids store carbohydrates in a different glucose polymer than typical starch — the glucose units are combined in a 1, 3 linkage, rather than the 1, 4 linkage found in normal starch. Euglenoids may also behave like heterotrophs and acquire material by ingestion (phagocytosis) or by absorption of solutes from its aquatic environment. Some forms of Euglena lack chloroplasts and are solely heterotrophic.
Interactions
Euglena can be important components of certain aquatic environments and play a role as both a primary producer, eaten by other organisms, and also as a decomposer (heterotroph) that consumes other organisms and breaks them down, or consumes dead organic material and breaks it down.
Certain Euglena species (e.g. Euglena sanguinea) can turn a pond red and can also produce toxins that kill fish.
Watch
A YouTube element has been excluded from this version of the text. You can view it online here: pb.libretexts.org/sdt34b/?p=485
A YouTube element has been excluded from this version of the text. You can view it online here: pb.libretexts.org/sdt34b/?p=485 | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.19%3A_Euglena-_a_unicellular_algae.txt |
Gingko (Ginkgo biloba) is a commonly planted tree that many have probably seen but may not have distinguished from other trees. In spite of the fact that its form is very similar to most trees it has a number of distinct features. In particular, most trees are flowering plants (angiosperms) or conifers, ginkgo is neither!
Taxonomy and phylogeny
Gingko is unique in all of life's diversity because it is the only species that is the sole member of an entire phylum. While there are numerous examples of a single species as the sole member of a genus, and a few examples of a species as a sole member of a family, still fewer examples of a species being the sole member of an order, etc., etc., there is only one example of a species being the sole member of a phylum, in this case the Ginkgophyta. What this means is that ginkgo is distinctly different in a number of ways from all other plants, and in particular from all other seed plants. Generally seed plants are divided into five groups, one of which is the Ginkgophyta; the others are: flowering plants, conifers, cycads, and gnetophytes. Ginkgo is an ancient group—the figures above shows a modern leaf beside a fossil revealed in 60 million year old rock.
The genus is over four times this age with recognizable leaves in 250 million year old deposits.
Structure
Ginkgo looks like a typical tree and, from a distance, because of its broad leaves, would be considered to be more closely related to angiosperm trees like oak and maple than to conifers like pine and hemlock. However, the wood of ginkgo, like that of pines, hemlock and all conifers, contains no vessels or fibers, only tracheids and parenchyma cells. Gingko, like some conifers (e.g., larch), has 'short shoots' (very slow growing shoots) and 'long shoots' (faster growing shoots). The short shoots look like spurs on the stems and make identifying ginkgo easy in the winter.
Sex and reproduction
Ginkgo produces seeds that develop in the female 'cones' , which resemble olive fruits. The species is dioecious, i.e. it has separate male and female plants. Male plants produce pollen in cones. The pollen is dispersed to female cones by the wind. Like Ephedra in the Gnetophyta group, the female cones of ginkgo produce a drop of liquid that helps to capture pollen. This drop, containing pollen, is pulled into the cone by capillary action as the drop dries. Once in the cone, the opening to the outside is closed and the pollen germinates and produces a small, fungal-like structure, the male gametophyte, which acquires nutrition from tissues of the ovule. The male gametophyte matures and releases mobile, flagellated sperm into the liquid that is present in the 'canal' at the end of the ovule. These swim to the female gametophyte and fertilize the egg to form a zygote. Flagellated sperm are present in all ferns, mosses, and liverworts but are extremely rare in seed plants, being found only in Gingko, the cycads and some gnetophytes.
Matter and energy
Ginkgo is a typical photosynthetic autotroph.
Interactions
Ginkgo are extensively planted as a shade tree. It has an appealing form and grows well in a variety of habitats, including urban ones where pollution and asphalt produce an environment where many trees fare poorly. A significant , but not well explained , feature of the plant , is that it grows well when planted but does not establish itself on its own. Many workers feel that there are no 'naturally-occurring' ginkgos, i.e. that it is only found where it has been planted and its current existence is due solely to the fact that humans have been planting them for the last 10, 000 years, most of that time in China, but more recently world-wide.
The 'fruits' (female cones) of ginkgo produce a foul smell (butyric acid) when ripening. In the past the female trees were sometimes removed when they were old enough to produce fruit but modern horticulture has allowed plants to be cloned and most of the trees now planted are male.
The leaves of ginkgo are thought by some to be an herbal medicine that improves brain function. Conclusive evidence of this is lacking. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.20%3A_Ginkgo.txt |
The Glomeromycota are a very common, yet rarely seen, group of fungi. They are ubiquitous partners with angiosperms, forming associations called mycorrhizae, more specifically 'endomycorrhizae', also called vesicular/arbuscular (VA) mycorrhizae. Most plants (more than 80%) are mycorrhizal and most of these form endomycorrhizae with a fungal associate in the Glomeromycota.
Taxonomy and Phylogeny
The Glomeromycota have long been considered a part of the bread mold (Zygomycota) group because of structural similarities (see below) , but recent studies, in particular molecular studies, have indicated that they are distinct from the bread molds and are closer to club fungi and sac fungi than to the bread molds. They are not a very diverse group (less than 500 species in the whole phylum) and morphologically they do not exhibit a great deal of variation.
Structure
Like most fungi, the Glomeromycota generally exist as filamentous hyphae, and like the bread molds, the hyphae have no cross-walls, i.e. the members are coenocytic. Commonly the hyphae produce relatively large spores. Unlike the club fungi and cup fungi they do not produce fruiting bodies. When inside plant cells most Glomeromycota produce characteristic structures called arbuscules that function to transfer materials between the fungus and plant. Also produced are vesicles, which are enlarged spherical parts of the hyphae where materials are stored.
Reproduction
Glomeromycota are strictly asexual. They produce spores but they do not appear to have any sexual process.
Matter and energy
Most, but apparently not all, members of the group are mycorrhizal (endomycorrhizal) and obtain carbohydrates from their photosynthetic associate (usually an angiosperm but there is one documented case of an association with a filamentous blue-green algae). All apparently obtain nutrients (i.e. minerals) from the soil and there is evidence that although most species are mycorrhizal, a few species also obtain food (i.e. carbohydrates) from the soil.
Interactions
Glomeromycota interact with many (nearly all) plant species and it is increasingly apparent that they significantly affect the behavior of their hosts, generally allowing them to grow more vigorously. The group was probably significant in the colonization of land by autotrophs and thus the origin of plants.
Further Reading
• “MYCORRHIZAL ASSOCIATIONS: The Web Resource” by Mark Brundrett
2.22: Gonyaulax- adinoflagellate
Gonyaulax is representative of a n important group of unicellular organisms, the Pyrrophyta (sometimes called Dinophyta). The common name for the group is the dinoflagellates. Like the Euglenophyta, the group contains both photosynthetic and non-photosynthetic forms. Gonyaulax and several other dinoflagellates are notable for their association with two familiar phenomena: ocean bioluminescence and red tides, although most dinoflagellates are not. And both bioluminescence and 'red tides' (algal blooms) are not restricted to dinoflagellates. The group as a whole is extraordinarily diverse in terms of their biology, interactions with other species and evolutionary history.
Taxonomy and Phylogeny
Because of certain 'prokaryotic' features associated with their nucleus and DNA, the dinoflagellate group was once were once thought to be a 'transitional' group between prokaryotes and eukaryotes but workers now believe that these features are 'derived' (i.e. appeared after the group originated) and not 'ancestral' (present in the original dinoflagellates). That is, it is thought that the dinoflagellates diverged from other eukaryotes and then developed these 'prokaryotic' features. Modern treatments often lump the dinoflagellates with two other unicellular groups that are completely heterotrophic: the ciliates (including Paramecium) and the ampicomplexans (mostly parasites, including Plasmodium, the causal organism for malaria). There is evidence that the ancestor of all these groups was in fact photosynthetic, the result of a secondary endosymbiotic event between a red algae and a heterotrophic eukaryote, but that photosynthetic ability was lost in all of these groups, only to be regained in some dinoflagellates by a another endosymbiotic event that apparently has occurred multiple times, with (photosynthetic) diatoms, cryptomonads and green algae.
Structure
Dinoflagellates are unicellular and range tremendously in size, from 5 um to 1 mm. They also vary tremendously in form although many are spherical with 'horns' . Many have a complex boundary, called a 'theca' between it and the outside that consists of several large, cellulose plates enclosed in vesicles, just inside the outermost membrane. Most possess two flagellae, one long and one short and have a characteristic 'whirling' motion as a result of flagellar movement.
Reproduction
Most reproduction is asexual and the sexual process has not been found in most of the members of this group. When there is sex the diploid cell quickly undergoes meiosis; therefore finding the diploid cells is rare.
Matter and energy
Dinoflagellates occur both as photoautotrophs and as heterotrophs. The heterotrophs may be predatory (i.e. kill and consume other living things), parasitic (i.e. live in, and sometimes, but not always, kill its host) or saprophytes (feeding on dead organic matter). Dinoflagellates also serve as the photosynthetic component for a number of symbiotic associations, in particular in corals, and thereby allow these associations to be photoautotrophic.
Interactions
Dinoflagellates are found primarily in marine systems but some are in fresh-water. A number of species produces a toxin which can kill fish and invertebrates and may kill humans if they eat organisms, in particular shellfish, that have consumed the dinoflagellates. Dinoflagellates sometimes have population spikes causing what are known as 'red tides' , so named because of the of a red carotenoid pigment often present in the cells.
Gonyaulax has been used to study the biological clock — it is bioluminescent with a 24 hour periodicity. Bioluminescence in several species is triggered by agitation as is shown in the picture below where the motion of breaking waves triggers luminescence.
Further Reading
• “Tree of Life Dinoflagellates” by Mona Hoppenrath and Juan F. Saldarriaga | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.21%3A_Glomeromycota-_important_mycorrhizal_fungi.txt |
Halobacterium is one of several organisms that can color high salt environments red, like the hypersaline pools in Owens Lake, California. Halobacterium is significant not just for its tolerance of extreme salinity but also because it is a member of the Archaea and because it has some peculiar metabolic abilities.
Phylogeny
Halobacterium is an oxymoron, because it is not a bacterium, it is an archaeon, a member of the Archaea, a group of prokaryotes that in 1977 was distinguishedfrom the rest of prokaryotes (organisms lacking cellular organelles) by virtue of a suite of characteristics, in particular the sequence of bases in the 16s ribosome(actually the sequences of bases in DNA that codes for the RNA of the 16s ribosome). Thus most workers now describe two groups of prokaryotes, Archaea and Eubacteria. Although initially thought to be representative of the most ancient forms of life (hence the name Archaea) workers now believe that the Archaea were derived from Eubacteria. Based on metabolic pathways and genes, it appears that and that eukaryotes and Archaea are more closely related than eukaryotes and Eubacteria.
Structure
Cells are rod-shaped and roughly 2-5 um in length with a single lipid bilayer membrane surrounded by a glycoprotein cell wall. Archaea cell membranes are made of phospholipids that are distinct from those found in bacteria and eukaryotes. Halobacterium cells are flagellated and capable of moving towards a source of light, especially light in the in the yellow-green, around 560 nm, which is where its photosynthetic pigment (bacteriorhodopsin, see below) has peak absorbance.
Sex and reproduction
Like all prokaryotes, Halobacteria are not sexual but they are capable of exchanging genetic material by other means. They reproduce by cell division but, like all Archaeons do not produce endospores.
Matter and energy
Halobacteriaare photoheterotrophs. Like other heterotrophs they need to eat (i.e. assimilate) organic compounds to provide themselves with material to grow, but they also use light energy to generate ATP. In contrast, photosynthetic organisms are autotrophic: they make food (carbohydrates) and then 'eat' some of it to make ATP and use the rest as building material. Regular heterotrophs 'eat' both to acquire material for growth and to obtain energy, usually via cellular respiration.. If Halobacteria are deprived of light they need to eat more because they will behave like a 'normal' heterotroph, using the food they eat both to make themselves bigger and also to provide for their energetic needs.
The pigment that interacts with light is bacteriorhodopsin, a form of rhodopsin, the same pigment that our eyes use to see. In both instances light causes a conformational change in the protein. In our eyes this causes a nerve impulse to be transmitted; in Halobacterium it causes protons to accumulate on one side of a membrane, allowing ATP to be synthesized. Halobacterium also possesses a second protein pigment, halorhodopsin, that can use light energy to pump chloride ions into the cell, increasing the solute concentration and preventing excessive water loss.
Interactions
Halobacterium is a classic example of an 'extremophile' , an organism that exists under extreme conditions, such as high temperature, high salinity, high acidity. Halobacterium can live, and indeed requires, salt concentrations far exceeding the tolerance levels of most other organisms. They can even survive in saturated brine solutions. Because of this they can actually be 'fossilized' in salt deposits and stay alive for thousands, perhaps millions of years. Tolerance of extreme conditions probably means reduced competition in such habitats.
Although many archaeons are extremophiles, not all are; and there certainly are extremophiles that are not archaeons (one you should be aware of is the bacterium, Thermus aquaticus). Another non-archaeon that lives in high salt conditions is the unicellular green algae Dunaliella salina which can produce large quantities of the pigment beta-carotene and at one time was once thought to be the source of red coloration in hypersaline lakes. Most workers now believe that archaeons like Halobacterium are what make the lakes red, but that Dunaliella may be responsible in making flamingos pink, a result of their consumption of brine shrimp that have feasted on the beta-carotene loaded Dunaliella. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.23%3A_Halobacterium.txt |
A tale of two Hemlocks
Eastern hemlock (Tsuga canadensis) is a common tree in the northeastern U.S. It is the only conifer that is common in eastern deciduous forests. Other conifers do occur in the eastern forests, on sites where they have been planted, or in specific habitats (higher elevations in the mountains, areas with sandy or boggy soils), or early in a successional sequence where they are eliminated with time. Western Hemlock (Tsuga heterophylla) is found in the Pacific northwest and generally occurs in coastal temperate rainforests. Other hemlock (Tsuga) species occur in Japan/China/Korea.
Taxonomy and phylogeny
Hemlock is a gymnosperm, a seed producing plant that does not have flowers. Gymnosperms are not considered monophyletic and therefore it is not a phylogenetic entity. The four groups that used to be lumped as gymnosperms (conifers, ginkgo, cycads and gnetophytes) are no longer grouped together unless the largest seed bearing group, angiosperms, is included as well. Hemlocks are in the pine family (Pinaceae) of the conifer phylum (Coniferophyta); other members of the Pine family are pines, firs, spruces and larch and other members of the Coniferophyta are junipers, redwoods and cedars. There are about ten species in the genus Tsuga.
Structure
Hemlocks are typical woody plants, with a main trunk capable of extensive secondary growth and reaching substantial girths and heights. Eastern hemlock can often reach 30 m and western hemlock more than twice that height, making it one of the tallest tree species. These are long-lived organisms, with Eastern Hemlock reaching over 500 years in age and western Hemlocks over twice that age.
Sex and reproduction
Hemlock produces seeds in small (~2 cm), woody cones which earlier are the site of meiosis and female gametophyte development, including the production of eggs. Male gametophytes (pollen) are produced in separate cones that are much smaller. Pollen is dispersed by the wind and completes its development inside the female cone, producing sperm that fertilize the egg. The seeds are small (1-2 mm), winged, and dispersed by the wind.
Matter and energy
Hemlock is a typical photosynthetic autotroph. Western hemlock occurs in coastal evergreen rainforests in habitats with relatively mild winter temperatures and where being evergreen has a distinct advantage. Eastern hemlock is unusual in being an evergreen species in a forest that is dominated by deciduous trees. It may gain some advantage by being able to acquire carbon in the winter but often photosynthesis is limited by low temperatures and especially when it is below freezing and water transport is restricted. Both species are known for being extremely shade tolerant, meaning that they can stay alive (have a positive carbon budget) in spite of low levels of light, this would require low respiration rates.
Interactions
An introduced insect species, the hemlock wooly adelgid (HWA), is causing significant mortality of eastern hemlocks, especially in the southern part of its range. The HWA exclusively feeds on hemlock species. Closely related to aphids, adelgids are sedentary insects that feed on phloem sap, using a stylet to penetrate phloem sieve tubes. They then acquire carbohydrates when the pressurized phloem sap is pushed into the insect’s body, similar to the way that pressurized capillaries of mammalian circulatory systems allow mosquitoes to acquire a blood meal. In neither case is the insect ‘sucking’ fluids, it is merely tapping a pressurized ‘pipe’. In the far east, where the HWA is native, it is controlled by predatory insect species and there is hope that introduction of these predators may help control the pest in North America.
Although a common tree, the eastern hemlock is not commercially useful. Its wood has a a number of features that make it ill-suited as lumber or pulp (for making paper). In contrast, the western hemlock is a highly desirable lumber species with considerable strength and a straight grain. Western hemlock pulp makes high quality paper. In the 18th and 19th century the bark of eastern hemlock was a source of tannins. Tannins are group of chemicals that are important both to the plants that produce them and for humans utilizing the plants. For plants, tannins are bitter tasting and deter feeding because of this. However, if eaten, tannins can interact with digestive enzymes and thereby impede digestion. Herbivore avoidance of tannin containing plants may be a learned and/or evolved consequence of these effects and not simply a ‘dislike’ for the taste. To humans tannins actually provide a desirable bitterness to (at least some) humans and consequently are desirable at a certain level in tea, chocolate, wine and other consumables. Another use for tannins is the process of tanning leather, where the ability of tannins to interact with proteins, specifically the collagen found in animal skin allows tanning to make animal hide more supple and less prone to decay.
Some fungi apparently like the taste of hemlock, Gamoderma tsugae , the hemlock varnish fungus, is distinctive because of its shiny, glossy surface. As the name implies, it grows (i.e. eats) hemlocks, although it occasionally is found on other conifers. Gamoderma tsugae is closely related to Gamoderma lucidum, known as Lingzhi ( Ling Chih ) in China and Reishi in Japan which is highly valued medicinally.
Further Reading
• “Tannins” by the US Forest Service | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.24%3A_Hemlock.txt |
Horsetails, the genus Equisetum, are a very easily recognized group of plants that are commonly found throughout the world. They represent a very small remnant, only a single genus with less that 100 species, of a group that in the Paleozoic was a much more conspicuous component of the earth's flora. From 100 million years, ending 250 million years ago, this group was a dominant in terrestrial habitats world wide and the group is responsible for much of our coal and oil deposits. They are common in most of the United States, sometimes as a roadside weed or in wet habitats.
Taxonomy and Phylogeny
The genus traditionally had been put in a phylum all by itself but more recent treatments lump the horsetails in the fern phylum (Pterophyta), usually putting them in an order (Equisetales) distinct from other fern groups. When treated this way , the orders of the Pterophyta diverged in the late Paleozoic era. Whether you consider horsetails to be a phylum by themselves or an order within the Pterophyta, they still are very easy to recognize because of their distinct structure.
Structure
Horsetails have a very distinctive form–they have jointed stems with small and inconspicuous leaves that appear as scales at the base of each section of stem. The stems are hollow and ribbed. The successive sections of stem get shorter and shorter, reminiscent of a logarithmic scale and there is a claim (I haven 't been able to verify this) that the plant was an inspiration to John Napierto invent logarithms. Napier invented logarithms in the 16th century to make calculations easier (many biology students don' t believe that logarithms make calculations easier!!). The stems sometimes have whorled branches (in which case they look a bit like a horse 's tail) but sometimes don' t (in which case they really do not look at all like a horse's tail!). Horsetails have extensive underground horizontal stems (rhizomes) off of which emerge roots and vertical above ground stems. The commonly seen plant is a sporophyte that produces spores in a terminal cone or strobilis. Some species are dimorphic, with vegetative stems that are green and photosynthetic but produce no spore-producing strobili, and fertile stems that are brown (no chlorophyll, no photosynthesis) but do produce strobili and thus are only involved in reproduction. Fossil members of the group had secondary growth and grew up to 18 m in height, with stems a half a meter across. These plants were significant components in the deposits that yield coal and oil.
Reproduction
Like all plants, Equisetum exhibits alternation of generations with a visible sporophyte and hard-to-find gametophyte. The gametophyte is is bisexual (thus the plants are homosporous, producing only one type of spore), small, uncommon, and quickly overgrown by the sporophyte that grows from the archegonia. Sperm are flagellated and swim to the egg.
Matter and energy
Equiesetum (both thesporophyte and gametophyte) is a typical photoautotroph, using the energy of sunlight to synthesize carbohydrates from carbon dioxide and then using the carbohydrates as an energy source in cellular respiration and as building material to synthesize a variety of biomolecules. Note that for dimorphic species the spore bearing stems are photosynthetic only briefly and are 'fed' by the photosynthetic branches for most of their existence. Significantly, the energy captured by horsetails 300 million years ago is now being utilized when coal and oil are burned, releasing carbon that has been trapped in molecules that were transformed into fossil fuels. The plant has afairly unusual nutrient requirement, silicon, which most plants do not have (many plants may take up and contain silicon but it is not a required element, i.e. they can grow without it). Silicon is also required by the diatoms (phylum Bacillariophyta), a group of unicellular algae. The presence of silica dioxide deposits in the cell walls of horsetails makes the stems particularly tough and accounts for the common name 'scouring rush' because pioneers used the stem of the plant as a scrub brush.
Interactions
Equisetum plants are commonly encountered both in 'weedy' habitats (the plant can be a problem in agricultural situations) and less disturbed habitats. The group generally requires high light conditions and most species are shaded out when trees are present. Like the club mosses, they do not appear to suffer much from herbivory; this is perhaps because of the silica deposits in the cell walls. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.25%3A_Horsetails_the_genus_Equisetum.txt |
Juniperus
Junipers are a widely distributed group of plants that are used extensively in landscape gardening, especially in commercial and academic settings where their diversity in form and texture are appealing to landscapers. As a result they are seen by most people in the United States although many may not recognize what they are seeing except that they are evergreens. They may be a small tree or an upright or prostrate shrub.
Taxonomy and Phylogeny
Junipers (the genus Juniperus) are conifers (Phylum Coniferophyta) and generally put into the Cupressaceae (cedar) family whose members generally have very small leaves that overlap one another, making it hard discern the individual leaves. Other members of the group include: cedars, incense-cedars, cypress and redwoods. The family appeared in the Triassic, around 200 million years ago, but junipers are much more recent additions.
Structure
Juniper is a woody, slow growing plant that sometimes grows as a small tree and sometimes is shrub-like with multiple stems and extensive branching. There also are a number of forms that have been selected for their prostrate growth, less than 30 cm tall and spreading along the ground. Generally the leaves are small (2-3 mm) and 'imbricated' (overlapping like shingles on a roof). A few species have longer needles that extend extend outward from the stem. And there are a few species produce both types of leaves with the pointy needles occurring on younger growth. The leaves generally senesce as a group, with entire branches browning and abscising rather than individual leaves
Reproduction
Like all seed plants, Junipers produce female gametophytes inside ovules. The zygote is formed when the egg, produced by the female gametophyte, is fertilized by a sperm nucleus produced by the male gametophyte (pollen). Pollen is produced in minute (1-3 mm) male cones. The zygote develops into a new sporophyte embryo that is packaged inside a seed, a mature (fully developed) ovule. Junipers produce 'berries' that are a good example of convergent evolution. Technically, berries are fruits and fruits are only produced by flowering plants as a result of development of the ovary of the flower following fertilization. In many cases fruits have characteristics (rewards) that attract frugivores to come and eat the fruit and subsequently disperse the seed, present in the fruit, by defecating somewhere distant from the plant where the fruit was collected. Juniper 'berries' are actually cones, like those of pine and hemlock, but the cone scales are not woody but are thick, fleshy and aromatic and attract frugivores who disperse the seeds. Fleshy fruits are found in some other non-flowering seed plants (gymnosperms) including ginkgo and some species of Gnetophytes (Ephedra).
Matter and energy
Juniper is a typical photoautotroph, using the energy of sunlight to synthesize carbohydrates from carbon dioxide and then using the carbohydrates as an energy source in cellular respiration and also as building materials to synthesize a variety of biomolecules. The wood of juniper is infused with chemicals that deter the growth of decomposer organisms, hence the carbon captured by junipers may last for a long time before be released back to the atmosphere. Some juniper individuals live for thousands of years.
Interactions
In arid parts of western North America at the lower elevations of mountains there exists a shrub-land, the 'Pinyon-Juniper' zone , named for its two dominant species, pinyon pine and juniper. Because of their abundance in these areas junipers have significant interactions with herbivores and other organisms. Because pinyon juniper woodlands are poor habitat for cattle, areas of pinyon-juniper are sometimes destroyed to promote the growth of grasses and shrubs that cattle prefer to eat.
Juniper is an alternate host for a rust species that also affects apples and hawthorns. Juniper berries are used to flavor gin and also as a spice in cooking.
Due to its resistance to decay, juniper stems have often been used as fence posts. The wood is often used in the making of 'cedar chests' for clothing because the aromatic wood repels moths. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.26%3A_Juniper.txt |
Like Focus (rockweed), Laminaria is representative of an interesting group of organisms that are commonly seen in the intertidal zone and washed up on beaches. Most of the organisms called 'seaweeds' are brown algae, although some are red algae and a few are green algae. Like most (but not all) brown algae, Laminaria is a large, multicellular organism that well-adapted to life in intertidal and shallow coastal waters, most commonly in relatively cool waters.
Taxonomy and Phylogeny
The brown algae are a small group of eukaryotes who traditionally were placed in their own phylum, the Phaeophyta, sometimes along with two groups of primarily unicellular algae, the golden algae and the yellow-green algae, based on similarities in pigmentation and other factors. Most modern treatments do not elevate this group to the phylum level but combine it with other 'heterokonts' , a group defined by having two characteristic flagella, one longer than the other. The heterokonts (sometimes called the Stramenopiles) also includes diatoms and the heterotrophic water molds (Oomycota). The pigmentation of photosynthetic stramenopiles is similar to that of the haptophytes like Emiliania huxlii, and the cryptophytes. This may not represent a common phylogeny but instead that all three groups separately became photosynthetic by acquiring the same photosynthetic endosymbiont. The photosynthetic members of these groups are thought to be produced by secondary endosymbiosis and their chloroplasts have four membranes (see discussion in the article ondiatoms).
Structure
Typical of most brown algae Laminaria is truly multicellular, and has three distinct multicellular organs: a holdfast, that attaches the organism to a substrate, a broad flat blade that carries out the bulk of photosynthesis, and a stipe (stalk) that connects the blade to the holdfast and is long enough to allow the blade to obtain light. Many brown algae also have 'floats' , air filled structures that cause the blade to be elevated. Brown algae have transport systems that allow photosynthate from the blade to be distributed throughout the plant.
Reproduction
Most brown algae are sexual and exhibit alternation of generations. The 'dominant' (i.e. larger and more visible) stage is usually the sporophyte (diploid) stage but there are some brown algae that show isomorphic alternation of generations (the sporophyte and gametophyte look identical) and a few where the gametophyte stage is dominant. Another brown algae, rockweed (Fucus), shows a life cycle like humans, with no alternation of generations and where the only haploid cells are gametes. Gametes are sometimes distinct from one another (egg and sperm)and sometimes all look the same (isogametes). Flagellated cells are common and include sperm, isogametes and zoospores, mobile cells that can attach to a substrate and grow into a new organism.
Matter and energy
Laminaria is a typical photoautotroph, using the energy of sunlight to synthesize carbohydrates from carbon dioxide and then using the carbohydrates as an energy source in cellular respiration and as building materials to synthesize a variety of biomolecules. The brown algae produce a distinct form of a carbohydrate storage polysaccharide called laminaran, made up of glucose units connect by a beta 1-3 linkage, rather than the alpha 1-4 linkage found in starch. They also have high concentrations of mannitol which serves as a transport carbohydrate, a role occupied by sucrose in most plants.
Interactions
Laminaria is an important member of cool, shallow coastal waters. Along with other members of the brown algae they form 'kelp forests' , providing food for a number of organisms and habitats for others. Rockweed (Fucus) is especially important in the intertidal zone for similar reasons. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.27%3A_Kelp-_Laminaria_a_brown_algae.txt |
Lungwort lichen is unique among the groups considered here because it is a very different biological entity that the other groups that are considered. In spite of the fact that it has been given a genus and species name, lichens are communities, assemblages of organisms and often biologists consider organisms to be genetically uniform.. But the definition of 'organism' is not rigid (see Chapter 1) and certainly lichens can be considered organisms. The fact that they can be given scientific names attests to this. Like 'regular' organisms, they are distinct in time and space. The boundary between the lichen and its environment is very evident and one could follow its development, if you live a long time and are patient, from its initiation to its demise. Traditionally lichens were considered to have two components: a photobiont, either a unicellular green algae or a cyanobacterium (bluegreen algae) and a fungus. Recent work has ind icated that lichens also contain a unicellular fungus, a yeast. And some lichens, including lungwort have two photobionts, meaning that it is a community of at least four organisms.
Taxonomy and Phylogeny
Lichens are able to be classified because of characteristic form, color and structure. While each component of the lichen may have an evolutionary history (phylogeny), it would be difficult to track the phylogeny of the composite organism. Lichens are classified on the basis of their fungal component but the same fungus can produce marked different structures depending upon its algal symbiont and other features, making it difficult to match form to scientific (taxonomic) name.
Structure
Lichens are typically grouped as foliose '—having flattened leaf-like features (like lungwort), ' fruticose '— having extensions that are typical round and stem-like, not leaf like, and ' crustose'— forming a crust, typically over a rock. Especially in foliose and crustose lichens there is an upper and lower layer of dense fungal hyphae all glued tightly together, with a middle layer where the fungal hyphae are more loosely arranged and where the photosymbiont is found. The fungal component of most lichens is an ascomycete fungus and commonly one can find cup-shaped apothecia, a structure associated with the sexual reproduction of ascomycetes (aka cup-fungi) on the lichen. The algal component is unicellular and usually a cyanobacterium or a green algae. Lichens are often very colorful with the coloration generally being determined by the photobiont.
Sex and reproduction
Lichens reproduce asexually by fragmentation, and this is often promoted by the production of soredia, small pieces of lichen that are easily dislodged and dispersed. The fungal component of the lichen is capable of sexual reproduction, as evidenced by the production of ascocarps, but to recreate the lichen requires the acquisition of the photobiont.
Matter and energy
The lichen can be considered a photosynthetic autotroph, using sunlight to capture carbon dioxide and form carbohydrates that are then used (1) structurally to make more lichen (both the photobiont and the fungus) and used (2) energetically to power the metabolism of both the photobiont and the fungus. It is thought that the fungus manipulates the photobiont to make it more likely to 'leak' carbohydrates. The other 14 elements (besides carbon, hydrogen and oxygen) required to make more lichen come from rain water, perhaps modified as it descends down tree trunks and acquired by the fungal component.
Interactions
Lichens are extremely common components of the landscape, be it forest, desert or tundra. Although they are rarely eaten, they often provide materials for birds to build nests. They are significant to soil development both by providing organic material and also by breaking down rocks. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.28%3A_Lungwort_Lichen_%28Lobaria_pumonaria%29.txt |
Marchantia, a 'complex, thalloid' liverwort
Marchantia is one of the most commonly encountered liverworts. It has a wide distribution (arctic to tropics) and is relatively large and with a distinctive form. It is often encountered in seeps near steep rocky outcrops next to brooks and streams.
Taxonomy and phylogeny
Marchantia is in the Phylum Hepatophyta in the Plant Kingdom. In the past, the three groups of non-vascular plants (mosses, liverworts and hornworts) were grouped together into some taxonomic entity, often a phylum, but recent studies have supported placing the three groups into three separate phyl a , reflecting a view that the liverworts, mosses and hornworts are not obviously connected with each other, other than all being plants.
Structure
(Gametophyte)—Of all the plant groups, the liverworts show the most diversity in form. While some liverworts bear a resemblance to mosses, having a stem axis with appendages ( 'leaves' ), Marchantia is representative of a group of liverworts described as having 'complex thalloid' structure, consisting of a flattened body (a thallus) that generally spreads across the ground surface and is differentiated into a top and bottom. Marchantia is characterized by repeated branching into two parts. The thallus has multiple layers of cells. The top layer has permanently open pores (visible to the naked eye as minute dots) that allow for carbon dioxide entry. Below this skin (dermal) layer lies a layer of chlorophyll containing cells that are loosely arranged with lots of air space to allow for the diffusion of carbon dioxide. Below this is a (usually) thicker layer of cells that lack chlorophyll, and finally the lower skin (epidermis) which has multicellular fish-scale like structures that help attach the liverwort to the substrate, and also rhizoids, cells with thread like extensions that also attach the liverwort to a substrate. The sporophyte is hard to find, being small (less than 1 mm) and imbedded on the underside of archegoniophores (see below).
Sex and reproduction
Like mosses, liverworts show alternation of generations with a 'dominant' gametophyte (dominant = more visible, longer lasting). Under the appropriate conditions the gametophyte of Marchantia (and some other liverworts) grows two types of vertically oriented, umbrella/mushroom shaped structures: antheridiophores and archegoniophores, both roughly 1 cm in height. The antheridiophores produce male structures that produce sperm on the upper surface of the umbrella.
The archegoniophores, which are like umbrellas that lack the webbing between ribs produce female structures, archegonia, on the underside of the ribs.
On the underside of the female structures are produced flask-shaped archegonia, at the base of which is a single egg. When mature, an opening ( 'canal' ) develops from the egg to the tip of the archegonia, providing a route for the sperm to access the egg and allowing for fertilization. After fertilization a small (barely visible to the naked eye) sporophyte is produced, embedded in the tissue that produced the egg. Spores from the sporophyte are dispersed in the air and germinate to produce more gametophytes. Marchantia has separate male and female gametophytes (some liverworts have bisexual gametophytes).
Marchantia also reproduces asexually, producing small cup shaped 'splash cups' with clusters of cells (gemmae) at the base. These can be ejected by rain drops and are capable of producing new gametophytes if the end up in a favorable location.
Matter and energy
Liverwort gametophytes are photosynthetic autotrophs. Minerals are obtained from the absorption of solutes in rainwater. The sporophytes are totally dependent on the gametophyte for nourishment.
Interactions
Marchantia generally appears to require moisture and a lack of competition. It is found on rocks in places where water is seeping through the substrate, or perhaps gently falling from above. Although Marchantia can grow on moist soil it probably is eliminated by organisms (vascular plants) that can grow upwards and outcompete them for light. However, these competitors generally cannot grow without soil, which is probably why Marchantia is usually found on rocks. Although it can grow in full sunlight if moisture is available it often is found in shady conditions. Marchantia benefits, as do most non-vascular plants, from being small and being able to function in conditions where small stature is useful. Marchantia contains a variety of secondary plant compounds that may explain the fact that it apparently is rarely eaten. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.29%3A_Marchantia-_thalloidliverwort.txt |
Marsilea is a genus of ferns that don't look much like ferns. Its leaves look more like a four-leaf clovers than the typical fern leaf. There are a number of species of Marsilea and it is common throughout temperate and subtropical regions of the world , usually growing in shallow water with a stem rooted to the bottom and leaves that extend up and float on the surface. In North America M. quadrifoliata is considered a weed, although it is commonly grown intentionally in water gardens. It is sometimes found emerging from moist soil as well.
Phylogeny and taxonomy
Marsileais in a group (generally considered an order—the Salviniales) that is known as 'water ferns' in the Phylum Pterophyta (ferns), the group that includes most seedless vascular plants (the other group of seedless vascular plants are the clubmoss group, Lycopodiophyta). Some water ferns, including mosquito fern and azollaare floating aquatic species, while Marsileais rooted and can tolerate seasonally dry conditions.
Structure
Marsilea produces a horizontally running stem across the surface of the substrate (which may be underwater). Like sensitive fern and some of the horsetails, water fern is dimorphic and the horizontal stem produces two types of leaves, green, photosynthetic leaves and non-photosynthetic leaves associated with reproduction. The vegetative leaves look like shamrocks. These elongate and make it to the surface of the water or, if growing on moist soil, grow to a height of ~ 10 cm. A second type of leaf is much smaller, with a shorter petiole ending in a sporocarp, a brown circular seed-like structure that dries out completely.
Sex and reproduction
Like all plants, Marsilea alternates between a haploid and diploid stage and like all vascular plants it is the diploid, spore producing, stage that is most visible. The sporocarp is seed-like in looks and behavior, but developmentally is something very different. The sporocarp is a highly modified spore-bearing leaf that develops to a certain point and then becomes dormant and dries out and is therefore capable of being dispersed. Eventually, when the hard coating of the sporocarp becomes scarred, either by mechanical forces (abrasion) or by biotic forces (decomposition), water can enter and hydrate the spore bearing leaf, which then emerges from the sporocarp. The leaf looks nothing like a regular leaf, it is very small and non-photosynthetic, but bears two types of sporangia, producing two types of spores: larger spores (megaspores) that develop into female gametophytes inside the spore case (endosporically) and smaller spores that release flagellated sperm.
Matter and energy
Marsilea sporophytes are photosynthetic autotrophs. The gametophytes live solely off material from the sporophyte incorporated in the mega and microspores.
Interactions
Marsilea sporocarps (the seed-like structures) are eaten by aboriginal Australians. Although the plant produces an enzyme, thiaminase, that breaks down vitamin B1, the plant is edible if prepared properly and the enzyme is de-activated.
2.31: Molds - Ubiquitous Fungi
The common molds Aspergillus and Penicillium are of tremendous importance to human endeavors for both positive and negative reasons. Both are 'spoilers' that can destroy crops before harvest or, more commonly, during storage. They also can spoil all sorts of non-food items: leather, clothing, shoes, carpeting, paintings, etc. Members of both genera produce chemicals that are toxins to other species, including humans. Most well known of such chemicals is the antibiotic penicillin, which is a toxin to many bacteria but is not toxic to (most) humans.
Another chemical produced my molds is aflatoxin, which doesn't affect bacteria but which is a toxin and a carcinogen for mammals, including humans. Both genera are of commercial importance in several ways: enzymes from Aspergillus are used to produce citric acid, an additive in soft drinks and a variety of candies, it is also used to produce soy sauce, a fermented liquid used as a flavoring. Besides being used to make antibiotics, Penicillium is used to produce brie, camembert and blue cheese.
Phylogeny and taxonomy
Most of the species in the genus Aspergillus and some of the genus Penicillium are fungi for which there is no known sexual stage. Until relatively recently, fungal classification was based almost exclusively on characteristics of the sexual stages. Consequently, fungi lacking sexual stages could not be categorized and were put into a category of their own called the Deuteromycetes or the Fungi Imperfecti. With the use of molecular characteristics these fungi can now be put into phylogenetic categories, and both Aspergillus and Penicilliumhave been put in the same family in the Ascomycete phylum.
Structure
As Ascomycetes, both genera are septate fungi that have a typical filamentous structure of hyphae that form mycelia. The relatively few members that reproduce sexually (usually only rarely) produce small spherical closed fruiting bodies called cleistothecia. What are much more commonly seen are the asexual reproductive structures called conidia. Penicillium produces minute 'paint-brush' conidia, with each 'hair' on the brush producing small, spherical conidiospores, while Aspergillus produces spherical structures with linear extensions of conidiospores.
Sex and reproduction
All members of these two groups primarily reproduce by means of conidia, asexual spores. The ones that reproduce sexually exhibit sexual reproduction typical of Ascomycetes : dikaryon hyphae are produced after plasmogamy of two different strains; asci are produced in which karyogamy and meiosis occur, followed by mitosis to produce eight haploid ascospores.
Matter and energy
Both Aspergillus and Penicillium are generalist heterotroph s , i.e. can feed on a wide-variety of materials, including most crops species. It is a common pest spoiling of corn and other grains.
Interactions
Aspergillus and Penicillium are both fast growing and more tolerant of lower humidity levels than most fungi. This allows them to grow in drier situations than other fungi. Additionally, some species can tolerate growth on media that have a high solute content, e.g. the high sugar levels on jams and jellies (high sugar contents generally act as preservatives because many bacteria and fungi cannot tolerate the 'dry' conditions that result from high solute levels). Molds might be considered 'weedy' fungi, growing on a wide variety of materials, in contrast to many fungal species that are much more discriminating in terms of where they will grow and what they will eat. Aspergillus is occasionally a human pathogen, primarily in people with weakened immune responses. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.30%3A_Marsilea_-_The_4-leaf_Clover_Fern.txt |
Nostoc is a genus of cyanobacteria that is common in a variety of habitats : soil, ponds and growing on the surface of rocks that are kept moist. It also lives symbiotically inside of other organisms. Because of its ability to metabolize nitrogen (see below) it can be significant to ecosystems and to the organisms it associates with. As discussed in Chapter 5 it might be considered multicellular because it has multiple cell types that communicate and cooperate with each other.
Phylogeny
Nostoc is in the group with the common name 'blue-green algae' , a group often called cyanobacteria. In a five-kingdom classification they are in the Kingdom Monera, Phylum Cyanobacteria. In other classification systems they may be put in Domain Eubacteria, Kingdom Bacteria, Phylum Cyanobacteria. Cyanobacteria are thought to be the endosymbiont that became the chloroplast of eukaryotic photosynthetic organisms.
Structure
Nostoc are filamentous with roughly spherical cells. I n addition to the normal cells t hey also produce two larger specialized cell types: heterocysts, which are cells specialized to fix nitrogen; and akinetes, which are a type of spore that is resistant to environmental extremes. Nostoc typically produces a large amount of polysaccharide mucilage that form s a sheath around the filaments and occasionally form hollow balls and other amorphous shapes that are up to several cm in size.
Sex and reproduction
Like all bacteria, Nostoc are not sexual but they are capable of exchanging genetic material by other means.
Matter and energy
Nostoc and the cyanobacteria are an important group of organisms that 'can do it all' , being able to acquire both carbon (via photosynthesis) and nitrogen (via nitrogen fixation) from the atmosphere. Nitrogen is acquired by the reduction of dinitrogen gas into ammonia that is subsequently used in forming amino acids. Although they lack chloroplasts, their photosynthesis is basically the same as that found in eukaryotic organisms and it produces oxygen. More so than most organisms, they can 'live on their own' , acquiring carbon and nitrogen without requiring the intermediaries of other organisms.
Interactions
Nostoc forms associations with several plants, including hornworts (a group of non-vascular plants), liverworts, ferns , and some flowering plants. Nitrogen fixation by Nostoc can be an important source of nitrogen in soils that are young and have few plants growing on them and therefore little nitrogen availability via the normal route, i.e. as a result of the decomposition of organic material. Nostoc is occasionally eaten by humans, particularly in Asia, although there are some reports of it producing toxins.
Some cyanobacteria can form toxic algal blooms on lakes, causing health officials to close beaches.
On a global scale, cyanobacteria like Nostoc were the cause of the 'Great Oxygenation Event' starting about three billion years ago Oxygen produced by the photosynthetic process started to accumulate in the atmosphere, causing a biological catastrophe by eliminating much of the life present at the time whose metabolism was poisoned by oxygen. (see https://www.scientificamerican.com/article/origin-of-oxygen-in-atmosphere/ )
2.33: Oedogonium- a filamentousgreen algae
Oedogonium is representative of a number of organisms in a very diverse group, the green algae. In this book we consider several members of the green algae that illustrate a range in form and structure. The other members of the green algae group are Chlamydomonas (small and unicellular), Acetabularia (large and unicellular) and Caulerpa (large and coenocytic), which are quite different in form and structure.
Taxonomy and Phylogeny
The filamentous life form is not a good phylogenetic characteristic, i.e. it does not unify a group that is considered to be closely related. It is found in several of the subgroups (orders and families) of the green algae as well as in other protist phyla (brown and red algae), and even in some prokaryote groups. In an alternate and more phylogenetically based classification of the green algae group (presented in the write up for Chlamydomonas), Oedogonium is in the Chlorophyaceae, a diverse group of algae that are in the branch of green algae (Chlorophyta) that is not thought to contain the ancestor of land plants. Like most green algae, and like all plants, Oedogonium has both chlorophyll a and b, stores carbohydrates as starch and has cellulose cell walls.
Structure
Oedogonium forms elongate filaments of cells, m ost of which are non-flagellated, cylindrical and have a cell wall that contains both cellulose and chitin. These cells are vegetative, i.e. are not associated with reproduction but only associated with photosynthesis and growth of the filament. Several additional cell types are produced that bring about reproduction and sex:
• zoospores — mobile, flagellated cells do not have cellulose cell walls. Zoospores are released from parental cells and can attach to various substrates, becoming immobile and dividing to form new filaments. Zoospores have contractile vacuoles; why do you think this is the case?
• oogonia — large cells that develop a pore in the cell wall that allows flagellated sperm cells to enter the cell
• sperm — mobile, flagellated cells that are released from parental cells and swim to the oogonia
• zygospores — produced after sperm fertilize eggs, these cells developed a thick cell wall. They eventually undergo meiosis and break open to release flagellated zoospores.
Reproduction
Oedogonium reproduces asexually via mobile zoospores and sexual ly via sperm , oogonia and zygospores. Sperm are released from parental cells and are chemo-attracted to the oogonia that house an egg. A pore in the oogonium cell wall allows the sperm to enter the oogonium and fertilize the egg. Fertilization occurs and the oogonium develops a thick wall , forming a structure called a zygospore. Eventually the cell inside the zygospore undergo meiosis and haploid daughter cells are released as mobile zoospores, which, like the zoospores produced asexually, swim to a substrate and attach themselves and elongate into filaments.
Matter and energy
Oedogonium is a typical photoautotroph, using the energy of sunlight to synthesize carbohydrates from carbon dioxide and then using the carbohydrates as an energy source in cellular respiration and as building materials to synthesize a variety of biomolecules.
Interactions
Oedogonium is common in fresh water habitats. It is eaten by a variety of herbivores including fish, mollusks and other invertebrates.
Further reading
• “The Filamentous Algae” on Micrographia
• Oedogonium Image-based Key | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.32%3A_Nostoc_-_The_Smallest_Multicellular_Organism.txt |
Physarum: a plasmodial slime mold
Physarum is a member of a group that is unfamiliar (to most) but whose members are actually relatively common. They can commonly seen on mulch used in landscaping and occur as a large thin, amorphous 'blob' of yellow or cream colored material that usually hardens in a day or two. They also are commonly found on decaying wood in the forest.
Phylogeny and taxonomy
Since they are heterotrophic, mobile and (generally) unicellular they used to be considered 'protozoa' ; other early treatments put them with fungi because they produce spores and fruiting bodies. Like a number of other 'misfit' groups, the plasmodial slime molds can be placed in the Protist kingdom, a heterogenous assemblage of eukaryotic groups that do not readily fall with animals, plants or fungi. In certain stages plasmodial slime molds look like a giant, multinucleate amoebae and they are sometimes grouped with other similar looking things (including the amoebae often seen in introductory biology classes as well as cellular slime molds (see Dictyostelium) in a group that may be called the Amoebazoa. However, looks can be deceiving and apparently not all amoebae-like things belong (phylogenetically) together, i.e. amoeboid 'looks' evolved more than once and a group with all amoebae-like things (e.g. the Rhizopoda)is paraphyletic (i.e. groups together organisms with different origins). Consequently, the Amoebazoadoes not include all amoebae-like things.
Structure
Physarum is eukaryotic and is capable of ingesting material by phagocytosis. The cells are multinucleate (coenocytic), forming a thin film called a plasmodium that spreads across its substrate, often with visible branching channels occurring within the structure. They often can become several centimeters in size, flowing over a substrate (soil, leaves, branches or logs. They exhibit an easily seen (with a hand lens or dissecting scope) cytoplasmic streaming, the result of the interaction of motor proteins with microfilaments (actin filaments). Their normal food is bacteria or other minute organisms. They also can live off of dead organic matter (e.g. oatmeal, which is often used to feed it in the laboratory). Under adverse conditions the cytosol thickens and dries out forming a structure called a sclerotia that can survive in an inactive state for a prolonged period.
Reproduction
The large cell often reproduces by fragmentation, which can also happen with the dried sclerotia. The plasmodium can also dramatically transform from a blob of cytoplasm to a rigid structure consisting of numerous sporangia, often stalked structures with a round capsule (sporangium) at their top, in which are formed haploid spores created as the result of a meiotic cell division that occurs in the developing sporangium. The spores are dispersed and, when they germinate, form uninucleate amoeboid (haploid) cells that grow and divide and can develop, also loose, a flagellum. At some point some of these cells are capable of fusing with each other and having their nuclei also fuse. This diploid cell is capable of growing and forming a large, multinucleate cell, the plasmodium.
Matter and Energy
Physarum is both predatory heterotroph, capturing (by phagocytosis) other living organisms (primarily bacteria) and also a saprophyte, feeding on dead organic material. In either case they break down their food's biomolecules into simple sugars, amino acids, etc. and reform them into their own biomolecules. That is, they are typical heterotrophs.
Interactions
Plasmodial slime molds interact in a trophic manner with their prey and with organisms that eat them (either the plasmodium or the spores). They need moist conditions to grow and changes in their growth pattern (spore germination, formation of sporangia and sclerotia) are triggered by environmental conditions.
Further Reading
Plasmodial slime molds have been shown to be capable of a type of 'reasoning' (depending upon how one defines it. In addition to the links listed below Youtube has several excellent videos of slime molds. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.34%3A_Physarum_-_A_Plasmodial_Slime_Mold.txt |
Phytophthorais an example of the water mold group—the Oomycetes (Oomycota). They are highly significant to humans as pathogens of plants, in particular late blight disease of potatoes, but also the pathogens that cause sudden oak death syndrome, downy mildew and 'damping off' disease. There are a few oomycetes that are pathogens of animals, in particular the fuzzy mold that is sometimes seen on fish (just before they die).
Phylogeny
Because of its structure , water molds were once considered to be fungi. However, a variety of features do not match with fungi and recent work either puts them as a distinct phylum in the Kingdom Protista, or in a separate Kingdom altogether (the Chromista or the Stramenopiles or heterokonts). They have affiliations with a number of photosynthetic groups (diatoms, brown algae, golden algae) and there is some debate as to whether the group started out without chloroplasts or whether the ancestor of the water molds lost chloroplasts.
Structure
Like the bread molds , most water molds have a filamentous structure where cells are not delineated with cross walls (i.e. they are siphonaceous). Although water molds exhibit a filamentous structure like fungi, the cell walls are composed of cellulose, not chitin as is found in fungi. The filaments explore the habitat (which is sometimes water and sometimes the inner part of other organisms) and obtain nutrients; in the case of Phytophthora , the habitat is the inside of potato leaves or potato tubers
Reproduction
Phytophthora can spread very rapid in moist weather using mobile zoospores, flagellated cells that can swim through the water. Although they are not long distance swimmers, movement of water by splashing , or by the wind and animals walking through vegetation , can aid in their dispersal. Phytophthora also reproduces sexually, producing large, immobile eggs and smaller, mobile sperm. Unlike the fungi, the typical (i.e. most commonly encountered) cell of a water mold is diploid.
Matter and Energy
Phytophthora is a typical heterotroph, needing to find organic material as a source of matter and energy. For part of its life, Phytophthora is what is known as a 'biotroph' which means that it associates with living cells and is able to acquire matter (sugars, amino acids) from them using a structure called an haustorium, a structure that penetrates the cell wall, associates with the host cell membrane and is able to induce materials to move from the cytosol of the host plant to the cytosol of the parasite. With time, this drain on plant nutrients can kill the host plant cells and the fungus necessarily shifts from being a biotroph, to a necrotroph, an organism that kills its food and then eats it, similar to killer whales, lions and spiders. Significant to researchers is the fact that biotrophs are impossible to culture without living plant cells, i.e. you cannot simply have a medium with 'good stuff' , like sugars and amino acids, and culture Phytophthora on it.
Interactions
There are a substantial number of Phytophthora species, mostly known because they affect a number of crop species (potato, leek, cucumbers, squash, soybean, cocoa) or ornamental species (rhododendron, azalea). These species are found in the wild, not just in agriculture, and affect wild relatives of these crops. Moreover, epidemics caused by Phytophthora do occur in the wild (sudden oak death syndrome in California) , not just in planted monocultures.
One species of Phytophthora, P. infestans has had a particularly significant influence on human history, being the cause of the potato famine in Ireland in the 1850's that killed over a million people and caused roughly twice that number to emigrate to the United States, significantly affecting the history of the U.S. (see last link below).
Further Reading | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.35%3A_Phytophthora.txt |
Pine trees should be familiar to just about everyone although some might confuse them with other evergreen trees. Most pines are distinct from other evergreens by the fact that their needles are longer, often 10 cm long or more, and they almost always occur in clusters (bundles), typically in groups of two, three or five with the number of needles per group being a useful identification aid.
Phylogeny
Pines belong to a distinct phylogenetic entity, the conifers, a group that is usually placed at the phylum level (Pinophyta). They have vascular tissue and produce seeds but do not produce flowers. Sometimes conifers and other seed plants without flowers (e.g. cycads and ginkgo) are grouped as gymnosperms but most workers do NOT consider this to be a sound phylogenetic entity , i.e. they are not a group unified by their evolutionary history. Conifers are by far the most commonly encountered gymnosperm and pines (the genus Pinus) are probably the most frequently encountered conifer. They are the largest genus within the phylum, containing over 100 of the approximately 600 species in the group.
Structure
Almost all pines are typical woody trees (a few might be considered large shrubs) with a branched, dendritic form that through time and with secondary growth produces the typical form that we recognize as trees. While some pines and most other conifers (spruces, firs and douglas fir) produce a 'Christmas tree' form, with triangular crowns that are usually quite steep, pines often have a broader base and less steep sides.
Sex and reproduction
Pines reproduce by seed, a multigenerational unit, which in the case of conifers contains both an embryo and the female gametophyte that produced the egg that was fertilized to form the zygote that grew into the embryo. Both these entities are packaged in a seed coat constructed of cells derived from the tree that produced the cone. Significant to the story is that pines, like ferns and mosses and also like wheat and aspen, do produce spores, i.e. seeds do NOT replace spores. Most species of pines have seeds that are winged and dispersed by the wind, but a few species have adapted to dispersal by birds (see below).
Matter and energy
Pines are typical photosynthetic autotrophs, acquiring carbon dioxide from the air and converting it into carbohydrates to be converted back to carbon dioxide in cellular respiration (yielding ATP) or to be used to synthesize biomolecules. The shape of of conifer leaves (cylindrical), coupled with a thick cuticle reduces water loss but also slows carbon dioxide acquisition when compared to a broad-leafed plant with a much greater surface area to volume ratio and thinner cuticles. In spite of the fact that individual leaves of pines and most other conifers have a much smaller surface area than broad-leaved plants, the total leaf area per branch may exceed that of broad-leaved plants because there often are lots of needles. Two other features are significant to the matter and energy relations of pines (and other evergreen conifers): (1) their evergreen life-style allows for year-round photosynthesis if conditions are appropriate, (2) leaves with longer lifespans are potentially beneficial to nutrient status because absorbed nutrients have a longer residence time in the plant.
Interactions
With climate:
Pines are primarily distributed in the northern hemisphere, and primarily occur at latitudes north of the tropics. They are particularly abundant in mountain habitats, as are other conifers. Many are tolerant of extreme cold and can live at upper elevations (e.g. lodgepole pine in the western US, Swiss pine in the Alps). As a group they are also tolerant of dry conditions, in particular, seasonally dry conditions, and pines are often associated with sandy soils, which hold less water than other soils.
With disturbance:
Many pines are 'fire-adapted' and are associated with habitats that burn frequently, e.g. long-leaf pine, found in the southeastern US; ponderosa pine, found in the western US.; pitch pine, found in the eastern US (e.g. in the Albany pine bush and the Pine Barrens of New Jersey). All these pines have features that actually promote fire, in particular their needles are flammable and they also have behaviors and anatomy that allow them to tolerate fire. These species are likely to be eliminated from sites if fires are suppressed.
With seed predators (i.e. things that eat seeds):
A number of pines have interesting relationships with birds, such as the Clark's Nutcracker, that feed on their seeds. The seeds of these pines are particularly large and are NOT winged. The birds have morphological features that allow them to easily extract the seeds from the cones and they also exhibit a 'caching' behavior: much like some squirrels they bury their food for consumption later in the year. The birds make caches that are some distance from where they forage. This, coupled with the fact that they generally bury more seeds than they end up eating, means that the birds both disperse the seeds and also plant them.
With humans:
Pines are an important timber species and chemicals from their 'sap' are useful in a variety of ways: as waterproofing, as organic solvents (turpentine), to improve grip for baseball hitters (pine tar on the bat), for baseball pitchers (resin bags), and for violin bows (rosin–to improve their 'grip' on the strings), pine tar is sometimes used medicinally. The seeds of a number of pines are eaten (pignoli).
Further Reading
• “Longleaf Pine Ecosystem” by Albert Way
• “Restoring a Disappearing Ecosystem: the Longleaf Pine Savanna” by Noreen Parks in Science Findings
• “Clark's nutcracker” by John Fraley
• fwp.mt.gov/mtoutdoors/HTML/articles/portraits/nutcracker.htm
• Photos and videos of Clark's Nutcracker in Macaulay Library | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.36%3A_Pinus_-_Pine_Trees.txt |
Polytrichium is a common moss that occurs across all of North America. It is large for a moss and regularly exhibits both the haploid and the diploid phases of its life cycle. Thus it is a useful example of what mosses are about. It is generally found in forests but can also be found on soil or gravel in open areas.
Phylogeny and taxonomy
In the past, the three groups of non-vascular plants (mosses, liverworts and hornworts) were put together in a taxonomic unit (Phylum Bryophyta = 'Bryophytes' = non-vascular plants), but there is little evidence that this is a unified group other than they are all plants. Mosses are distinct from the other two non-vascular groups and vascular plants are probably more closely related to liverworts than to mosses. Mosses are now generally put into their own phylum (division), the Bryophyta, distinct from the phylum of liverworts (Hepatophyta) and hornworts (Anthocerophyta). Within the Bryophyta there are around 12, 000 species.
Structure
The gametophyte (haploid form) of mosses is the form that is usually seen. It is green, (photosynthetic) and lives for several years. Polytrichium has an erect unbranched stem with small pointed 'leaves' emerging off the sides. Technically it lacks 'true' vascular tissue because it lacks lignin. But it does produce cells, comparable to vascular cells, that are specialized for transport. Even without lignin for support Polytrichium can produce a stalk standing 4-10 cm tall. The plants have thread-like rhizoids emerging from the base of plant and attaching it to the substrate.
The gametophyte gets its name because it produces gametes. Polytrichium, but not all mosses, is dioecious, meaning that it has separate male and female plants. The gamete-producing organs appear at the tips of the stems, in structures (antheridia) that produce many mobile (flagellated) sperm on the male plants and structures (archegonia) on the female plants in which is produced a single, immobile egg.
The diploid form of the plant is called a sporophyte and it grows out of the structure that produces the egg (the archegonium). It has a typical spore-producing structure (cf. that of the cellular slime mold, Dictyostelium, or mushrooms) with a stalk (often over 5 cm) elevating a spore producing capsule at its top. The elevation provided by the stalk (seta) allows the spores to be more readily dispersed by the wind. Most moss capsules have one or two rings of teeth surrounding the opening of the capsule that can open and close, releasing spores under favorable (dry) conditions when they will be transported further by the wind.
Reproduction
Mosses exhibit the typical plant sexual life cycle that involves an 'alternation of generations', alternating between a haploid gametophyte and a diploid sporophyte and the sexual cycle requires both. Unlike familiar animals who reproduce by directly making replicas of themselves, plants, including mosses like Polytrichium, alternate between two forms: the sporophyte makes gametophytes and the gametophytes make sporophytes. Note that, if one rigidly holds to a definition of organisms being entities distinct in space, then the sporophytes produced by gametophytes are not 'new individuals', just appendages off of old ones! The gametophyte of most mosses can reproduce asexually both growing in a clonal manner. Some mosses also can reproduce asexually by producing groups of cells (gemmae) that break off and can be dispersed, but these are not found in Polytrichium. In Polytrichum, only one sporophyte is produced for each female gametophyte. In some other mosses a single gametophyte may produce a several sporophytes but for all mosses it is the sporophyte generation does the bulk of the reproduction, producing many, many spores. Of even more significance, the production of spores is what allows the moss to spread to new areas, i.e. performs a dispersal function.
Matter and Energy
Hairy cap moss is a photosynthetic autotroph, it makes food (carbohydrate) through the process of photosynthesis and then uses this carbohydrate both as a material to make biomolecules and also to provide energy for metabolic activities. For the gametophyte this is true throughout its existence. The sporophyte is usually only photosynthetic during its period of growth, if at all, and often loses its chlorophyll, and thus its ability to feed itself, as it matures, becoming dependent upon the gametophyte that it is growing out of for its food.
Mineral nutrition of mosses is different from that of vascular plants, whose roots obtain nutrients from the soil solution. The rhizoids of mosses are limited in extent and lack the ability of transporting nutrients to the above ground portion because they lack vascular tissue. Most of the nutrients obtained by mosses probably comes through the leaves of the gametophytes that provide substantial surface area and, unlike the leaves of vascular plants, are generally not coated with a waterproof cuticle that retards absorption of water or dissolved solutes. The nutrients in the solution surrounding the leaves are provided by dust particles blown in the wind, solutes dissolved in precipitation and solutes added to precipitation as it flows down the trees and shrubs in the forest canopy (if there is one), as well as solutes that may be carried up with capillary water from the substrate that the moss is growing on. Sporophytes of mosses lack leaves and are not in contact with the soil and thus probably obtain all their nutrients from the gametophyte that they grow out of.
Interactions
Mosses are very common in a variety of habitats and are particular significant in some of them (e.g. Sphagnum moss in bogs). They are rarely eaten extensively and generally (with the significant exception of Sphagnum) produce very little biomass compared to vascular plants, thus their contribution to the trophic structure of most ecosystems is slight. However, they do provide habitat for a number of small invertebrates (see the article on tardigrades linked below), they can sequester nutrients, including carbon, and are often very important in soil formation on sites that previously have lacked a soil, i.e. in primary succession.
Further Reading
• General information at Wikipedia:
• Bryophyte Ecology by Janice Glime: A tremendous source of information on moss ecology:
• “Tardigrades” by William Randolph Miller: An interesting article on tardigrades, fascinating tiny animals that often live in the environment surrounding moss leaves: | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.37%3A_Polytrichium_-_Hairy_Cap_Moss.txt |
Aspens, cottonwoods, poplars: the genus Populus
Trembling Aspen (Populus tremuloides) is the most widely distributed tree in North America, occurring from the east coast to the west coast and from Alaska to Mexico. Thegenus Populus, which includes several other aspen species and also cottonwoods, has aworldwide distribution in the northern hemisphere. While cottonwoods, like P. deltoides and P. fremontii are typically found along streams and rivers, aspens like P. tremuloidesand P. grandidentataare found in a variety of upland habitats, often forming monotypic standsbecause they grow clonally(see below).
Phylogeny
Populus is a genus of flowering plants in the willow family with around 25 species, many of which are familiar and are commonly seen. The willow family is a taxonomic grouping that used to be small (three genera), but recent studies using molecular information have enlarged the family greatly (56 genera) by merging it with several otherfamilies.Although the group was once thought to be primitive based on floral characteristics, including the fact that most are wind-pollinated, most plant taxonomists now consider the family to be of relatively recent origin.
Structure
Most members of this genus are fast-growing and relatively short-lived trees. They exhibit typical tree-like above-ground form but are relatively unusual because of their below-ground behavior, producing underground stems (rhizomes) that spread horizontally below ground and sporadically produce vertical shoots that form new trees. As a consequence , several members of the genus (especially aspens) are typically found as clones, stands of genetically identical individuals all connected (or previously connected) by below-ground structures. Some other trees that behave similarly are black locust and beech. This kind of growth pattern with spreading below ground stems is also found in shrubs (e.g., creosote bush of the Mojave desert) and herbaceous (non-woody) plants (e.g., Kentucky bluegrass, a common lawn grass).
Although individual aspen trees (above ground stems) are relatively short lived (typically less than 200 years) aspens clones represent some of the longest-lived organisms. One of the best-studied clones lives in Utah and has been named 'Pando' . It is estimated to weigh over six million kilograms, extend over 43 hectares, and may have an age of 80, 000 years (see http://discovermagazine.com/1993/oct/thetremblinggian285#.UhC20RZ96FI ).
Reproduction
As described above, aspens 'reproduce' asexually by spreading below ground, although one could argue that this isn't reproduction at all, it is simply organismal growth. Aspen is also capable of the sexual reproduction typical of angiosperms, producing mobile male gametophytes (pollen) which are dispersed to the location of the female gametophytes (the ovules of flowers). The gametes that are subsequently produced unite to form a zygote that grows and is packaged into a seed. One relatively unusual feature for Populus, compared to most flowering plants, is that individual trees and (therefore) clones are unisexual; the flowers are unisexual and any one tree/clone produces only one kind of flower, either male or female.Both the male and female flowers occur in catkins, drooping clusters of flowers that lack obvious petals. Cottonwoods (P. deltoides) in particular but all members of the genus are known for producing copious quantities of seeds, each packaged in a cottony tuft of hairs.
Matter and Energy
Aspens are typical photosynthetic autotrophs. Individual plants accumulate carbon dioxide from the atmosphere and use it to form carbohydrates that are both used to enlarge the plant (i.e., grow) and also to be 'burned' in cellular respiration to provide energy for the plant. Aspens are typical seed plants, requiring 17 elements: carbon, hydrogen and oxygen(obtained as carbon dioxide and water), plus an additional 14 'minerals' that are obtained from the soil solution by the root system.
Interactions
Because it is a common, wide-ranging genus there is a multitude of interactions that aspens exhibit. Among them are the following:
Fire ecology
In parts of its range aspen depends upon fire to eliminate competitors. Conifers (e.g., spruce and fir) do not grow as fast as aspens but can grow taller and can eventually outcompete aspens by shading them out, killing trees and root sprouts. Fire can kill conifer competitors while only eliminating the above-ground part of aspens. Thus, fire allows aspens, sprouting from underground stems, to quickly re-colonize the area. In western North America, avalanches may serve as a different form of disturbance that eliminates aspen competitors and facilitates continued aspen presence.
Beaver interactions
Beaver are herbivores that feed primarily on tree bark and shoots. They are particularly fond of aspen and some of its relatives. As a consequence , beaver can have a very substantial influence on forest composition, drastically decreasing the occurrence of aspen and increasing the frequency of species less desirable to beaver. Because beaver can significantly affect communities by building dams and flooding areas, the preference for aspen can influence what areas get flooded as a result of beaver activity.
Further Reading
'Pando' and large organisms
Ecology of aspen — Bryce Canyon National Park
• www.nps.gov/brca/naturescience/quakingaspen.htm
Ecology of aspen: fires, predators and pathogens
Ecology of aspen: beaver
• www.ecology.info/beaver-trees.htm | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.38%3A_Populus.txt |
Potatoes (Solanum tuberosum) are an herbaceous plant, native to South America, that has been cultivated by indigenous peoples for five to ten thousand years but only became cultivated world-wide in the last 500 years. Growingat high elevations of Peru and Bolivia, it was a staple crop of the Incas, who developed a freeze-dry preservation technique, producing 'chuno' . This was possible in thesehigh elevation sites (10, 000 feet or more) where the combination of clear nights and bright sunny days allowed for the freezing and drying. The spread of potato in Europe was slowed because people recognized that it was related to plants that were known to be poisonous, e.g. several species of nightshade. The potato family is interesting in that it has produced a number of important crops (potato, tomato, pepper, eggplant) and also important poisons and drugs (nicotine, novocaine, atropine).
Phylogeny
Potato (Solanum tuberosum) isa flowering plant (angiosperm) and would typically be classified as: Plant Kingdom, flowering plant phylum (Magnoliophyta = Anthophyta), dicot class (now usually considered the Eudicot class), potato order (Solanales), potato family(Solanaceae). Other members of this family include: tomato, pepper, tobacco, nightshade, jimsonweedand petunia.
Structure
Potato is an herbaceous plantwith a typical plant structure of below-ground roots and above-ground shoots with leaves. Like tulips and a number of other plants, the above-ground stem and leaves are 'annual' , i.e. they die every year. The plant is perennial because a below-ground portion survives and perpetuates the organism. The perennatingpart is a structure called a tuber, a branch shoot that is produced and remains below ground. These stems do not produce leaves or branches but their tips swell and produce tubers. These are the result of producing much more parenchyma tissue than is found in a normal stem. Tubers (or functionally similar, but anatomically different, structures called corms and rhizomes) are a common feature that allows plants to survive in areas where the above groundclimate is hostile (cold or dry) for part of the year. The above ground portion of the plant dies, but the below-ground part, present in the more favorable (i.e. warmer/moister) environment of the soil, is able to survive and can sprout new 'normal' (i.e. upward growing) branches when it 'knows' that favorable above-ground conditions have returned. Parenchyma cells of the tuber possess numerous starch storing plastids (amyloplasts) that provide material and energy to power growth when it resumes. The 'stem nature' of a potato tuber is revealed in its 'eyes' , which are lateral buds, i.e. embryonic branches. They, like the leaves and branches of the above ground stems, are distributed in a spiral fashion around the shoot. Farmers vegetatively propagate potatoes by cutting the tubers into sections with at least one eye and planting them.
Sex and reproduction
Potatoes reproduce sexually by flowers but are generally propagated vegetatively from the tubers. Although it is grown as an annual crop, it is perennial in the wild.
Tubers are planted in the spring and the tubers are harvested in the fall after the annual shoots have died.
Matter and energy
Like most plants, p otatoes are photosynthetic autotroph s, acquiring carbon from the atmosphere, water from the soil and another 14 essential elements from ions and solutes dissolved in soil water.
Interactions
Potato's interactions with humans have been extremely significant, both by being the primary food source for several regions and also for the disruption caused when crops failed, disruptions whose consequences are felt for many years in multiple regions (read about the Irish potato famineand its effects on the United States). The causal organism for the famine is late blight of potato (Phytophthora infestans), and the interaction between late blight and potato reveals some interesting features significant to disease interactions specifically and biotic interactions in general:
The interaction involves three 'players' (the disease triangle, see chapter 30):
• the host—Phytopthora infestansinfects potato (Solanum tuberosum) and also tomato (Solanum lycopersicon). Within both host species there are varieties that are more and less susceptible but as yet, no variety that is completely resistant.
• the parasiteInterestingly, it appears that Phytopthora infestansoriginated outside the native range of either of its hosts, where it survived by feeding on other species of Solanum. Host and parasite were brought together when potato cultivation spread from its origin in South America and the parasite 'jumped' hosts.
• the environmentoutbreaks of the disease are associated with cool and moist conditions, conditions that favor the growth, reproduction and spread of the parasite.
Other interesting interactions involving potato are:
The Colorado potato beetle shows some similarities to late blight of potato: it feeds on (i.e. 'has a taste for' ) a group of related plants: potato, tomato, pepper, indicating that diet preferences are probably related to the secondary chemistry of the hosts. Like late blight, the beetle originated in an area where potato/tomato was not present but, given the opportunity, developed a taste for these new arrivals.
Tuber formation in potato, something essential for its utility as a crop, involves a complex combination of interactions with the conditions the plant encounters. Tuber formation is is promoted by short day photoperiods, cool night temperatures, and relatively low soil nitrogen levels.
There are many many varieties of potato and only a small portion of these are available commercially in the U.S. Among other differences (such as color and shape) potatoes also vary in the type of starch present and this can impact their utility in cooking: some potatoes (considered 'starchy' ) have almost all of their starch as unbranched polymers of glucose—this produces a potato better suited for mashing or baking. Other potatoes (considered 'waxy' ) have a greater portion of their starch existing as branched polymers of glucose, which allows the potato to retain its shape and firmness even after cooking and is better suited for use in potato saladsand othersituations where it is desirable for the potato to maintain its shape (e.g. in a soup or stew). | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.39%3A_Potatoes-_Solanum_tuberosum.txt |
Porphyra is representative of a diverse and important group, the red algae (Rhodophyta), one of three algal groups that have members that include multicellular, macroscopic forms (the other two are the brown algae (Phaeophyta) and the green algae (Chlorophyta) ). Like the green algae, but not to the same extent, the red algae phylum also has members that are unicellular or filamentous.
Taxonomy and Phylogeny
The red algae are eukaryotes and usually placed in their own phylum, the Rhodophyta. Their affinities with cyanobacteria are reflected in their chemistry (in particular their photosynthetic pigments), but they are clearly eukaryotic with nuclei, chloroplasts and mitochondria. Like the green algae, the chloroplasts o f red algae have two membranes, one thought to be the remnant of the membrane of the cyanobacterium that was engulfed during the endosymbiotic event and a second membrane that was produced during phagocytosis when the cell was engulfed, the phagosomal membrane. The chloroplasts of other photosynthetic groups of algae (e.g. diatoms, brown algae) are considered to have been the result of secondary endosymbiosis, a second engulfing (phagocytosis) event where an already eukaryotic cell consumed, but did not digest, another eukaryotic cell that was a red or green algae. These chloroplasts have four membranes, two from the chloroplast of the red/green algae, one from the plasma membrane of the (prim i tive) red or green algae cell that was engulfed and a fourth membrane, again a remnant of a phagosomal membrane, derived from the engulfing cell.
Structure
Although large, often up to 20 cm in extent, Porphyrais not truly multicellular, i.e. parenchymatous(three-dimensional). It has a very simple two-dimensionalform, existing as sheets which are either one or two cells thick. The algadoes producefilamentous 'rhizoids' that attach one end of the sheet to a substrate.
Reproduction
Sexual reproduction in all the red algae is complex and involves alternation of generations , but instead of alternating between a haploid form and diploid form there are three fo rms: (1) a haploid (gamete producing) form that develops from haploid spores; (2) a diploid form that develops from a zygote, stays attached to its parental gametophyte and produces diploid spores that are dispersed; and (3) a diploid form that develops from these diploid spores and in turn produces haploid spores following meiosis.
Matter and energy
Porphyra is a typical photoautotroph, using the energy of sunlight to synthesize carbohydrates from carbon dioxide and then using the carbohydrates as an energy source in cellular respiration and as building materials to synthesize a variety of biomolecules. The red algae produce a distinct form of starch, floridian starch, that is not found in other eukaryotes.
Interactions
Porphyrais generally found in cool, marine waters. It is an important component of shallow marine waters into the intertidal zone. As an autotroph it is an important base to marine food chains. It is also a type of 'seaweed' that is commonly eaten by humans and is called 'nori' or 'laver' . More recently it has become popular in the U.S. in sushi. Porphyrais cultivated in the oceans off Japan and elsewhere, being grown on rope networks hung in the water.
Other red algal species are important to humans to produce agar. Polysaccharides in the cell wall are extracted , purified and dried to a powder. This can then be used to make gels suitable for growing a variety of organisms.
For vegetarians Porphyra is thought to be a source of vitamin B 12 , a nutrient usually derived from animal sources. There are some reports that chemical found in Porphyra , although similar to vitamin B 12 , does not perform the necessary functions, but most researchers believe that Porphyra can be a source of vitamin B 12. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.40%3A_Porphyra-_an_edible_red_algae.txt |
The name ' redwood ' is applied to two distinct entities, both found in California: the ' Coast Redwood ' of the northern California and the ' Giant Redwood ' , or ' Big Tree ' or ' Giant Sequoia ' of the western slope of the Sierra Nevada mountains in southern California. The habitats of these two areas are significantly different: the Coast Redwood only occurs in areas that are frequently in a coastal fog. The fog significantly alleviates dry conditions and the trees actually obtain moisture from it. The Giant Sequoia occurs in a much drier montane habitat and is a fire-adapted species, having a number of features that allows it to do well in areas that burn. Although both species can become very big, their shapes are distinctly different, with the coast redwoods being taller and thinner. The tallest tree is a coast Redwood with a height of 115.55 m and a volume of 530 m 3. . This is about one-third the volume of the largest (by volume) tree, a Giant Sequoia, which has a volume of 1487 m 3 but is ' only ' 84 m tall.
Phylogeny
Both the coastal redwood and the giant sequoia are sole representatives of their genera (Sequoiaand Sequoiadendron, respectively) with additional species being described from the fossil record. Most workers put these two genera in the Sequoioidae subfamily of Cupressaceae (cedar) family of the conifer group. A third genus in this subfamily is Metasequoia, the dawn redwood, a tree that was first described from fossils before living representatives were found. All three genera are endangered and have limited distributions, although throughout most of the Cenezoic era (the last 65 million years) these species were common and much more widely distributed. Other members of the cedar family include junipers and cedars, both of which have small, scale-like leaves that overlap each other on the stem, a feature that is also found in the Giant Sequoia. In contrast, the coast redwood has needles.
Structure
Except for their potential size these are typical woody trees and obviously have extensive secondary growth. The wood that is produced is high in tannins and this accounts for both its durability (i.e. resistance to decay) and color, features that are found in all the members of the cedar family. The cells that conduct water (trachieds) have features that allow them to operate at the extreme tensions that are required to pull water up to the tops of these tall trees. The long distance that water has to be moved, coupled with the fact it is moving against the force of gravity means that the tensions are extreme and the tracheids found in the uppermost leaves have features, including an ability to collapse, that make it possible for the transport system to function.
Sex and reproduction
These are seed-bearing trees that produce seeds in cones, not in flowers. The cones of Giant Sequoia are fire adapted, opening in response to heating created by a fire. Coast Redwood has an ability rarely found in conifers, the ability to sprout from the trunk of the tree if the top is damaged and or killed. Sprouting is the result of the creation and activation of new apical meristems in response to some signal (perhaps reduction in carbohydrate supply) that indicates that the top of the plant is not functioning. As a consequence of this ability one can sometimes find straight rows of Coast Redwood trees reflecting their origin from the trunk of a downed stem, or a ring of trees that have sprouted from the base of a felled tree. Sprouting is fairly common in angiosperm trees but much less common in conifers.
Matter and energy
Redwoods are typical photosynthetic autotrophs.
Interactions
Both species have distributions that reflect interactions with physical conditions: Coast Redwood requires the foggy conditions only found along the coast; Giant Sequoia is a classic fire-adapted species, requiring fire both to open cones and release seeds and also to remove litter from the surface because successful germination requires the seeds to have contact with the mineral soil.
Only recently have ecologists accessed the canopies of these trees and found, especially in those of the Coast Redwood, remarkable communities of lichens, mosses, vascular plants, and associated animals. Some of the needles that are shed from the top of the trees accumulate on the intertwining branches below. Soils actually develop on these sites located 50-100 m in the air and allow for a rich diversity of epiphytes and associated animals. Nearly 200 'species' of lichens and nearly 50 species of bryophytes and a similar number of vascular plants have been found growing in this arboreal environment ( www.ecology.info/redwood.htm ). | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.41%3A_Redwoods-_the_tallest_and_largest_trees.txt |
Rhizobiaare one of several group of bacteria capable of 'fixing' nitrogen, i.e. converting dinitrogen gas into ammonia and then into organic molecules such as amino acids. Because of this ability, nitrogen fixing bacteria are significant conduits between an extremely large pool of nitrogen in the atmosphere and living things who otherwise could only obtain nitrogen by recycling it from existing pools of organic nitrogen(e.g. amino acids, ammonia, nitrate and nitrite). Unlike many nitrogen fixing bacteria that can fix nitrogen when 'free-living' (i.e. when not living inside a host plant) Rhizobiacan only fix nitrogen when associated with a plant that provides it with carbohydrates. The carbohydratesprovide energy for a process that requires substantial inputs of energy (both ATP and the reducing power of NADH). Rhizobiaonly associate with legumes, members of the pea family. (But not all legumes associate with Rhizobiaand somethat have nitrogen fixing associates may have bacteria other thanRhizobia).
Taxonomy and Phylogeny
Rhizobia are members of the Domain Bacteria. They are gram negative bacteria that are usually flagellated and motile. The ability to associate with legumes, like the ability to fix nitrogen, is NOT thought to be significant phylogenetically. The ability to fix nitrogen appears to have evolved separately several times (i.e. convergent evolution) as evidenced by its presence in Archaea, Cyanobacteria (see Nostoc ) and several other bacterial groups not phylogenetically related. Similarly, t he ability to associate with legumes (which might be considered a type of parasitism) is thought to have been transferred horizontally and consequently is not a good indicator of phylogeny (which reflects vertical gene transfer). The Rhizobia group is thus considered to be paraphyletic.
Structure
Rhizobia are rod shaped bacteria, 0.8 um in diameter and 2 um in length, often with flagellae. They assumea different shape when inside their host, being irregularly shapedandoften 'Y' -shaped.Their presence induces a novel structure within root hair cells called an infection thread. Sensing the presence of Rhizobia, root hairs curl and bacteria are lodged in the crook of the curl. At this point the root cell wall is degraded and the bacteria proliferate in a space outside the root hair cell membrane. A tubular infection thread is then produced and grows down the root hair into the root itself. The thread has cell wall materials and essentially is an elongate invagination of the cell wall, with materials contributed both by the plant and by the bacteria. The infection thread eventually fuses with cell membrane at its base, adjacent to the root cortex. The infection thread then extends to enter (infect) cortical cells, inside of which the bacteria proliferate. As the thread develops the cortical cells have de-differentiated and have become meristematic, producing the tumor (nodule) that characterizes Rhizobiuminfection of roots.
Sex and reproduction
Like all bacteria, Rhizobia are not sexual but they are capable of exchanging genetic material by other means.
Matter and energy
Rhizobiaare heterotrophs that are capable of associating with photosynthetic plants that will provide them with carbohydrates ( 'food' ) as well as whatever nutrients (i.e. mineral elements) they need, excluding the nitrogen which they obtain from the air, where it is abundant. Particularly important to the nitrogen fixation process is the element molybdenum. When Rhizobiaare living outside of a plant they are typical heterotrophs feeding on dead organic material and use the material obtained both as 'building material' for growth and to provide substrates that are oxidized in cellular respiration to provide energy.
Interactions
The ability to associate with legumes requires elaborate communication (signaling) between Rhizobiumand its host plant. Factors secreted by both the plant and the bacteria affect the gene expression and behavior of the other. Among other features, the cells of the gall producea form of hemoglobin called leghemoglobin that is able to bind oxygen and thereby reduce the levels of free oxygen, which is a poison to the nitrogen fixation process. Nodules develop vascular connections, allowing the nodules to be 'fed' with carbohydrates produced by the host plant. These are used primarily to power the substantial energy demands of the nitrogen fixation process but also provide carbohydrate molecules to which the fixed nitrogen is attached. The bacteria acquire N2and excrete ammoniathat is incorporated by the host plant into organic acids forming amino acids or other nitrogen containing compounds. There are forms of Rhizobiathat are complete parasites, being fed by the plant but providing no fixed nitrogen. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.42%3A_Rhizobium-_nitrogen_fixing_bacteria.txt |
Bread Mold (Rhizopus) is one of the most frequently encountered members of the Kingdom Fungi, appearing not only on bread but on a variety of other foods (e.g. strawberries, peaches) if not eaten soon enough.
Taxonomy and Phylogeny
The genus Rhizopus has the same common name, bread mold, as the entire phylum, Zygomycota, in which it is found. The Zygomycota are in the Kingdom Fungi, a group unified by a several characteristics including a filamentous structure, the presence of cell walls formed of the polysaccharide chitin and a lack of cross-walls (i.e. it is coenocytic, see below). Molecular evidence supports both the Kingdom Fungi and the Zygomycota phylum , i.e. it is thought to be a good phylogenetic entity.
Structure
Like most fungi, Rhizopusconsists of filaments (hyphae)that branch to form a feeding structure, a mycelium. All the bread molds, including Rhizopus, are coenocytic, that is, the filaments contain multiple (haploid) nuclei that are not partitioned into individual compartments (cells). Thehyphaegrow from the tip, extending the filaments, andmore nuclei are produced as they grow.
Initially the Rhizopusmycelium 'mines' its substrate, acquiring food from whatever it is growing on. Later it produces three distinct structures, all coenocytic: (1)vertically oriented sporangiophores that bear at their tip round structure that produce numerous asexual spores, (2) root-like 'rhizoids' located below the sporangiophores. Theyare imbedded in the substrate and allow the sporangiophores to grow upward(3) horizontally running 'stolons' that spread the fungus laterallyand produce sporangiophores and rhizoids where they attach to the substrate. Only within the the spore producing structure are cell walls formed around individual nuclei, forming uninucleate cells which develop into spores and are dispersed.
Sex and r eproduction
Rhizopusreproduces asexually by producing sporangia at the end of sporangiophores. Sporangia open to release numerous spores. Occasionally hyphae of two different mating types ( '+' and '–' ) encounter each other and, under appropriate conditions, will induce each other to grow together to effectsexual reproduction. The hyphae meet and fuse; cross walls are formed on each side of the junction, creating a cell that contains haploid nuclei from each of the mating types. Pairs ofnuclei, one from each mating type, are formed andfuse to form (multiple) diploid nuclei. All this occurs as the cell containing the now diploid nuclei develops into a zygospore with a thick cell wall with projections extending outward. Thezygospore typically becomes dormant and the hyphae connected to it die. The zygospore can bedispersed by wind or water before any growth occurs. When it germinates a single filament emerges, forming a sporangiophore with a spore producing sporangiumat its end. As this develops, the diploid nuclei undergo meiosis, creating haploid nuclei, each of which develop cell walls and forming spores that are subsequently dispersed when the sporangium splits open at the end of its development.
Matter and energy
Rhizopus is a heterotroph, like humans, but it digests food outside of the organism, not inside , as is the case for most familiar animals. Both fungi and humans secrete enzymes to break down food but humans secrete the enzymes inside a tube running through their body, while fungi secrete enzymes into the environment that they live in.
Interactions
Bread molds like Rhizopusare very important heterotrophs who collectively eat a great deal of organic material, thereby releasing nutrients that autotrophs can use. Occasionally bread molds, including some forms of Rhizopus, can cause diseases of both plants and animals. Because Rhizopus is relatively easy to culture, it is used industrially to carry out some important chemical conversions, e.g. the conversion of plant steroids into specific chemicals like cortisone and the production of fumaric acid from sugar. Rhizopus is also used to produce tempeh, a soybean 'curd' food consisting of crushed soybeans partially decomposed by Rhizopusand held together by fungal hyphae. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.43%3A_Rhizopus.txt |
Riceis our most important cultivated plant, feeding more people than any other crop. It is anannualor short-lived perennialgrass speciesnative to Asia. Its domestication (i.e. cultivation and modification by humans) started 8 to 13 thousandyears ago. Much of the world, especially Asia, has rice as its primary food source and rice production is critical for feeding the world. Rice requires warm, moist conditions for growth and is grown world-wide in tropical and warm temperate habitats. As is the case in all 'cereal grains' the 'cereal' — the portion eaten — is a one-seeded fruit with the cells of a very thin fruit fused to those of the seed coat.
Taxonomy and Phylogeny
Oryza sativa is by far to most utilized species, although a second species ( Oryza glaberrima ) is grown in western Africa. 'Wild rice' ( Zizania aquatica and Z. palustris ) are in the same tribe (a level of classification between genus and family) but are not generally considered a type of rice. Wild rice was and is harvested by Native Americans and has a very limited amount of production, being used primarily for the gourmet food industry. Virtually all of the world's production of rice is Oryza sativa, and there are numerous varieties. (The Rice Association states that there are over 40, 000 varieties and if you visit a grocery store you might see a dozen or so different types.) Oryza is in the monocot group and is in the grass family (Poaceae).
Structure
Rice has a typical grass structure with a series of leaves that form a false stem through which emerges the main stem when the plant flowers and fruits. Although there are some perennial varieties, most rice varieties are annuals with the plant senescing as it develops fruit. The few perennial varieties have annual shoots but are able to sprout new stems from a below-ground shoot system. Particularly significant to its growth in flooded conditions is the fact that the leaves have a thick cuticle and a vertically corrugated surface that allows the grooves to form air-filled capillaries. These allow for the movement of both oxygen and carbon dioxide.
Sex and reproduction
Ricereproduces sexually, producing bisexual flowers that develop into fruits (cereal grains) after pollination and fertilization. As is the case for most grasses, pollination is by the wind and the flower has features to promote pollination: long stamens that are exerted (extended out of) the flower and elongated stigmas that also extend out of the flower. Most rice varieties are annual and show little vegetative spread. But perennial rice varieties do spread laterallybelow ground and can produceof new, erect branchesafter the first is harvested. In this manner the plant may yield crops for up to 30 years. Riceis difficult to propagate vegetativelyand most rice that is planted is sprouted from seeds and then transplanted as seedlings.
Matter and energy
Rice is a photosynthetic autotroph that uses the C 3 photosynthetic pathway. Like all plants, rice requires 14 mineral elements in order to grow, with nitrogen often being the limiting factor for growth and crop yield. In common with most plants, rice can acquire minerals that are not essential, including minerals that are toxic to the plant and/or toxic to organisms that eat the plant. An example is arsenic. Arsenic is not required by rice or by any plant, but is required in trace amounts by at least some animals. Arsenic is sometimes accumulated by plants, occasionally to levels that some consider unsafe. Rice is a crop that is much more likely to accumulate arsenic than other crop species, probably due to the fact that it is usually cultivated in aquatic situations that can promote arsenic accumulation. While no one is stating that all rice should be avoided, there are some concerns being raised and the arsenic content of rice is being monitored.
Interactions
Like wheat and corn, the most significant of rice's interaction is with humans: their efforts to cultivate rice are of overwhelming significance to the plant. Three other interactions related to its cultivation are worth noting:
• flooding is not required by rice but it is an effective weed prevention technique. Most weeds (and plants in general) do not thrive under flooded conditions, hence the practice of flooding rice paddies cuts down on the number of competitors that rice must face.
• one plant that does thrive in flooded conditions and that is often present in rice paddies is Azolla , a small, floating aquatic fern. Azolla harbors a cyanobacterial symbiont that is capable of fixing nitrogen, and Azolla ' s presence can increase rice yield substantially while avoiding the cost of nitrogen fertilizer.
• Rice is affected by many pests/diseases including fungi, bacteria and viruses. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.44%3A_Rice.txt |
Rust fungi are a common, interesting and economically significant group of fungi. They are obligate parasites of flowering plants, including a number of important crop species: corn, wheat and most cereal grains. Many rust fungi are heteroecious, meaning that they alternate between two hosts. Others are autoecious and only infect one type of host plant. They are particularly challenging to study because, unlike most fungi, which can be cultured on nutrient media, rust fungi can only be grown on living plants, so in order to grow the fungus you have to grow the plant.
Phylogeny
The Pucciniales are an order (i.e. a group of related genera) in the Basidiomycota (club fungi). The group had long been recognized based on their behavior (life cycle) and the structures that they produce on their host plants. Modern molecular studies have confirmed the group as a phylogenetic entity. Many of the structures produced by rusts are orange, hence the common name 'rust fungi' .
Structure
Many of the structures of these fungi are small and not readily observed without a microscope, but some result in the production of characteristic galls on their host plants. A particularly significant feature of these fungi is an haustorium, the structure that occurs inside infected cells and is constructed both of the membrane of the fungus and that of the host plant cell. It is through this haustorium that nutrients pass from the plant to the fungus, allowing it to grow and reproduce.
Sex and reproduction
Rust fungi life cycles are complex. They have multiple stages, typically four or five, that are distinguished by a number of features, including the host plant on which it grows, the structures that are produced, and the 'ploidy' number of the cells (whether they are haploid, diploid or dikaryon). Most of these stages start and end with a type of spore, hence rusts typically produce four or five different spore types and often have a spore produced on one plant species (e.g. hawthorn trees) that is capable of infecting another species of plant (e.g. juniper trees).
Matter and energy
These fungi are heterotrophs that feed upon material produced by other living organisms. They are unusual because they can only be fed by living cells of their host. Even though the nutrients that they need (e.g. sugars, amino acids) might be supplied from non-living sources, these 'obligate biotrophs' cannot absorb nutrients except from the haustorium, the structure produced inside a living cell of its host.
Pictured above is a juniper branch with dormant gall caused by a rust fungus. For a brief period in the spring it turns bright orange (see previous picture) and produces 'horns' from which spores are dispersed that infect its alternate host, which may be apple, crab apple, hawthorn or a number of other species. The leaf on the right is a crab apple showing galls on the underside of the leaves. Often the top of the leaf shows orange spots. Spores produced by the galls infect juniper, completing the life cycle.
Interactions
Depending upon the rust species, the impact on the host can vary from negligible to devastating. Rust diseases are very significant to several crop species including wheat, corn, coffee and white pine, where they can have serious economic impact. In this area rust fungi are commonly seen on both hawthorn and its alternate host, juniper, and also on blackberries (this fungus is autoecious and has no alternate host).
Some of the spores are produced in a sugary substance (nectar) that attracts insects who feed on the nectar and can transport the spores to other plants.
Further Reading
“The Rust Fungi” by Kolmer, Ordonez, and Groth
“Stem rust of wheat” by Schumann and Leonard | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.45%3A_Rust_fungi_%28order_Pucciniales_formerly_Uredinales%29.txt |
Sagebrush ( Artemisia tridentata ) dominates large portions of western U.S., a region that are too dry to support forests or grasslands. Similar areas are found in several other parts of the world (central Asia, southern South America, southern Africa) and are described sometimes as a 'shrub-steppe' community. Some of these areas are also sometimes described as 'cold deserts' with low rainfall and cold winters. Interestingly, although these areas do not support trees, smaller woody plants with multiple branches (i.e. shrubs) are successful.
Phylogeny
Artemisia is a large genus in the sunflower family (Asteraceae) of the angiosperm (flowering plant) group. There are 200-400 species depending upon how much a worker decides to 'lump' groups together. Many members of the genus are herbaceous, including s everal cultivated species: A. drucunculus is the source of the spice tarragon; A. absinthium (aka wormwood) is used to flavor some wines and to produce the liquor absinthe; A. stelleriana ( 'dusty miller' ) is a common ornamental plant; A. vulgare (mugwort), is a common weed. All members of the genus produce chemicals that are aromatic (in an olfactory sense), hence their use as flavorings. Some of the chemicals produced by Artemisia have been used medicinally (either directly or after some chemical modification) to treat malaria, internal parasites and morphine addiction. The common name sagebrush comes from the superficial similarity in scent with the herb sage, an unrelated species. The common name sagebrush is applied to a group of roughly twenty species of shrubs found in the western U.S.
Structure
Shrubs are woody plants that have extensive branching and do not grow particularly tall. Sagebrush is rarely over two m tall and, although it often has a main stem, it branches extensively and may send up multiple stems from its base. Because they rarely have taller plants around them, shading is not a problem and their spreading habit allows them to intercept more sunlight. Although woody, they have an unusual pattern of secondary growth where the vascular cambium often does not form a complete ring around the stem/branch, producing branches that are not round in cross section. Sagebrush leaves are evergreen, roughly five cm in length, have three 'teeth' at the end and have a whitish 'bloom' , the result of many small hairs. The physical structure of sagebrush is important to a wide variety of other species in providing an improved thermal environment both in the summer through shading, and in the winter by reducing wind speed and convective heat cooling. Sagebrush roots often penetrate several meters into the soil to obtain water. They also produce a root system closer to the soil surface (less than a meter) and studies have shown that at night sagebrush carries out 'hydraulic lift' , moving water which actually ends up moistening surface layers of the soil and providing water to both sagebrush and potentially to other plants.
Sex and reproduction
Sagebrush is a typical angiosperm, producing spores in flowers that develop male gametophytes (pollen) that generally are dispersed to other flowers where they complete their development by growing to the location (an ovule) of the female gametophyte (embryo sac) that developed from a haploid spore. Members of the Asteraceae have 'flowers' that are actually inflorescences. Many familiar members of the Asteraceae (asters, sunflowers) have two types of flowers in the inflorescence: ray flowers ( 'petals' ) and disk flowers. Other members of the family (dandelion) have only ray flowers. Sagebrush represents a third type of Asteraceae inflorescence, one that has only disc flowers. Sagebrush is also able to reproduce asexually by sprouting from underground rhizomes.
Matter and energy
Sagebrush is a photosynthetic autotroph which uses the C 3 photosynthetic pathway.
Interactions
Sagebrush is often a dominant species in the areas where it grows and is an extremely important species to these communities, providing food for animals, including numerous insects, pronghorn antelope, rodents, and birds (e.g. sage grouse). The plant is not desirable for ranchers because cattle avoid the bitter foliage and considerable effort has been taken to remove sagebrush and replace it with more palatable species. But efforts are underway to preserve sagebrush and the unique habitat it is associated with, known as 'the sagebrush sea' ( http://www.sagebrushsea.org ). | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.46%3A_Sagebrush.txt |
One of the more common groups of carnivorous plants in North America is the genus Sarracenia. Carnivorous plants of various types have evolved independently at least seven times. One category of carnivorous plants are those that produce pitchers, a structure that collects water and has other features that enhance the likelihood of trapping insects in that water. Carnivorous plants utilizing pitchers evolved independently in several different plant families. Although insects are the primary 'prey' , occasionally frogs and even mice are captured. Death is not directly caused by actions of the plant but is the result of 'drowning' or an inability to escape to feed themselves. Decomposition of the prey is accomplished primarily by microorganisms living in the pitcher but may be aided by enzymes secreted by the plant. In addition to pitchers carnivorous plants may capture prey by glue mechanisms (e.g. sundews, bladderworts) or mechanical traps (Venus flytrap, bladderworts). Carnivory is associated with habitats that are nutrient poor, generally because the soils are acidic and oxygen-poor (e.g. bogs), conditions where decomposition and the consequent release of nutrients, is limited. The pitchers are habitats on the plant where conditions for decomposition are more favorable and released nutrients are directly absorbed by the plant through the leaves or leaf parts that form the pitcher.
Taxonomy and Phylogeny
Carnivorory is found in over 500 plant species, in over 10 genera and over 10 families in both the monocot and eudicot groups. There is one species of monocots that produces pitchers but most are edicts., found primarily in two unrelated families, the Nepenthaceae, found in Africa, and the Sarraceniaceae, found in both North and South America. The plants described here are in the genus Sarracenia , which has about ten species, all in North America.
Structure
The pitchers are highly modified leaves whose margins have sealed for most of its length, creating a water retaining pitcher with a short unsealed terminal portion forming a flange at the top. Leaves occur in clusters on a short vertical stem rising from a rhizome. Flowers are very large and observers often don't recognize that they are part of the same plant that is producing the pitchers.
Reproduction
Sarracenia is a typical flowering plant, p roducing seeds that have a rather limited dispersal ability. It can also spread vegetatively by means of its rhizomes.
Matter and energy
Carnivorous plants nicely reflect the contrast between heterotroph and autotroph nutrition. When heterotrophs 'eat' something, they acquire both food (i.e. carbohydrates and other materials to burn in cellular respiration) but also nutrients (i.e. the 14 minerals) that all life requires. In contrast, autotrophs make their own 'food' (carbohydrates), generally in photosynthesis, and need to acquire minerals in a completely distinct process that requires specialized structures, roots. Carnivorous plants don 't ' eat ' in the same sense as heterotrophs; they derive no carbohydrates from the process. They ' eat' solely to acquire mineral elements because they live in situations where the standard structure of nutrient acquisition (roots) is of limited effectiveness. Pitcher plants have reduced levels of photosynthesis because, although green, leaves are not displayed in a way to maximize light acquisition. If pitcher plants are grown in environments with higher levels of nutrients (available from the roots) they reduce the size and number of pitchers, allowing them to increase photosynthesis.
Interactions
The pitcher provides a habitat for a variety of decomposer organisms: bacteria, protozoans, water molds and others. In fact the pitchers have their own food webs with not only decomposers but also organisms that feed higher up on the food chain: rotifers, midge larvae and others. Several mosquito species specialize in laying their eggs in pitcher plants and their larvae are often the 'top carnivore' in the ecosystem. The midge and mosquito larvae are adapted to aquatic conditions and are not killed in the pitchers. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.47%3A_Sarracenia_a_carnivorous_plant.txt |
Fucusis representative of an interesting group of organisms that are commonly seen attached to rocksand visible at low tide in the intertidal zone. Most of the organisms called 'seaweeds' are brown algae, although some are red algae anda few are green algae. Like most (but not all) brown algae, Fucusis a large, multicellular organism that well-adapted to life in intertidal and shallow coastal waters, most commonly in relatively cool waters.
Taxonomy and Phylogeny
The brown algae are a small group of eukaryotes whotraditionally wereplaced in their own phylum, the Phaeophyta, sometimes along with two groups of primarily unicellular algae, the golden algae and the yellow-green algae, based onsimilarities in pigmentation and other factors. Most modern treatments do not elevate this group to the phylum level but combine it with other 'heterokonts' , a group defined by having two characteristic flagella, one longer than the other. The heterokonts (sometimes called the Stramenopiles) also includes diatoms and the heterotrophic water molds (Oomycota). The pigmentation of photosynthetic stramenopiles is similar to that of the haptophytes like Emiliania huxlii, and the cryptophytes. This may not represent a common phylogeny but instead that all three groups separately became photosynthetic by acquiring the same photosynthetic endosymbiont. The photosynthetic members of these groups are thought to be produced bysecondary endosymbiosis and their chloroplasts have four membranes (see discussion in the article ondiatoms).
Structure
Typical of most brown algae Fucus is truly multicellular, and has three distinct multicellular organs: a holdfast, that attaches the organism to a substrate ; flattened, dichotomously branching stems/blades (similar to thalloid liverworts) that carry out photosynthesis; and air bladders, often part of the stems, that carry the blades upward in the water column. Brown algae have transport systems that allow photosynthate from the blade to be distributed throughout the plant.
Reproduction
Most brown algae are sexual and exhibit alternation of generations. The 'dominant' (i.e. larger and more visible) stage is usually the sporophyte (diploid) stage but there are some brown algae that show isomorphic alternation of generations (the sporophyte and gametophyte look identical) and a few where the gametophyte stage is dominant. Rockweed (Fucus), shows a life cycle like humans with no alternation of generations and where the only haploid cells are gametes. In Fucusthe gametes are distinct from one another (egg and sperm)and in some brown algae theyall look the same (isogametes). Within the brown algae flagellated cells are common and include sperm, isogametes and zoospores, which are mobile cells that can attach to a substrate and grow into a new organism.
Matter and energy
Fucus is a typical photoautotroph, using the energy of sunlight to synthesize carbohydrates from carbon dioxide and then using the carbohydrates as an energy source in cellular respiration and as building materials to synthesize a variety of biomolecules. The brown algae produce a distinct form of a carbohydrate storage polysaccharide called laminaran, made up of glucose units connect ed by a beta 1-3 linkage, rather than the alpha , 1-4 linkage found in starch. They also have high concentrations of mannitol which serves as a transport carbohydrate, a role occupied by sucrose in most plants.
Interactions
Fucus is is especially important in the intertidal zone, providing food for a number of organisms and habitats for others.
Further Reading
• “Fucus” by M.D. Guiry | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.48%3A_Seaweed_Fucus-_a_brown_algae.txt |
Onoclea sensibilis
Sensitive fern is a very common fern throughout most of the country east of the Rocky Mountains, occurring in wetter spots in the woods. It is an easily recognized fern, with a large leaf that shows the classic 'dissected' leaf pattern. In comparison with other ferns, note that the leaf on the right is dissected once into roughly 17 'leaflets' and that each leaflet is serrated with large rounded teeth. In other ferns the 'teeth' are more distinct, creating a leaf that may be 'dissected' or 'cut' multiple times, i.e. the leaflets have leaflets. Sometimes a fern leaf may be cut as many as four times (the leaf has leaflets, which have leaflets, which have leaflets, which have leaflets). (see wood fern ).
Sensitive fern is a perennial plant with a below ground stem that lives for many years, sending up leaves each spring that senesce and wither in the fall.
Taxonomy and Phylogeny
Sensitive ferns clearly belong in the fern group, which most workers consider to be a phylum, the Pterophyta. Among other things the group is united in having vascular tissue but not producing seeds. Recently, many workers have lumped horsetailsand 'wisk ferns' together with the ferns. While horsetails (one genus) and wisk ferns (two genera) are very small groups, the fern group is large (over 12, 000species) and possesses considerable diversity in form. Although most of the members of this group look 'fern-like' , i.e. they are herbaceous with relatively large leaves that are dissected into leaflets, some ferns look very 'un-fern-like' , including some that look a bit like clover (Marsilea), some that are tiny/small floating aquatic plants (Azollaand Salvinea) and some 'tree ferns' that are over 3 m tall and resemble palms because of their dissected leaves. Fern ancestry goes back to the Paleozoic, 350 million years ago.
Structure
Sensitive fern has an underground stem (rhizome) from which emerge the leaves, which, unlike some ferns, are not distinctly clustered together. While m ost ferns just produce one type of leaf that both photosynthesizes and also can produce spores , sensitive fern is dimorphic, meaning it produces two types of leaves that are specialized in their functioning: green leaves (on the left in the accompanying figure) that photosynthesize but produce no spores and separate spore-producing leaves that do not look much at all like leaves (on the right of the accompanying figure). The below ground stem (rhizome) lives for many years, sending up leaves each spring that senesce and wither in the fall. Other common dimorphic species are Ostrich fern, Cinnamon fern and Marsilea (water clover), while a number of other ferns (Christmas fern, Interrupted fern) have dimorphic leaflets, i.e. the leaflets of some of the leaves are specialized for spore production.
Reproduction
Like all plants, sensitive fernexhibits alternation of generations with a visible sporophyte and hard-to-find bisexualgametophyte that is small, uncommonly seen, and quickly overgrownby the sporophyte that grows out from the archegonium. Sperm are flagellated and swim to the egg.
Matter and energy
Sensitive fern is a typical photoautotroph, using the energy of sunlight to synthesize carbohydrates from carbon dioxide and then using the carbohydrates as both energy source in cellular respiration and as building materials to synthesize a variety of biomolecules. Note that the spore bearing leaf is in a sense a parasite on the photosynthetic part, relying on it for sugars to supply its energy and material needs. The same is true of flowers.
Interactions
Sensitive fern contains a number of toxins and is rarely grazed. It is poisonous to cattle, who by and large avoid eating it. Sensitive fern requires moist, shady conditions. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.49%3A_Sensitive_fern.txt |
Soybean, Glycine max, is an important annual crop throughout much of the temperate regions of the world but especially in the United States, which leads the world in soybean production, followed by Brazil and Argentina. Much of the U.S. production is exported. Soybean is particular notable because of the many ways it is used. It is eaten fresh and dry. The seeds can be processed to yield soy oil or to make soy milk (produced by grinding soy seeds in water, producing an emulsion of protein and oil). Soy milk is used to make tofu. The insoluble remnants of these extractions are used in animal feed.
Soybean shares a name (the genus name, Glycine) with one of the twenty amino acids, not because soybean is protein ri ch, although it is, but because of a connection to sweetness. In the 1700 's Linnaeus gave a genus of plants the name 'Glycine ' because of the sweetness in the root of one of its species (not G. max). In the 1800' s the chemical glycine (the amino acid) was isolated from gelatin, and because of its sweetness the chemical was given the name glycine. The sweetness found in plants of the genus Glycine is not due to the amino acid, it comes from sugars present in the roots.
Phylogeny
Soybean is a flowering plant (angiosperm) and is a dicot (eudicot), in the Fabaceae, the pea family, a large and economically important family containing species that are used for food, medicine and lumber plus many species that are important ecologically. The cultivated species is derived from a wild ancestor, Glycine soja, which grows wild in Japan, Korea, China and Russia.
Structure
Soybean is an annual herbaceous species that typically grows to roughly 1 meter in height and may be branched or not depending on the cultivar and planting density. Leaves are compound and generally trifoliate. Small flowers are produced on short branch shoots growing from the axial buds at the base of leaves. Flowers are self fertile and develop into pods (official fruit name is legume) that are typically less than 10 cm long and contain 2-3 seeds.
Sex and reproduction
It is a typical flowering plant with bisexual flowers that produce male gametophytes (pollen) and female gametophytes located in ovules present at the base of the flower, the ovary. The flowers are self fertile; pollen from a flower can be transferred to the stigma of the same flower and it will germinate, grow to the ovule, and fertilize the egg produced by the female gametophyte. Since meiosis does occur in the production of both gametophytes some variability results from the sexual process but much less than would occur if flowers were fertilized by pollen from different plants.
Matter and energy
Soybean is a photosynthetic autotroph which uses the C3 photosynthetic pathway, producing sucrose that can be used as an energy source in cellular respiration or as a material source, providing carbohydrates. Like many members of the pea family, soybean often houses Rhizobium bacteria in nodules (galls) on its roots. The Rhizobium bacteria provide a source of nitrogen to the plant, but they also represent a sizable drain on photosynthate because substantial amounts are needed to 'feed' the bacteria, mostly to provide energy for the nitrogen fixation process. Whether or not the soybean benefits (grows more) from its interaction with Rhizobium depends on the amount of available nitrogen. But symbiotic nitrogen fixation by Rhizobium lessens the nitrogen fertilizer needs for growing soybeans and also enriches the soil with nitrogen for subsequent crops.
Interactions
Soybean is a short-day plant, although the specific requirements vary with cultivar. One of the reasons soybean is not grown near the equator is because the daylength is never sufficiently short to trigger flowering. In addition to the interaction with Rhizobium, soybean has significant interactions with a large group of pathogens and herbivores (nematodes, water molds ( Phytophthora ), rust diseases, a variety of bacterial diseases, and a large number of insect herbivores, most of which attack other crops as well.
Other edible members of the pea family: beans and others
Even more than the grass family, the pea family (Fabaceae) is the source of a variety of edible crops. These are generally divided into 'pulse' crops where the seeds (often called beans) are harvested dry, and green vegetable crops that are harvested and eaten before drying. Some, like soybean and green beans may be harvested both ways.
Harvested green
• Phaseolus vulgaris — green bean, string bean
• Phaseolus lunatus — lima beans (sometimes called butter bean)
• Pisum sativa — peas
• Glycine max — soybean, but when harvested green, it is called edamame
Harvested dry
• Glycine max — soybean
• V igna unguiculata — cowpea, including 'black eyed peas'
• V igna angularis — adzuki b ean
• V igna radiata — mung bean
• Cicer arietinum chickpea, garbanzo bean
• Phaseolus vulgaris — pinto bean, black bean, kidney bean
• Lens culinaris — lentil
• Arachis hypogaea — peanuts
• Vicia fava — fava beans
All of the seeds of the Fabaceae family contain secondary chemicals that can have toxic effects on humans, although most of the widely cultivated plants are generally not toxic to most people. Red kidney beans and lima beans should be thoroughly cooked before eating and fava beans are toxic ( 'favism' ) to individuals lacking a specific enzyme. Wild members of the pea family are commonly toxic and include 'locoweeds' , rosary pea, some species of Lathyrus. Note that not all 'beans' come from members of the Fabaceae, e.g. castor bean, cocoa bean, vanilla bean, coffee bean. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.50%3A_Soybeans_%28and_other_beans%29.txt |
Peat moss
The genus Sphagnum is by far the most important non-vascular plant group on earth. The 120 species in the genus are primarily found in cool, moist habitats, mostly in the Northern Hemisphere (northern U.S., Canada, northern Ireland, Scotland, northern Europe, Siberia) but some do occur in the southern part of the Southern Hemisphere (Chile, New Zealand). The genus is important because it can dominate large areas and change conditions at these sites, making them less hospitable for some species and more hospitable for others.
Phylogeny and taxonomy
Sphagnum is the only genus in the family Sphagnaceae, which is the only family in the Class Sphagnales, which is the only class in the order Sphagnopsida, i.e. a single genus is the only representative of an entire Class. Sphagnum is distinctive in form. Its distinctiveness is also borne out in molecular studies of the group.
Structure
The gametophyte (haploid form) generally occurs in dense mats. Individual plants may be quite long, over 30 cm, but this is including the slowly decomposing basal parts, with the green portion typically 10 cm or less. Plants are erect and have a cluster of branches near the top that give it a characteristic look. The leaves of sphagnum consist of strands of narrow living cells with abundant chloroplasts, surrounding bands of much larger cells that quickly die after being produced. The ability of sphagnum to hold so much water is related both to the large quantity of non-living cells that can absorb water and also to the fact that the mat of plants itself can hold water in between individual plants.
The sporophyte is less commonly seen and includes a roughly spherical capsule that opens explosively to release spores. In most mosses ( e.g. Polytrichium) the sporophytes (the diploid part) have two components: a stalk and a capsule situated at the top of the stalk. However, in Sphagnum the sporophyte is solely the capsule and the stalk that it sits on is haploid and part of the gametophyte.
Reproduction
Sphagnum exhibits the typical alternation of generations found in mosses, with a haploid gamete producing plant (gametophyte) that is relatively large, long-lived and noticeable, and a much smaller, shorter-lived diploid sporophyte that is produced on the gametophyte, produces spores, and then is shed.
Matter and Energy
Sphagnum is a photosynthetic autotroph, it makes food (carbohydrate) through the process of photosynthesis and then uses this carbohydrate both as a material to make biomoleules and also to provide energy for metabolic activities. For the gametophyte this is true throughout its existence. The sporophyte is usually only photosynthetic during its period of growth, if at all, and often loses its chlorophyll, and thus its ability to feed itself, as it matures. It thus becomes dependent for food on the gametophyte that it is growing out of.
Mineral nutrition of mosses is different from that of vascular plants, whose roots obtain obtain nutrients from the soil solution. The source of mineral nutrition for most mosses is not the soil, it is precipitation (sometimes altered in chemistry as it flows down tree trunks) and dust. This is especially true for sphagnum moss because it generally occurs as a carpet sitting on top of a large mat of poorly decomposed material (usually sphagnum plants themselves). At least some species of sphagnum are unusual in their ability to use amino acids as a source of nitrogen in addition to nitrate and ammonia.
Interactions
Sphagnum interacts with other species a number of ways. Most significant is its ability to alter water and nutrient conditions on a site. Specifically, sphagnum can make areas of land waterlogged, acidic and nutrient poor. This is advantageous for sphagnum because it eliminates competitors that might shade out the sphagnum. It is also significant for other species (e.g. pitcher plants and sundews) that thrive in open, waterlogged habitats, again because potential competitors are kept at bay. Interestingly, not only can sphagnum make terrestrial habitats waterlogged it can also make aquatic habitats (e.g. ponds) somewhat terrestrial, by growing across the surface and producing a mat capable of supporting terrestrial plants, although the habitat is waterlogged and not truly terrestrial.
The remnants of bogs are often 'mined' for the un-decomposed material, called peat, that can be used as a fuel source. Like coal and oil, the energy captured in photosynthesis is still available in the peat because the plant material has not been oxidized in cellular respiration of decomposer organisms. Dried peat is also a common soil additive in gardening.
Further Reading | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.51%3A_Sphagnum-peat_moss.txt |
The sunflower is a familiar plant that has the distinction of being the only widely used crop species that originated in North America. Although Native Americans domesticated the plant and selected for plants with single heads and larger seeds, its initial use after being introduced into Europe was primarily as an ornamental plant in gardens. It first became popular as a crop plant in Russia, largely as a consequence of edicts from the Eastern Orthodox Church concerning diet restrictions during Lent. During Lent, consumption of oils from a variety of plants (e.g. olive, palm, sesame) was forbidden, but sunflower, a recent arrival, was not banned and sunflower became an important crop in Russia by being a source of oil during Lent. It is now the national flower of both Russia and the Ukraine. Early in the 20th century sunflower came back to North America as a crop grown primarily for its oil in both the northern U.S. and in Canada. In the southern hemisphere, Argentina is a major producer of sunflower. The oil from sunflower is used both in cooking and also industrially (e.g. as a base for paints). It can be used as a substitute for diesel oil directly or after first being converted to biodiesel. After oil has been extracted the remaining seed can be used for animal feed. To a very limited extent sunflower seeds are eaten directly, especially by baseball players!
Phylogeny
Helianthus is a genus in the sunflower family (Asteraceae), one of the largest families angiosperms. There are roughly 70 species, both annual and perennial, with H. annuus (an annual) being the most important crop species. A perennial species ( H. tuberosus ) called Jerusalem artichoke, is occasionally grown for its edible tubers.
Structure
Sunflower is an herbaceous annual. Although wild representatives are usually branched, the cultivated form typically does not branch and consists of a single stem that maybe well over 2 m in height with the single large head inhibiting the production of branches. The stem produces a vascular cambium but does not form wood (a continuous cylinder of secondary xylem) instead it adds to the existing vascular bundles. Although it does not produce wood the stem is remarkably ' woody ' , meaning tough, durable and resistant to deformation. Most cells in the primary xylem and phloem are extensively lignified and produce a strong stem, able to stand several meters tall and hold a head that may weigh as much as two kilograms or multiple much smaller heads. The stem often more than 5 cm in diameter, with most of the width from primary growth. The bulk of the stem is pith and the strength comes from a ring of vascular bundles near the margin of the stem.
Fields of mature sunflowers are striking because all the heads, regardless of the time of day, are facing the same direction, east. In contrast, younger flower heads, before they start to flower, show a daily movement, tracking the sun from east to west during the day and then returning to the east overnight. The control of the movement probably involves both an endogenous biological clock and a responsiveness to incident light.
The heads of sunflowers are a good place to observe the spirals associated with plant architecture. Spirals rotating in both clockwise and counter-clockwise directions are evident. And the number of spirals usually relates to two numbers in the Fibonacci sequence (momath.org/home/fibonacci-numbers-of-sunflower-seed-spirals/). See also the following link connecting the Fibonacci series to the 'golden angle' , an interesting mathematical and artistic concept (www.mathsisfun.com/numbers/nature-golden-ratio-fibonacci.html).
Sex and reproduction
Sunflowers reproduce utilizing seeds produced in the normal pattern for angiosperms. The flowers are characteristic of the Asteraceae family. The 'flower' is actually an inflorescence, a structure of several hundred flowers of two types: the 'petals' of a sunflower are ray flowers, with a large petal that is actually composed of five fused parts and is is asymmetrically oriented, extending out to one side of the flower. Ray flowers are often sterile, lacking both male and female parts. The central disk flowers that make up the bulk of the inflorescence have much smaller petals arranged in a ring. They are bisexual and have a distinct phenology (timing). For the head as a whole the central 'disk' flowers mature from the outside inward, i.e. the first flowers to open are on the outside. Each individual flower also has a pattern of development. The anthers mature first, making pollen available to pollinators, primarily bees. After the pollen has been available for several days a stigma pushes up through the ring of anthers. Self-pollination of a particular flower by itself is unlikely unless the flower has not been visited by pollinators, in which case there may still remain abundant pollen. While the annual H. annuus , must set seed to reproduce, the perennial H. tuberosa can reproduce via its tubers which, like potatoes, are produced on underground stems (rhizomes) that allow the plant to spread laterally and is part of the reason that H.tuberosa can be a problem weed.
Matter and energy
Sunflower is a photosynthetic autotroph which uses the C 3 photosynthetic pathway.
Interactions
Sunflower probably represents a classic case in the evolution of crops. It is a 'weedy' species in an ecological sense, one that thrives in disturbed habitats. Because of this, it probably frequented the areas close to primitive human habitation. Subsequently humans recognized its utility and started actively cultivating it and thereby developing it as a crop. A similar scenario may also apply to wheat and other crop species. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.52%3A_Sunflower_-_Helianthus_annuus.txt |
The fungus Rhytisma lives inside tree leaves and produces large black spots on the leaves late in the growing season (August and September) as the leaves start to senesce. The most common species in the northeastern U.S. occur on maples but there are other species that occur on other tree species. The black spots form when the fungus produces large black masses of hyphae ( 'stroma' ) that break through the epidermis of the leaf. In the spring of the year, spores produced in these black spots are released and can be dispersed by the wind. Some fortunate spores end up on newly produced leaves where they can germinate and penetrate through the epidermis to get inside the leaf. The tar spot fungus is an example of an endophyte, an organism (usually a fungus) that lives inside of plants. Generally endophytes are not very apparent and they are not generally thought of as causing disease. Some endophytes are even thought to be a positive presence, providing benefits such as disease and stress resistance while at the same time benefiting from being fed and protected by the plant
Phylogeny and taxonomy
Rhytisma is an ascomycete fungus. As is common for a number of fungi, Rhytisma was described with both a sexual form (placed in the Ascomycota) and an asexual form (placed in the Fungi Imperfecti) but it is now recognized that there is one entity that sometimes reproduces sexually and sometimes does not. (Placing fungi into phyla used to require the observation of sexual stages; and fungi lacking sexual stages were placed in the 'Fungi Imperfecti' ). With modern molecular techniques fungi can be placed into groups without observation of the sexual stages.
Structure
Tar spot fungus consist of septate hyphae (i.e. filaments with cross walls) that spread through part but not all of the leaf that they have penetrated, typically spreading 1-3 cm. If sexual reproduction is to occur hyphae from two different mating strains need to find each other and some of their hyphae fuse (plasmogamy) to form a dikaryon cell that grows to produce dikaryon hyphae where each cell has two haploid nuclei. In late summer both the haploid hyphae (i.e. those of each mating type) and the dikaryon hyphae intertwine to form a stroma, a thick mass of hyphae. Within the stroma are produced small, cup shaped 'apothecia' . Within these structures the tips of some of the dikaryon cells produce the the characteristic asci–elongate cells where karyogamy occurs to make the cell temporarily diploid. This is the only diploid cell produced by tar spot fungus or any ascomycete. The diploid nucleus undergoes meiosis followed by mitosis to produce a cell with eight haploid nuclei, each of which develops a cell wall to form ascospores. The ascospores of tar spot fungus are quite narrow and pointy.
Sex and reproduction
Tar spot fungus can reproduce both sexually and asexually. Sexual reproduction, described above, is in a manner typical of Ascomycetes.
Matter and energy
Tar spot fungus is a herbivore, obtaining matter and energy from its host. Hyphae apparently can acquire nutrients from host cells without the presence of haustoria, evidently obtaining materials that 'leak' from cells. Because of the fungus 's modest growth habits (it doesn't grow particular fast and does not grow extensively, i.e. it does not go through the entire leaf) there is minimal damage to its host.
Interactions
Recently some endophytes, like tar-spot fungus, have been recognized to benefit their host in a variety of ways: by producing toxins that deter other herbivores, by somehow making their host more able to fight off other diseases, by making their host better able to withstand harsh environmental conditions (e.g. drought).
Another endophytic interaction that you may have heard of is ' St. Anthony' s fire', a human disease caused by the consumption of grain (e.g. wheat, rye) infected with an endophytic fungus. The fungus produces alkaloids related to LSD that can cause hallucinations and death if grain harvested from plants infected by the fungus are consumed.
Further Reading | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.53%3A_Tar_Spot_Fungus.txt |
T. aquaticus is the organism that makes PCR (polymerase chain reaction) possible. It is an 'thermophile', capable of living in high temperatures, specifically at temperatures over 70 °C (150 °F). It was discovered in 1969, at a time when biologists assumed that no living thing could survive at temperatures over 55 °C. While Thermus can 'only' withstand temperatures up to 80 °C, other organisms can live at temperatures even closer to the boiling point of water.
Phylogeny
Unlike many thermophilic (heat-loving) prokaryotes Thermus is not in the Domain Archaea but is a genus in the Domain Bacteria. Along with one other genus Thermus forms a distinct and ancient lineage within the bacteria.
Structure
Thermus aquaticus cells are rod-shaped and sometimes filamentous , non-flagellated gram negative bacteria often occurring as filaments. Gram negative bacteria have a peptidoglycan cell wall layer sandwiched between an inner and outer phospholipid membrane.
Sex and reproduction
Like all bacteria, Thermus are not sexual, but they are capable of exchanging genetic material by other means.
Matter and energy
Thermus is a heterotroph and acquires matter and energy by absorbing organic compounds from its environment , organic compounds that that are derived from other living organisms either by excretion or degradation of the biomolecules that once was part of an organism.
Interactions
Thermus is found in sites with elevated temperatures, hot springs and near thermal vents in the oceans. It occasionally is found in hot water systems and in areas of thermal pollution (e.g. near power plants). It feeds off organic matter produced by other thermophiles including both other members of the Domain Bacteria (including some photosynthetic cyanobacteria) as well as members of the Domain Archaea (see Halobacterium)
Polymerase Chain Reaction
In the last 20 years the PCR technique has revolutionized biology research and plays a very significant role in 'applied biology' (e.g. testing for Wuhan flu, paternity testing, diagnosis of hereditary disease, forensic science, security). These are situations where having multiple copies of a certain portion of the DNA molecule are needed and PCR techniques allow the synthesis of multiple copies of a specific part (often a 'gene' ) of DNA. Synthesizing DNA is accomplished by the DNA polymerase enzyme, an enzyme found in all cells. In the normal process carried out by all cells, two enzymes (topoisomerase, helicase) separate a portion of double strand DNA into two single-strands and DNA polymerase is then able to extend DNA strands complementary to each of the single strands that have been revealed. In PCR, heat is used to separate ( 'melt' ) the double stranded DNA into single strands. Then the mixture is cooled slightly to allow one of two 'primers' to bind (anneal) to the single strands. The primers are two short sequences of single stranded DNA (one for each strand) complementary to each end of the gene that is to be copied. The annealing of the primers produces a two stranded 'starting point' from which DNA polymerase can add nucleotides, there by extending a DNA molecule complementary to the existing single strand. The DNA polymerase from Thermus aquaticus (called 'Taq polymerase' ) is useful in this process because it can be heated to a temperature high enough to melt DNA yet is still able to function. The PCR machine (called a 'thermocycler' ) performs repeating cycles of high temperature, melting the double stranded DNA, then cooling slightly to allow primer sequences to bind 'anneal' to the single strand, and thereby allowing Taq polymerase to work to extend the primer strand in a manner complementary to the single strand. This process (a thermal cycle) is repeated multiple times to get multiple copies of the DNA under study. Although the technique is feasible using polymerases not from thermophilic bacteria, one would have to add additional enzyme after each heating because most enzymes are destroyed by the temperatures required to melt double stranded DNA. Taq polymerase can be added at the beginning and it remains stable through the multiple cycles (usually about 30) needed to produce enough (usually millions!) copies of the gene. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.54%3A_Thermus_aquaticus.txt |
Wheat should be familiar to everyone although perhaps only as a food and not very much as an organism. Wheat is one of the oldest crop species, originating in Turkey probably close to 10,000 years ago, although some researchers place its origin even older. As described below what we call 'wheat' is at least three different entities, differing in chromosome number, evolutionary history and also features related to harvesting and baking.
Phylogeny and taxonomy
Wheat is a flowering plant. Multicellular, terrestrial, photosynthetic organisms (“land plants”) are generally put in the Plant Kingdom. The most important group within this kingdom, based on a number of different measures (number of species, economic importance, ecological importance) is a group that produces flowers, (flowering plants = angiosperms = the phylum Magnoliophyta). Within the angiosperms there are two main groups, monocots and dicots (now called eudicots). Wheat is in the monocot grouping, generally considered at the class level (Liliopsida), although modern treatments recognize the group but may not assign it a particular rank. In contrast to the dicots, monocots are considered monophyletic (originating from a single ancestor) and therefore a sound taxonomic entity. In contrast, the old dicot group is not considered monophyletic. This is why the grouping 'eudicot' came into being, it contains just those dicots (almost all of them) that are united by being monophyletic. Wheat is in the Poaceae, the grass family, one of the four most important families of flowering plants and the family that includes all our important 'cereal grains' (wheat, rice, corn, barley, oats).There are several different species called 'wheat' and these are related by polyploidy: one is diploid (eikorn wheat), two are tetraploid (emmer and durum wheat) and one is hexaploid (bread wheat).
Structure
Wheat is a fairly typical 'herbaceous' (i.e. non-woody) plant. Like almost all organisms that are considered plants, wheat consists of cylindrical structures, shoots and roots. Both these structures have an embryonic region (apical meristem) at their tip that produces cells whose expansion elongates the cylinder. The shoot apical meristem also produces organs (leaves) that are typically broad and thin. The cellular organization of both roots and shoots shows a radial organization(i.e. a pattern from the inside to the outside) but the cells show few changes as you move up or down a root or shoot, except in the region close to the root or shoot tip where the cells are younger and have yet to develop some features. Given the proper stimulus, at least some of the shoots will develop into clusters of flowers (inflorescences) that will develop into fruits containing seeds. Grasses only exhibit primary growth, the growth resulting from the embryonic regions at the tips of roots and shoots, including branch shoots and branch roots. There is no secondary growth, growth that makes the roots and shoots of some plants wider and woody. Like most grasses, the wheat apical meristem does not elongate until the time of flowering and most leaves that the stem produces elongate before the main stem, producing what appears to be a stem but is actually a series of cylindrical leaf bases extending from the still unelongated stem.
Reproduction and sex
Wheat reproduces sexually in a manner typical of flowering plants. Seeds develop from the fertilized ovules present in the ovaries of flowers. All grasses produce flowers that have a single ovule per ovary and this develops into a one-seeded fruit with the fruit wall fused to the seed coat. A wheat seed consists of three parts: the embryo, stored food (endosperm) and a seed coat fused with with the fruit wall. These components are important to human nutrition. White flour is produced after milling the grains to remove: (1) the embryo, which is sold separately as wheat germ, (2) the seed coat and fruit coat, which is also sold separately and called wheat bran. The remaining endosperm is primarily starch but does contain roughly 10% protein, including two proteins that combine to form gluten as flour and water mixtures (do ugh) are massaged (i.e. kneaded). The germ represents only a small part of the fruit but it contains substantial amounts of protein, fats, minerals and vitamins. The bran is largely indigestible fiber but it does contain some protein and fat. This is what makes whole-wheat flour 'more nutritious' , i.e. more protein, minerals, vitamins and fat than white flour. Unfortunately, 'more nutritious' also applies to fungi and bacteria and whole wheat flour is considerably more likely to spoil than white flour, which is part of the reason white flour became favored. Other reasons were white flour 's improved baking qualities and the ideal of' purity'.
Matter and Energy
Wheat is a typical photosynthetic autotroph. Individual plants accumulate carbon dioxide from the atmosphere and use it to form carbohydrates that are both used to enlarge the plant (i.e. grow) and also to be 'burned' in cellular respiration to provide energy for the plant. Wheat is typical of seed plants, requiring 17 elements, carbon, hydrogen and oxygen(acquired as water and carbon dioxide), plus an additional 14 'minerals' that are obtained from the soil solution by the root system.
Interactions
The most significant interactions of wheat are with humans who actively foster its growth by planting it and culturing it. Like many crop species (but not like most plants) it is an 'annual' species:it has a finite lifetime that is less than a year, resulting from the fact that the shoot apical meristem is converted into a flowering meristem within a year of planting. Once the conversion to a flowering meristem occurs, no further growth of the shoot is possible. Moreover, as flowers and fruits develop, the nutrients in the existing plant structure, especially leaves, are mobilized and delivered to the developing seeds, providing them with nutrients but eliminating the ability of leaves to photosynthesize. Wheat can be harvested in as little as 100 days after planting, and can be planted in late spring and harvested in late summer ( 'spring wheat' ) or can be planted in early fall and harvested in late spring ( 'winter wheat' ). The latter varieties need a cold treatment ( 'vernalization treatment' ) to induce flowering.
Important to the interaction between wheat and humans are interactions between wheat and:
1. climatic and soil conditions–wheat grows best in 'temperate' regions, i.e. not in the tropics or in arctic regions. It can tolerate relatively dry conditions but does not handle flooding well.
2. herbivores — a number of insect herbivores can drastically affect wheat growth and yield
3. diseases — a variety of diseases, caused by fungi, bacteria and other agents affect wheat growth. These diseases are trophic in nature and could be considered parasites, because the disease causing organism is eating the plant. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.55%3A_Wheat.txt |
The wood ferns (genus Dryopteris) are a group of over 400 species and are commonly seen throughout temperate areas, especially in forests. Many are planted as ornamental plants and they are commonly used in landscaping and gardens. The group is known for hydridization, polyploidy and subsequent speciation which accounts for the large number of species (see discussion of speciation through polyploidy in Chapter 28).
Taxonomy and Phylogeny
Wood ferns are members of the Pterophyta, the fern group, which includes ferns, horsetails and wisk ferns. Most observers recognize ten orders within the group, the largest of these is the Polypodiales, which contains roughly 80% of the roughly 12, 000 species put in the Pterophyta and is the order that contains the Dryopteridaceae, the family of roughly 1700 species that contains Dryopteris. Among other features that unite the Polypodiales is a sporangium with a band of cells, the annulus, that is interrupted by the stalk that attaches the sporangium to the fern leaf.
Structure
Wood ferns have an underground stem (rhizome) from which emerge the leaves. In most of the wood ferns the leaves are produced in clusters that produce an urn-like, circular groups of leaves. Leaves emerge in the spring as fiddleheads, exhibiting what is know as 'circinate vernation' i.e. they are coiled and unfurl from the base upwards. The leaves of most wood ferns are dissected 2-4 times. The petiole (stipe) of the leaf generally has large, scale-like outgrowths. Sporangia are produced on the underside of leaves in clusters called 'fruit dots' . There is a flap of tissue called an indusium that covers the cluster of sporangia.
Reproduction
Like all plants , wood ferns exhibits alternation of generations with a visible sporophyte and hard-to-find bisexual gametophyte that is small, uncommon ly seen, and quickly over grown by the sporophyte that grows out from the archegonia. Sperm are flagellated and swim to the egg.
The sporangia of all ferns in the Polypodiales are small stalked structures less than a millimeter tall.
They have a band of specialized cells, called an annulus (red arrow on the top), that run, starting at the stalk, around roughly 80% of the circumference of the sporangium. As the sporangium starts to dry the sporangium splits between two cells just below the annulus (green arrow, on the right). The cells of the annulus have specialized thickenings that can store energy as the sporangia dries and the annulus shortens to fully open the sporangium. The shrinkage generates a tension in the annulus that eventually overcomes the strength of water columns that are holding the annulus together. When the water columns break, the top of the sporangium rapidly snaps back, dispersing the spores into the air.
Matter and energy
Wood ferns (both the sporophyte and gametophyte) are a typical photoautotroph s , using the energy of sunlight to synthesize carbohydrates from carbon dioxide and then using the carbohydrates as an energy source in cellular respiration and as building materials to synthesize a variety of biomolecules.
Interactions
Wood ferns contains a number of toxins and are rarely grazed by mammals but are eaten by some caterpillars. Wood ferns are found throughout the eastern U.S., generally in forested situations. | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.56%3A_Wood_Ferns.txt |
Yeast—Saccharomyces cerevisiae
Brewer's (aka baker's yeast or commercial yeast), is the organism that is used to make bread rise and produce wine from the fruits of grape. It also is extremely important as a 'model organism' in biology. It was the first eukaryote to have its entire genome sequenced and studies using S. cervisiae have been highly significant in developing our understanding of meiosis, mitosis and cancer. The translation of the scientific name is: saccharo = sugar, myces = fungus, cerevisiae = beer, reflecting its ability to make beer out of sugar water. It accomplishes this feat in a manner that several organisms can, by carrying out a processes termed fermentation, an anaerobic respiration process that releases carbon dioxide while converting six-carbon sugars (glucose and/or fructose) into ethanol. This same ability is important in bread making, not for the production of alcohol but for the production of carbon dioxide, which acts as a 'leavening agent' , releasing carbon dioxide gas into a matrix of hydrated starch and protein molecules (bread dough), thereby producing a product with a light, aerated texture. In both bread/beer making and in scientific experimentation, what makes yeast particularly useful is the fact that it is easily cultured — it can be readily grown (i.e. it is not fussy about growth conditions) and is easy to keep alive/viable (i.e. it is tough to kill) and actually can be kept viable under what is often considered harsh conditions — cooling, freezing, drying.
Phylogeny and taxonomy
The name yeast is a morphological term referring to unicellular fungi. Used in this context it does not relate at all to phylogeny. Convergent evolution has resulted in unicellular fungi in several different groups including Zygomycetes (bread molds), Basidiomycetes (club fungi) and Ascomycetes (cup fungi). Most unicellular fungi (yeasts) are ascomycetes but even within this phylum there are yeasts that are not closely related. Commercial yeast (Saccaromyces cervisiae) is an ascomycete, as is fission yeast ( Schizosaccharomyces pombe ), another yeast used in brewing and also an important model organism with its entire genome sequenced. Although fission yeast and baker's yeast have a similar ecology and are in the same phylum they are not closely related, having diverged from each other over 300 – 1000 million years ago.
Structure
Yeasts in general are unicellular fungi and in form and size very similar to bacteria. Like all fungi, they have a cell wall composed of chitin and possess a nucleus and other organelles, in particular, mitochondria. In many ways they represent fungi that have evolved to become 'bacteria-like' in their form and ecology. Baker's yeast is typical of yeasts in generally — they typically are roughly spherical and around 5 um in diameter.
Sex and reproduction
Brewer's yeast primarily reproduces asexually, by ' budding ', which is basically cell division but where the daughter cell starts as an outgrowth (bud) of the parent cell and eventually separates. Brewer's (and fission) yeast are capable of sex when the diploid cells undergo meiosis, forming cells that can fuse with each other (i.e. serve as gametes) to restore the diploid condition. Both fission yeast and commercial yeast can occur as haploid or diploid cultures. Haploid cultures can be maintained by not bringing together different mating strains, while diploid cultures can be maintained because specific culture conditions (nitrogen starvation) are needed to bring about meiosis. When haploid cells of different mating strains encounter each other, chemical communication (pheromones) trigger the production of extensions ( 'Shmoo's ') that allow cells to fuse with each other (plasmogamy). In the diagram below the blue ' a ' strain produces a mobile chemical (pheromone) designated by the blue circles and has receptors (red ' football goalposts ') that can bind the pheromone (red squares) produced by red 'alpha' strain. Similarly, the red alpha strain has receptors for the pheromone produced by the blue ' a' strain. In both strains the binding of pheromones produced by compatible strains induces the production of a schmoo and the eventual creation of a diploid cell.
Matter and energy
Saccharomyces is a heterotroph with a sweet tooth—it prefers living off of simple sugars, although some strains can breakdown sugar polymers, e.g. starch, into simple sugars, thereby broadening its diet. Its mineral needs are obtained by absorbing small organic molecules (amino acids) and minerals like phosphate. Various strains differ in their ability to breakdown organic matter and absorb and metabolize nutrients; these features may be useful in genetic/cell biology experiments.
Interactions
Obviously yeast have significant interactions with humans in providing food products and beverages. The 'native habitat' of both Brewer's yeast and fission yeast is the skins of sugar containing fruits such as grapes, apples and pears, making the ' invention ' of wine-making relatively easy. In addition to ethanol, genetically engineered yeast are used to produce a variety of compounds including insulin. While brewer' s yeast is non-pathogenetic some yeast species can cause disease in humans and other organisms.
Further Reading | textbooks/bio/Botany/Inanimate_Life_(Briggs)/02%3A_Organisms/2.57%3A_Yeast.txt |
• 1.1: Plants, Botany, and Kingdoms
Botany is the scientific study of plants and plant-like organisms. It helps us understand why plants are so vitally important to the world. Plants start the majority of food and energy chains, they provide us with oxygen, food and medicine. Plants can be divided into two groups: plants1 and plants2 . Plants1 contain all photosynthetic organisms which use light, H2O, and CO2 to make organic compounds and O2 . Plants1 are defined ecologically (based on their role in nature).
• 1.2: Styles of Life and Basic Chemistry
Life obtains energy in a few different ways: (1) from sunlight (phototrophy); (2) from chemical reactions with inorganic matter (lithotrophy); (3) from breaking organic molecules into inorganic molecules, typically carbon dioxide and water (organotrophy). To make its body, living beings obtain building blocks either by (a) from the assimilation of carbon dioxide (autotrophy), or from other living beings (heterotrophy).
01: Introduction to the Introduction
Botany is the scientific study of plants and plant-like organisms. It helps us understand why plants are so vitally important to the world. Plants start the majority of food and energy chains, they provide us with oxygen, food and medicine. Plants can be divided into two groups: plants$_1$ and plants$_2$. Plants$_1$ contain all photosynthetic organisms which use light, $\ce{H2O}$, and $\ce{CO2}$ to make organic compounds and $\ce{O2}$. Plants$_1$ are defined ecologically (based on their role in nature). Some plants$_1$ can be bacteria or even animals! One example of this a green slug, Elysia chlorotica (see Figure $1$). Green slugs collect chloroplasts from algae and use them for their entire life as food producers. Therefore, green slugs are both animals and plants$_1$.
Plants$_2$ are all organisms from Vegetabilia kingdom. Normally, plants$_2$ are green organisms with a stem and leaves. We can define them also as multi-tissued, terrestrial, and primarily photosynthetic eukaryotes. This definition is taxonomical (based on evolution).
It is possible for the organism to be plant$_2$ but not plant$_1$ (Figure $2$). Those who fall into that category, are fully parasitic plants (mycoparasites like Pterospora, root parasites like Hydnora, stem parasites like Cuscuta, and internal parasites like Pilostyles) which do not practice photosynthesis but have tissues, terrestrial lifestyle and originated from photosynthetic ancestors. Plants may be understood on several levels of organization: (from top to bottom) (a) ecosystems or taxa, (b) populations, (c) organisms, (d) organs, (e) tissues, (f) cells, (g) organelles, and (h) molecules (Figure $3$). Botany is considered to be a “slice science” because it covers multiple levels of organization.
Taxonomy
Taxonomy, systematics and classification are terms with similar meanings; they are all about the overwhelming diversity of living organisms, for there are more than 2,000,000 species (and 300,000 of them belong to plants$_2$). Phylogenetics is a more fashionable term; it emphasizes the evolutionary history (phylogeny) of taxonomic groups (taxa). This taxonomic organization is hierarchical. Most scientists accept seven main levels of taxonomy (ranks): the highest is kingdom, followed by phylum, class, order, family, genus, and lastly, species.
The highest rank, kingdoms are easy to understand as the pyramid of life (Figure $4$) which is divided into four levels—kingdoms. At the bottom is Monera, which consists of prokaryotes (Bacteria and Archaea). This is the first level of life: Monera have simplest cells without nucleus. The next level is Protista. These are eukaryotes (nuclear cells) without tissues; some examples are algae and fungi. The final level consists of two groups: Vegetabilia and Animalia. They both have tissues but have obtained them for completely different purposes. Animals have tissues to hunt and digest, while plants have tissues mainly to survive on land. Viri which are mentioned sideways, are not living things but merely pieces of DNA or RNA which “went astray” out of cells of living organisms of all four kingdoms. Despite of being non-living, viruses are capable of evolution.
Plants$_2$ (kingdom Vegetabilia) contain more than 300,000 species and divided in multiple subgroups (Figure 5.1.1).
Ranks are used to compare taxonomic groups (taxa) from different major groups. No precise definitions are available for particular ranks, but it is believed that they are
associated with the time of divergence (separation) between taxa. In addition to seven ranks mentioned above plant taxonomy uses intermediate ranks like subfamily, subclass or superorder—when taxonomic structure is too complicated.
Below is and example of names used for different ranks. Please note that names used for some ranks have standardized endings (underlined):
English Latin Example 1 Example 2
Kingdom Regnum Vegetabilia Animalia
Phylum Phylum Spermato Chordata
Class Classis Angiospermae (Magnoliopsida) Mammalia
Order Ordo Liliales Primates
Family Familia Asparagaceae Hominidae
Genus Genus Chlorophytum Homo
Species Species Chlorophytum comosum (Thunb.) Jacq. Homo sapiens L.
It is frequent when one species has several geographical races without clear borders between them. The example might be the stinging nettle, Urtica dioica. In North America, many nettles have narrower leaves and are less stinging than in Eurasia. However, there are many intermediate forms between these races. To reflect this, taxonomists introduced two subspecies: in this case, Urtica diuica subsp. dioica (“Eurasian”) and U.
dioica subsp. gracilis (“North American”). Another frequently used under-species category which is cultivar. Cultivars are frequently used in gardening. For example, many roses in cultivation belong to different cultivars of Rosa banksiae, and yellow roses are often Rosa banksiae cv. ‘Lutea’ where the last part of name is for the cultivar.
Names of species are binomials which consist of the name of genus and species epithet:
$\overbrace{\underbrace{\strut\mathrm{Chlorophytum}}_{\mbox{Name of genus}} \underbrace{\strut\mathrm{comosum}}_{\mbox{Species epithet}} \underbrace{\strut\mathrm{(Thunb.)}}_{\mbox{First author}} \underbrace{\strut\mathrm{Jacq.}}_{\mbox{Second author}} \underbrace{\strut 1862}_{\mbox{Year of description}}} ^{\mbox{ Name of species}}$
If one does not know the exact species, “sp.” shortcut is used instead of epithet, and “spp.” is used as a shortcut for multiple unknown species. It is required to use slanted font when one prints a name of species or genus. All scientific names are capitalized, but the second word in a species name (species epithet) always starts from lower case letter. It is a well-known fact that some species have a hybrid origin, and in these cases, botanists use a multiplication sign ($\times$). For example, common plum (Prunus $\times$domestica) is a hybrid between blackthorn and cherry plum: Prunus spinosa $\times$ Prunus cerasifera.
The group of plants or animals must have one and only one name. Ideally, the name should be a stable ID for all occasions. But since biology is a “science of exceptions”, some plant families are allowed to bear two names. As an example, legumes (Leguminosae) are frequently named “Fabaceae”, and grasses (Gramineae) have the second name “Poaceae”.
Throughout the long history of taxonomy, too many names were given to the same taxa. At the moment, we have almost 20,000,000 names to describe 2,000,000 species. These 18,000,000 “excess names” are synonyms which should not be used in science. To regulate the use of names, nomenclature codes were created. These codes specify, for example, the rule of priority: when two names are given for the same group, only earlier name is valid. Consequently, it is recommended to list the author and the year of description along with a name: “Homo sapiens L. 1758”, which means that founder of taxonomy, Carolus Linnaeus (“L.” shortcut) described this species in 1758.
Another important concept of nomenclature is the nomenclature type. Practically, this means that every species name must be associated with the physical museum specimen. In botany, these museums are collections of dried and pressed plants, called herbaria. Type specimens are of immense importance because there are no labels in nature, and only these specimens will “tell” about real plants or animals associated with particular names.
Names of taxa higher than species also have nomenclature types, but in these cases they are other names, not specimens. This example may clarify the use on nomenclature types. Initially, oleaster family (Elaeagnaceae) contained two genera, Elaeagnus (oleaster) and Hippophaë (sea-buckthorn). The second genus included Hippophaë rhamnoides (Siberian sea-buckthorn, type species) and Hippophaë canadensis (North American plant). Thomas Nuttall decided to split sea-buckthorns in two genera. Since one of them contains Hippophaë rhamnoides, the type species, it should keep the name Hippophaë. The second genus can be named arbitrarily. Nuttall gave it name “Shepherdia”. As a result, the species which had name Hippohaë canadensis L., became Shepherdia canadensis (L.) Nutt.
Plant taxonomy is a science. That means that our understanding of plant groups will always change. It also means that there always are different competing opinions, the taxonomic hypotheses which describe plant diversity in different ways. As a result, some groups of plants could be accepted in a broad sense, including as many subgroups as possible. For example, there might be an opinion of Homo sapiens s.l. (sensu lato = wide sense) including not only contemporary humans but also Neanderthal men. As a contrast, other opinions may accept groups in a strict sense, and Homo sapiens s.str. (sensu stricto = strict sense) includes only contemporary humans. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/01%3A_Introduction_to_the_Introduction/1.01%3A_Plants_Botany_and_Kingdoms.txt |
Life obtains energy in a few different ways: (1) from sunlight (phototrophy); (2) from chemical reactions with inorganic matter (lithotrophy); (3) from breaking organic molecules into inorganic molecules, typically carbon dioxide and water (organotrophy). To make its body, living beings obtain building blocks either by (a) from the assimilation of carbon dioxide (autotrophy), or from other living beings (heterotrophy).
These ways combine in six lifestyles. For example, plants$_1$ are by definition photoautotrophs. Most plants$_2$ are also photoautotrophs, but there are exceptions: full parasites (see above). Carnivorous plants (like sundew, Drosera or the Venus flycatcher, Dionaea) are all photoautotrophs. They “eat” animals in order to obtain nitrogen and phosphorus, so the dead bodies serve not as food but as a fertilizer. Note that plants are also organoheterotrophs like animals because in addition to photosynthesis, all plant cells can respire.
To understand life of plants, a basic knowledge of chemistry is needed. This includes knowledge of atoms (and its components like protons, neutrons and electrons), atomic weight, isotopes, elements, the periodic table, chemical bonds (ionic, covalent, and hydrogen), valence, molecules, and molecular weight. For example, it is essential to know that protons have a charge of $+1$, neutrons have no charge, and electrons have a charge of $-1$. The atomic weight is equal to the weight of protons and neutrons. Isotopes have the same number of protons but different number of neutrons; some isotopes are unstable (radioactive).
One of the most outstanding molecules is water. Theoretically, water should boil at much lower temperature, but it boils at 100$^\circ$C just because of the hydrogen bonds sealing water molecules. These bonds arise because a water molecule is polar: hydrogens are slightly positively charged, and oxygen is slightly negatively charged (Figure $1$).
Another important concept related to water is acidity. If in a solution of water, the molecule takes out proton (H$^+$), it is an acid. One example of this would be hydrochloric acid (HCl) which dissociates into H$^+$ and Cl$^-$. If the molecule takes out OH$^-$ (hydroxide ion), this is a base.
An example of this would be sodium hydroxide (NaOH) which dissociates into Na$^+$ and hydroxide ion.
To plan chemical reactions properly, we need to know about molar mass and molar concentration. Molar mass is a gram equivalent of molecular weight. This means that (for example) the molecular weight of salt (NaCl) could be estimated as $23 + 35$, which equals 58 units. Consequently, one mole of salt is approximately 58 grams. One mole of any matter (of molecular structure) always contains $6.02214078 \times 10^{23}$ molecules (Avogadro’s number).
The density of a dissolved substance is the concentration. If in 1 liter of distilled water, 58 grams of salt are diluted, we have 1M (one molar) concentration of salt. Concentration will not change if we take any amount of this liquid (spoon, drop, or half liter).
Depending on the concentration of protons in a substance, a solution can be very acidic. The acidity of a solution can be determined via pH. For example, if the concentration of protons is 0.1 M ($1 \times 10^{-1}$, which 0.1 grams of protons in 1 liter of water), this is an extremely acidic solution. The pH of it is just 1 (the negative logarithm, or negative degree of ten of protons concentration). Another example is distilled water. The concentration of protons there equals $1 \times 10^{-7}$ M, and therefore pH of distilled water is 7. Distilled water is much less acidic because water molecules dissociate rarely.
When two or more carbon atoms are connected, they form a carbon skeleton. All organic molecules are made of some organic skeleton. Apart from C, elements participate in organic molecules (biogenic elements) are H, O, N, P, and S. These six elements make four types of biomolecules: (1) lipids—hydrophobic organic molecules which do not easily dissolve in water; (2) carbohydrates or sugars, such as glucose (raisins contain lots of glucose) and fructose (honey); by definition, carbohydrates have multiple $-$OH group, there are also polymeric carbohydrates (polysaccharides) like cellulose and starch; (3) amino acids (components of proteins) which always contain N, C, O and H; and (4) nucleotides combined from carbon cycle with nitrogen (heterocycle), sugar, and phosphoric acid; polymeric nucleotides are nucleic acids such as DNA and RNA. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/01%3A_Introduction_to_the_Introduction/1.02%3A_Styles_of_Life_and_Basic_Chemistry.txt |
• 2.1: Introduction to Cells
In 1838, Schleidern and Schwann stated that (1) all plants and animals are composed of cells and that (2) cell is the most basic unit (“atom”) of life. In 1858, Virchow stated that (3) all cells arise by reproduction from previous cells (“Omnis cellula e cellula” in Latin). These three statements became the base of the cell theory. Discovery of cells is tightly connected with the development of microscopy.
• 2.2: Mitochondria and Chloroplasts
To escape from competition, cells which were prokaryotic became larger. To facilitate communication between all parts of this larger cell, they developed cytoplasm mobility using actin protein. In turn, this mobility resulted in acquiring phagocytosis, which is when a large cell changes shape and can engulf (“eat”) other cells. This way, cells that used to be prey became predators. These predators captured prey by phagocytosis and digested bacteria in lysosomes, which use enzymes that destroy th
• 2.3: Cell wall, Vacuoles, and Plasmodesmata
Plant cells do not have well-developed internal cytoskeleton, but cell wall provides an external one. There are two kinds (or, better, two stages of development) of cell walls, the primary and the secondary. The primary cell wall is typically flexible, frequently thin and is made of cellulose, different carbohydrates and proteins. The secondary cell wall contains also lignin and highly hydrophobic suberin. These chemicals completely block the exchange between the cell and the environment.
• 2.4: Other Parts of the Cell
The central dogma of molecular biology states that DNA will be converted into RNA by a process called transcription and RNA will be converted to protein by a process called translation. Translation in non-reversible whereas transcription could be reverted: there are viruses, such as HIV, that can make DNA from RNA with the enzyme called reverse transcriptase. The nuclear envelope is built from a double-layered membrane.
02: Symbiogenesis and the Plant Cell
In 1665, Robert Hooke looked at cork under a microscope and saw multiple chambers which he called “cells”. In 1838, Schleidern and Schwann stated that (1) all plants and animals are composed of cells and that (2) cell is the most basic unit (“atom”) of life. In 1858, Virchow stated that (3) all cells arise by reproduction from previous cells (“Omnis cellula e cellula” in Latin). These three statements became the base of the cell theory.
Discovery of cells is tightly connected with the development of microscopy. Nowadays, there are basically three kinds of microscopy: light microscopy, transmission electron microscopy (TEM), and scanning electron microscopy (SEM). Light microscopes use normal light, it can magnify transparent things 1,000 times. Transmission electron microscopes give a more detailed view of the internal organization of cells and organelles. They use an electronic beam, which kills objects as it passes through. In addition, for examination under a TEM, objects are often stained with heavy metals like osmium, and for SEM with gold which is highly reflective for electronic rays. A TEM can magnify things 10,000,000 times. Scanning electron microscopes show an image of the surface of cells and organisms using reflected electronic beam. It can magnify things 1,000,000 times. It is possible to see atoms on these photographs!
The minimal cell should have three things: protein-synthesizing apparatus (from DNA to RNA and proteins), space designated for all other chemical reactions (jelly-like cytoplasm) and the oily film separating cell from its environment (membrane). This is like fruit jelly covered with thin layer of butter; “fruit pieces” are protein-synthesizing parts.
The cell membrane of all cells has two layers. One end of each layer is polar and hydrophilic, while the other end is hydrophobic. These layers are made with phospholipids which are similar to typical lipids but have polar head with phosphoric acid, and two hydrophobic, non-polar tails (Figure \(2\)). Apart from phospholipinds, membrane contains embedded other lipids like cholesterol (in animal cells only) and chlorophyll (in some plant membranes), proteins and carbohydrates. Proteins are extremely important because without them, membrane does not allow large hydrophylic molecules and ions to came trough.
Cells which have DNA in a membrane-bound nucleus are known as eukaryotic, while those which do not are known as prokaryotic. Prokaryotic cells have their DNA surrounded by the cytoplasm. Some have also prokaryotic flagella (rotating protein structure), a cell wall, vesicles and membrane folds/pockets (Figure \(1\)). Eukaryotic cells have their DNA in a nucleus which separates it from the cytoplasm.
There are many other parts of the eukaryotic cell (Figure 3.2.1). The nucleus of the cell contains DNA and proteins. Nucleoli are in the nucleoplasm, this is the place where ribosomal RNAs are assembling. Ribosomes, found in the cytoplasm, help to synthesize proteins. The endoplasmic reticulum (ER), usually found near edge of the cell, is where proteins are synthesized, packaged and transported. In many cells, ER is connected with nucleus membrane. The Golgi apparatus directs proteins and other substances to the part of the cell where they need to go. Eukaryotic cells must have mitochondria and might have chloroplasts, both originated via symbiogenesis (see below). Mitochondria are covered with two membranes, the inner membrane has intrusions called cristae. Mitochondria break down organic molecules into carbon dioxide and water in a process known as oxidative respiration.
Cell membranes are semi-permeable (Figure \(3\)), they allow some molecules (typically small and/or non-polar) to go through but others (big and/or polar) will stay outside or inside forever, or until specific pore opens. Water always “wants” to equalize concentrations on both sides of membrane and water molecules typically flow through the membrane to where concentration of other molecules (salts, acids) is higher (and, naturally, concentration of water is lower). This is osmosis.
Cell wall (common in plants and fungi) surrounds the cell and limits how far the cell can expand due to osmosis (Figure \(4\)). Since osmosis may result in uncontrollable expansion of cell, cells without cell walls must find a way to pump out the excess water. Vacuole(s) is the large vesicle(s) which can do a variety of things for the cell, for instance store nutrients, accumulate ions, or become a place to store wastes. It plays an important role in the turgor (Figure \(4\)). | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/02%3A_Symbiogenesis_and_the_Plant_Cell/2.01%3A_Introduction_to_Cells.txt |
To escape from competition, cells which were prokaryotic became larger. To facilitate communication between all parts of this larger cell, they developed cytoplasm mobility using actin protein. In turn, this mobility resulted in acquiring phagocytosis, which is when a large cell changes shape and can engulf (“eat”) other cells. This way, cells that used to be prey became predators. These predators captured prey by phagocytosis and digested bacteria in lysosomes, which use enzymes that destroy the cytoplasmic components of the bacterial cells.
The threat of predators result in cells became even larger, and these cells will need a better supply of ATP. Some prey which were not digested, and turned out to be useful in providing ATP. Of course, predator cells should also invent a proper transport through the resulted double membrane! Due to natural selection, those prey, which were purple bacteria, became the cell’s mitochondria. This is symbiogenesis, or the formation of two separate organisms into a single organism (Figure \(2\)).
Another result of a larger cell (eukatyotic cells are typically 10–100 fold larger than prokaryotic) is that the size of DNA will increase, and to hold it, the cell will form a nucleus. The new predator cells also needed to prevent alien organisms from transferring their genes which will delay the evolution.
The other reason is that the nucleus protects the DNA by enclosing it; in case if DNA virus comes into the cell and tries to mock up cell DNA, eukaryotic cell immediately destroys any DNA found in the cytoplasm. One more reason to make nucleus is pressure of antibiotics: nucleus improves isolation from these harmful chemicals. Nucleus formation and symbiogenesis leaded cells to become eukaryotic.
To be called an eukaryote, it is more important to have phagocytosis and mitochondria then nucleus because (1) nucleus is not always exists, it could disappear during the division of cell and (2) some prokaryotes (planctobacteria) also have membrane compartments containing DNA.
On next step, some eukaryotes also captured cyanobacteria (or another photosynthetic eukaryote), which became chloroplasts. These photosynthetic protists are called algae.
In all, eukaryotic cells are “second-level cells” because they are cells made up of multiple cells. Cells of all eukaryotes have two genomes, nuclear usually has biparental origin whereas mitochondial genome normally originates only from mother. Plant cells, in turn, have three genomes, and chloroplast genome is usually also inherited maternally.
Chloroplasts synthesize organic compounds whereas mitochondria produce most of the cytoplasmic ATP. Both organells are covered with two membranes and contain circular DNA and ribosomes similar to bacterial. Chloroplasts have thylakoids, or inner membrane pockets and vesicles. Chloroplast thylakoids could be long (lamellae) or short and stacked (granes). In turn, mitochondria could be branched and inter-connecting.
Chloroplasts are normally green because of chlorophyll which converts light energy into chemical energy. Some chloroplasts lose chlorophyll and become transparent, “white”, they are called leucoplasts. Other chloroplasts could be red and/or orange (chromoplasts), because they are rich of carotenes and xanthophyls. These pigments facilitate photosynthesis and are directly responsible for the fall colors of leaves. Since starch is a more compact way of storing energy than glucose, chloroplasts store carbohydrates as starch grains. Transparent amyloplasts contain large granules of starch. Storage tissues of potato tubers, carrot roots, sweet potato roots, and grass seeds are examples of tissues rich in amyloplasts.
Having chloroplasts and cell walls are not directly connected, but almost all organisms with chloroplasts have also cell walls. Probably, this is because cell walls do not facilitate cell motility, and for those protists which already have cell walls, obtaining chloroplast will be the nice way for coming out of competition with organotrophic beings. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/02%3A_Symbiogenesis_and_the_Plant_Cell/2.02%3A_Mitochondria_and_Chloroplasts.txt |
Among eukaryotic cells, plant cells are largest. Some of them (for example, cells from green pepper and grapefruit) are well visible with the naked eye. Plant cells do not have well-developed internal cytoskeleton, but cell wall provides an external one. There are two kinds (or, better, two stages of development) of cell walls, the primary and the secondary. The primary cell wall is typically flexible, frequently thin and is made of cellulose, different carbohydrates and proteins. The secondary cell wall contains also lignin and highly hydrophobic suberin. These chemicals completely block the exchange between the cell and the environment which means that the cell with secondary wall will soon die. Dead cells can still be useful to plants in many ways, for example as a defense against herbivores, support and water transport. In fact, more than 90% of wood is dead.
Since every plant cell is surrounded with a cell wall, they need a specific way of communication. This is done through plasmodestata—thin cytoplasmic bridges between neighbor cells. A symplast is the name of continuous cytoplasm inside of cells. An apoplast is cell walls and space outside the cell where communication and considerable metabolic activity take place. Both the symplast and apoplast are important to the transportation of nutrients needed by the cell (Figure \(1\)).
If cells are surrounded by a smaller concentration of salts than in the cytoplasm, the water will flow into the cell. This process is called osmosis. In plant cells, most of the water with diluted chemicals is concentrated in vacuole(s). Turgor pressure is the combined pressure of the cell and vacuoles wall that supports the shape of cell (Figure 3.1.4).
You may think of plant tissue as about staked cardboard boxes where every box is made from wet cardboard paper (cell wall) but has the inflated balloon (vacuole) inside, and when the pressure of vacuole decreases (water deficit), plant organs droop. Please see the video http://ashipunov.info/shipunov/school/biol_154/mov/balloon.mp4 to understand this better.
Comparing with animal cells, plant cells have chloroplasts, vacuoles, cell walls, and plasmodesmata but they hardly have any phagocytosis and true cytoskeleton (Figure \(2\)). They are easy to explain: animals do not photosynthesize (no chloroplasts), instead, they need to move quickly (no cell walls and plasmodesmata); animals will support the shape of cell from cytoskeleton (no need for vacuole turgor system) and use molecular pumps to counterpart the osmosis.
2.04: Other Parts of the Cell
Protein Synthesis: from the Nucleus to the Ribosomes
The central dogma of molecular biology states that DNA will be converted into RNA by a process called transcription and RNA will be converted to protein by a process called translation. Translation in non-reversible whereas transcription could be reverted: there are viruses, such as HIV, that can make DNA from RNA with the enzyme called reverse transcriptase. The nuclear envelope is built from a double-layered membrane. The inner and outer membranes of the nuclear envelope connect to form pores which are complicated structures controlling travel between the nucleus and the cytoplasm. Inside of the nuclear envelope there is the nucleoplasm.
Nuleoplasm contains chromatin (chromosomes). Chromosomes store genetic information in the form of DNA molecules. Each chromosome consists of a chain of nucleosomes, which are condensed long DNA molecules and their associated histone proteins. Chromatin is just another word for non-condensed chromosomes. Visible parts of chromatin (globules, filaments) correspond with non-functional DNA.
Ribosomes, which are particles that contain RNA and proteins, synthesize proteins. The rough endoplasmic reticulum (RER) has ribosomes along its surface, and the proteins they create are either secreted or incorporated into membranes in the cell. The Golgi apparatus (AG) is made of membranous sacs which are flattened and stacked, it modifies, packages, and sorts proteins and carbohydrates for the cell; this is not an essential component of cell.
Other Vesicles
Plant cells frequently have smaller vesicles: lysosomes which digest organic compounds and peroxisomes which, among other functions, help in photosynthesis (see above). In addition, many plant cells accumulate lipids as oil drops located directly in cytoplasm.
Cellular Skeleton
The cellular skeleton is a collection of protein filaments within the cytoplasm. Microtubules are key organelles in cell division, they form the basis for cilia and flagella and are guides for the construction of the cell wall. Cellulose fibers are parallel due to the microtubules. The movement in microtubules is based on tubulin-kinesin interactions. In contrast, the movement of microfilaments is based on actin-myosin interactions. Microfilaments guide the movement of organelles within the cell. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/02%3A_Symbiogenesis_and_the_Plant_Cell/2.03%3A_Cell_wall_Vacuoles_and_Plasmodesmata.txt |
• 3.1: Discovery of Photosynthesis
The history of the studies done on photosynthesis dates back into the 17th century with Jan Baptist van Helmont. He rejected the ancient idea that plants take most of their biomass from the soil.
• 3.2: Light Stage
The light stage participants include photosystems (“chlorophyll”), light, water, ATPase, protons, and a hydrogen carrier (NADP+). The basic idea of light stage is that the cell needs ATP to assemble (later) carbon dioxide into sugar. To make ATP, the cell needs electrical current: proton pump. To make this current, the cell needs the difference of electric charge (difference of potentials) between thylakoid (vesicle or membrane pocket) and matrix (stroma) compartments of the chloroplast.
• 3.3: Enzymatic Stage
The enzymatic stage has many participants. These include carbon dioxide, hydrogen carrier with hydrogen (NADPH), ATP, ribulose biphosphate (RuBP, or C 5 ), and Rubisco along with some other enzymes. Everything occurs in the matrix (stroma) of the chloroplast.
• 3.4: C₄ Pathway
Rubisco is the enzyme of extreme importance since it starts the assimilation of carbon dioxide. Unfortunately, Rubisco is “two-faced” since it also catalyzes photorespiration. Photorespiration means that plants take oxygen instead of carbon dioxide. Rubisco catalyzes photorespiration if there is a high concentration of oxygen (which usually is a result of intense light stage).
• 3.5: True Respiration
The common misconception about plants is that their only energy-related metabolic process is photosynthesis. However, as most eukaryotes, plants have mitochondria in cells and use aerobic (oxygen-related) respiration to obtain energy. Typically, plants spend much less oxygen in respiration than they make in photosynthesis. However, at nights plants do exactly the same as animals, and make only carbon dioxide!
Thumbnail: Plant cells with visible chloroplasts (from a moss, Plagiomnium affine). Image used with permission (CC BY SA 3.0 Unported; Kristian Peters).
03: Photosynthesis
The history of the studies done on photosynthesis dates back into the 17th century with Jan Baptist van Helmont. He rejected the ancient idea that plants take most of their biomass from the soil. For the proof, he performed willow tree experiment. He started with a willow tree of 2.27 kg. Over 5 years, it grew to 67.7 kg. However, the weight of the soil only decreased by 57 grams. Van Helmont came to the conclusion that plants must take most of their weight from water. He did not know about gases.
Joseph Priestley ran a series of experiments in 1772 (Figure $1$). He tested a mouse, a candle, and a sprig of mint under hermetically sealed (no air can go in or out) jar. He first observed that a mouse and a candle behave very similarly when covered, in that they both “spend” the air. However, when a plant is placed with either the candle or mouse, the plant “revives” the air for both.
Further ideas were brought about in the late 1700’s. Jan Ingenhousz and Jean Senebier found that the air is only reviving in the day time and that CO$_2$ is assembled by plants. Antoin-Laurent Lavoiser found that “revived air” is a separate gas, oxygen.
But what is the oxygen “maker”? There are many pigments in plants, and all accept and reflect some parts of rainbow. To identify the culprit, Thomas Engelmann ran an experiment (Figure $2$) using a crystal prism. He found that Spirogyra algae produce oxygen mostly in the blue and red parts of the spectrum. This was a huge find. It tells that the key photosynthetic pigment should accept blue and red rays, and thus reflect green rays. Blue-green chlorophyll best fits this description.
Another important fact was discovered by Frederick Blackman in 1905. He found that if light intensity is low, the increase of temperature actually has very little effect on the rate of photosynthesis (Figure $3$). However, the reverse is not exactly true, and light is able to intensify
photosynthesis even when it is cold.
This could not happen if light and temperature are absolutely independent factors. If temperature and light are components of the chain, light was first (“ignition”) and temperature was second. This ultimately shows that photosynthesis has two stages. The first is a light stage. This stage relates to the intensity of the light. The second stage is the enzymatic (light-independent) stage which relates more with the temperature. Light reactions depend on the amount of light and water; they produce oxygen and energy in the form of ATP. Enzymatic reactions depend on carbon dioxide and water; they take energy from the light reactions and produce carbohydrates. Sometimes, enzymatic stage is called “dark” but it is not correct because in darkness, plant will run out of light-stage ATP almost immediately. Only some C$_4$-related processes (see below) could run at night.
Since water molecules are spent on light stage to make oxygen and at the same time are accumulating (see below), one of the best “equations” describing photosynthesis as a whole is ${CO}_2 + {H}_2{O} + {light} \rightarrow {carbohydrates} + H_2O + O_2$ | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/03%3A_Photosynthesis/3.01%3A_Discovery_of_Photosynthesis.txt |
The light stage participants include photosystems (“chlorophyll”), light, water, ATPase, protons, and a hydrogen carrier (NADP\(^+\)).
The basic idea of light stage is that the cell needs ATP to assemble (later) carbon dioxide into sugar (Figure \(2\)). To make ATP, the cell needs electrical current: proton pump. To make this current, the cell needs the difference of electric charge (difference of potentials) between thylakoid (vesicle or membrane pocket) and matrix (stroma) compartments of the chloroplast (Figure 2.3.1). To make this difference, the cell needs to segregate ions: positively charged go from outside and stay inside, negatively charged go from inside to outside. To segregate, the cell needs the energy booster—sun rays caught by the chlorophyll molecules embedded in the thylakoid membrane. The chlorophyll molecule is non-polar (similarly to membrane lipids) and contains magnesium (Mg). It is easy to excite the chlorophyll molecule with light; excited chlorophyll may release the electron if the energy of light is high enough.
To make carbohydrates from carbon dioxide (CO\(_2\) apparently has no hydrogen), the cell needs hydrogen atoms (H) from hydrogen carrier, NADP+ which at the end of light stage, becomes NADPH.
The main event of the light stage is that chlorophyll reacts with light, yielding electron (\(e^-\)) and becoming oxygenated, positively charged molecule. Then electron, proton and NADP\(^+\) react to yield NADPH which will participate in enzymatic reactions later on. The positively
charged chlorophyll is extremely active chemically, therefore it splits water molecules (“photolysis of water”) into protons (which accumulate inside thylakoid), oxygen (O\(_2\)) and electron. The electron returns to chlorophyll. When increasing gradient reaches the threshold, the proton pump starts to work as protons (H\(^+\)) pass along the gradient. The energy of passing protons allows for the ATP synthesis from ADP and P\(_i\) (inorganic phosphate). On the other side of membrane, these protons make water with hydroxide ions.
In the previous paragraph, “chlorophyll” is actually two photosystems: photosystem II (P680) and photosystem I (P700). Photosystem II (contains chlorophyll and carotenes) is more important. It splits water, makes proton the gradient and then ATP, and forwards electrons to photosystem I. Photosystem I contains only chlorophylls and makes NADPH.
Ultimately, the light stage starts from light, water, NADP\(^+\), ADP and results in an accumulation of energy (ATP) and hydrogen (NADPH) with a release of oxygen which is a kind of exhaust gas (Figure 2.3.1).
3.03: Enzymatic Stage
The enzymatic stage has many participants. These include carbon dioxide, hydrogen carrier with hydrogen (NADPH), ATP, ribulose biphosphate (RuBP, or \(\ce{C5}\)), and Rubisco along with some other enzymes. Everything occurs in the matrix (stroma) of the chloroplast.
The main event of the enzymatic stage is \(\ce{CO2}\) assimilation with \(\ce{C5}\) into short-living \(\ce{C6}\) molecules. Assimilation requires Rubisco as an enzyme. Next, this temporary \(\ce{C6}\) breaks into two \(\ce{C3}\) molecules (PGA). Then, PGA will participate in the complex set of reactions which spend NADPH and ATP as sources of hydrogen and energy, respectively; and yields (through the intermediate stage of PGAL) one molecule of glucose (\(\ce{C6H12O6}\)) for every six assimilated molecules of \(\ce{CO2}\). NADP\(^+\), ADP and P\(_i\) will go back to the light stage. This set of chemical reactions returns RuBP which will start the new cycle of assimilation. Consequently, all reactions described in this paragraph are part of the cycle which has the name “Calvin cycle” or “\(C_3\) cycle” (because the C\(_3\) PGA molecules here are most important).
In all, enzymatic stage starts with \(\ce{CO2}\), NADPH, ATP and \(\ce{C5}\) (RuBP). It ends with glucose (\(\ce{C6}\)H\(_{12}\)O\(_6\)), NADP+, ADP, P\(_i\) and the same \(\ce{C5}\). With an addition of nitrogen and phosphorous, glucose will give all other organic molecules (Figure \(3\)).
To summarize, the logic of photosynthesis (Figure \(4\)) is based on a simple idea: make sugar from carbon dioxide. Imagine if we have letters “s”, “g”, “u”, and “a” and need to build the word “sugar”. Obviously, we will need two things: the letter “r” and the energy to put these letters in the right order. The same story occurs in photosynthesis: it will need hydrogen (H) which is the “absent letter” from \(\ce{CO2}\) because sugars must contain H, O and C. NADP\(^+\)/NADPH is used as hydrogen supplier, and energy is ATP which is created via proton pump, and the proton pump starts because light helps to concentrate protons in the reservoir. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/03%3A_Photosynthesis/3.02%3A_Light_Stage.txt |
Rubisco is the enzyme of extreme importance since it starts the assimilation of carbon dioxide. Unfortunately, Rubisco is “two-faced” since it also catalyzes photorespiration (Figure $1$). Photorespiration means that plants take oxygen instead of carbon dioxide. Rubisco catalyzes photorespiration if there is a high concentration of oxygen (which usually is a result of intense light stage). Rubisco oxygenates C$_5$ (RuBP) which turns into PGA and PGAL, becoming glycolate. This glycolate is returned to the Calvin cycle when the cell uses peroxisomes and mitochondria, and spends ATP. The process of photorespiration wastes C$_5$ and ATP which could be more useful to the plant in other ways.
If concentration of CO$_2$ is high enough, assimilation will overcome photorespiration. Consequently, to minimize the amount of photorespiration and save their C$_5$ and ATP, plants employ Le Chatelier’s principle (“Equilibrium Law”) and increase concentration of carbon dioxide. They do this by temporarily bonding carbon dioxide with PEP (C$_3$) using carboxylase enzyme; this results in C$_4$ molecules, different organic acids (like malate, malic acid) with four carbons in the skeleton. When plant needs it, that C$_4$ splits into pyruvate (C$_3$) plus carbon dioxide, and the release of that carbon dioxide will increase its concentration. On the final step, pyruvate plus ATP react to restore PEP; recovery of PEP does cost ATP. This entire process is called the “C$_\mathbf{4}$ pathway” (Figure $2$).
Plants that use the C$_4$ pathway waste ATP in their effort to recover PEP, but they still outperform photorespiring C$_3$-plants when there is an intensive light and/or high temperature and consequently, high concentration of oxygen. This is why in the tropical climate, C$_4$-crops are preferable.
Two groups of plants use the C$_4$ pathway. Many desert or dryland plants are CAM-plants which drive the C$_4$ pathway at night. They make a temporal separation between the accumulation of carbon dioxide and photosynthesis. CAM-plants make up seven percent of plant diversity, and have 17,000 different species (for example, pineapple (Ananas), cacti, Cactaceae; jade plant, Crassula and their relatives).
“Classic” C$_4$ plants drive C$_4$ pathway in leaf mesophyll cells whereas their C$_3$ is located in so-called bundle sheath cells. This is a spatial, rather than temporal separation. These C$_4$-plants make up three percent of plant biodiversity and have more than 7,000 different species (for example, corn, Zea; sorghum, Sorghum and their relatives). In all, both variants of C$_4$ pathway relate with concentration of carbon dioxide, spatial or temporal (Figure $3$). Both are called “carbon-concentrated mechanisms”, or CCM.
There are plants which able to drive both C$_3$ and C$_4$ pathways (like authograph tree, Clusia), and plants having both “classic” C$_4$ and CAM variants (like Portulacaria).
3.05: True Respiration
The common misconception about plants is that their only energy-related metabolic process is photosynthesis:
CO$_2$ + H$_2$O + energy $\longrightarrow$ carbohydrates + O$_2$
However, as most eukaryotes, plants have mitochondria in cells and use aerobic (oxygen-related) respiration to obtain energy:
carbohydrates + O$_\mathbf{2}$ $\longrightarrow$ CO$_\mathbf{2}$ + H$_\mathbf{2}$O + energy
Typically, plants spend much less oxygen in respiration than they make in photosynthesis. However, at nights plants do exactly the same as animals, and make only carbon dioxide! | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/03%3A_Photosynthesis/3.04%3A_C_Pathway.txt |
• 4.1: Mitosis and the Cell Cycle
Mitosis is a process of equal cell division, where each of the new cells receives the same number of chromosomes as the original cell. Mitosis does not change the cells’ genotype. The goal of mitosis is to distribute pre-combined genetic material equally. Actually, mitosis is a kind of karyokinesis, or splitting of the nucleus, as opposed to cytokinesis, which is the splitting of the whole cell. Karyokinesis and cytokinesis are parts of the cell cycle.
• 4.2: Syngamy and Meiosis
A sexual process is important to the survival of a species. First, it makes the population more diverse, which allows more flexibility to adapt via natural selection. Natural selection means that all organisms are different, but if environmental conditions change, only most adapted will survive. If the population is uniform, it has less chance of survival. Second, it prevents lethal mutations from being transferred to the offspring, because those with the mutations will die and not pass on genes
• 4.3: Life Cycle of the Unicellular Eukaryote
The life cycle of a unicellular organism begins with syngamy: one cell unites with cell having different genotype. The life cycle has all three possible ways of reproduction: sexual (ploidy doubles: syngamy), asexual (ploidy reduces: meiosis of zygote) and vegetative (ploidy does not change: mitotic divisions)
• 4.4: Life Cycle of the Multicellular Eukaryote
Cells do not always part after mitosis, but sometimes stay together to form multicellular organisms. Cells in the multicellular body are not connected forever. Sometimes, one or few cells escape and start a new body. This body will be exact copy (clone) of the previous one (vegetative reproduction). It is also possible that when these “escaped cells” go the different route: they become “sex delegates”, gametes.
Thumbnail: Principal scheme of meiosis. Only one of two telophase I variants is shown.
04: Multicellularity the Cell Cycle the Life Cycle
Mitosis is a process of equal cell division, where each of the new cells receives the same number of chromosomes as the original cell. Mitosis does not change the cells’ genotype. The goal of mitosis is to distribute pre-combined genetic material equally. Actually, mitosis is a kind of karyokinesis, or splitting of the nucleus, as opposed to cytokinesis, which is the splitting of the whole cell. Karyokinesis and cytokinesis are parts of the cell cycle.
All prokaryotes (Monera) have a simple cell division called “binary fission”. DNA duplicates (replication), segregates and then cell splits in two (Figure $1$).
Eukaryotes have much more DNA than prokaryotes. This is why their cell division is more complicated. There are four stages: prophase, metaphase, anaphase, and telophase. Prophase is the longest, nucleus disintegrates (except some protists like fungi) and the DNA is super-spiralized into chromosomes (“archived”). In metaphase, the chromosomes go to the cell equator, and every “double”, “X-like” chromosome is then split in two halves which schematically can be shown as
$X \rightarrow I + I$
In anaphase, microtubules move these $I$-like chromosomes to different poles of the cell. In telophase, the endoplasmic reticulum will form nuclear envelopes and DNA despiralizes (Figure $2$).
Figure $1$ Binary fission of prokaryotes.
When mitosis is over, cell starts to divide (cytokinesis). Plant$_2$ cells use vesicles to form the border whereas many protists and animals form a constriction which finally separates two cells. Normally, chloroplasts and mitochodria are equally distributed between daughter cells along with the other cell content. Chloroplasts and mitochondria may also independently divide in “bacterial” (binary fission) way.
Mitosis is the part of the bigger cell cycle (Figure 4.2.1). Cell cycle includes pre-synthetic stage, synthetic stage, post-synthetic stage (they are parts of interphase), karyokinesis (= mitosis) and finally cytokinesis. Apart from mitosis and cytokinesis, the most important stage of cell cycle is the synthetic stage (S-stage) when every DNA molecule (despiralized chromosome) duplicates: $I \rightarrow X$
To simplify understanding of these numerous stages, one could use the following scheme. Cell cycle here has three main phases, and mitosis has four subphases:
Figure $2$ Principal scheme of mitosis. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/04%3A_Multicellularity_the_Cell_Cycle__the_Life_Cycle/4.01%3A_Mitosis_and_the_Cell_Cycle.txt |
Sexual Process and the Syngamy
A sexual process is important to the survival of a species. First, it makes the population more diverse, which allows more flexibility to adapt via natural selection. Natural selection means that all organisms are different, but if environmental conditions change, only most adapted will survive. If the population is uniform, it has less chance of survival. Second, it prevents lethal mutations from being transferred to the offspring, because those with the mutations will die instead of passing on these genes. The later happens when the mutated gene is either duplicated or alone in genotype.
(Genotype is a gene content of the organism. A gene is a piece of DNA, which is equal to one protein. A mutation is a “mistake” in DNA. A protein (many of them are enzymes) is made up of amino acids chained together. A population is a group of organisms which potentially may interbreed and have no isolation barriers.)
Figure $1$ Cell cycle: I interphase, D cell division, G$_1$ pre-synthetic stage, S synthetic stage, G$_2$ post-synthetic stage, M mitosis (karyokinesis), C cyto
To make populations more diverse, organisms need to exchange DNA. One way that cells exchange genes is through syngamy. Syngamy (frequently labeled by “Y!”), is the fusion of two cells, resulting in a cell that has twice as many chromosomes. The two cells which are fused together are called gametes, and the resulting cell is a zygote. The goal of syngamy is the renovation of genetic material. The new cells have genotype different from the gametes. Continuous syngamy will increase the amount of DNA, so cells use meiosis (frequently labeled by “R!”) to counterbalance this side-effect of syngamy: $\mbox{Y!} \rightarrow \mbox{R!}$
Syngamy results in diploid cell:
$X + X \rightarrow XX$
In diploid organisms, chromosomes form pairs (these paired chromosomes are known as homologous), whereas in halploid organisms they remain single.
There are three types of syngamy (Figure $2$): isogamy, heterogamy, and oogamy.
• Isogamy happens when the gametes that fuse together are similar. To avoid self-fertilization, they must have an advanced system of recognition. Different genotypes (mating types) recognize each other with the help of surface proteins, like cells of immune system.
• Heterogamy is when the gametes are of two different sizes. This difference makes rec848ognition easier, but even more important is division of labor: the female is larger because it has resources to care for the offspring, whereas the males are smaller and can increase in number to allow competition and make fertilization more likely.
• Oogamy is when the gametes also have different mobility. In oogamy, the non-motile female is known as the oocyte, and the flagellate male as the spermatozoon, which is only one mobile gamete here. In some organisms (red algae, sponges, crustaceans, most seed plants), spermatozoon become non-motile spermatium so it will need external agents to move it. Both spermatozoa and spermatia are called sperms.
Figure $2$ Three types of syngamy.
Meiosis
Syngamy is the way for organisms to become more genetically diverse, but since it increases the amount of chromosomes, it needs to be balanced by meiosis. Meiosis reduces the number of chromosomes, recombines the chromosomes, and allows chromosomes to exchange their genetic material. Meiosis is a reductive form of cell division, where each new cell receives half of the original cell’s chromosomes. Unlike mitosis, meiosis does change the genotype of cells because whole chromosomes are recombined and also exchanged their genetic material. Another difference is that in mitosis, ploidy (“twoness” of chromosomes) stays constant, while in meiosis, ploidy halves.
There are two problems of meiosis: first, how to find out which chromosomes are homologous; and second, how to split chromosomes which were already duplicated in S-phase. First problem is solving with “gluing” homologous chromosomes together; this happens because similar chains of DNA can attach each other. Second problem is usually solving with the second stage of meiosis which is quite similar to ordinary mitosis.
There are two stages of meiosis: a reductive division (meiosis I, unique) and an equal division (meiosis II, similar to mitosis). Each of these stages are divided into prophase, metaphase, anaphase, and telophase.
In prophase I, chromosomes conjugate (form synapses), and start to exchange DNA (crossing-over).
In anaphase I, chromosomes from each pair will go independently to different poles. Independence means that if we label “mother” and “father” chromosomes with, saying $a$ and $b$, then two variants are possible:
$X{_a}X{_b} + Y{_a}Y{_b} \rightarrow (X{_a} + Y{_a}) + ({X_b} + Y{_b})$
or
$X{_a}X{_b} + Y{_a}Y{_b} \rightarrow (X{_a} + Y{_b}) + ({X_a} + Y{_b})$
because chromosomes do not know which is “father’s” and which is “mother’s”.
Telophase I usually flows into prophase II. This second division of meiosis is very similar to mitosis without synthetic stage before it. Frequently, nuclei do not form until telophase II (Figure $3$).
In the first division, cell needs to split pairs of homologs to reduce ploidy. The second division of meiosis is necessary because DNA was already duplicated in the synthetic stage of the cell cycle. Consequently, every $X$-like chromosome needs to be split into two $I$-like chromosomes: $XX \rightarrow X + X \rightarrow I + I + I + I$
This is why there are two divisions and four cells in the end (sometimes, however, only one of these four survives). If DNA would not be duplicated before, it is also possible for meiosis to happen in one stage instead of two. This kind of meiosis is described in some protists. Inverted meiosis, when reductive division is the second and equal the first, is rare but also exists in nature (e.g., in some rushes, bugs and butterflies).
Figure $3$ Principal scheme of meiosis. Only one of two telophase I variants is shown.
It is possible that meiosis won’t work properly, which results in a cell receiving a double set of chromosomes. If, in turn, that cell goes to syngamy, the resulting zygote will have 3 sets of chromosomes. Cells with more than two sets of chromosomes are called polyploids. Rarely, only some chromosome pairs do not want to split. In this case, after the syngamy, some chromosomes will be “triplicated” (trisomy). This is aneuploidy. One example of frequent (1/800 births) aneuploidy in humans is Down syndrome.
4.03: Life Cycle of the Unicellular Eukaryote
The life cycle of a unicellular organism begins with syngamy: one cell unites with cell having different genotype. To recognize each other, cells which are going to fuse (gametes) frequently use surface proteins, like cells of our immune system. If these proteins are same (same genotype), gametes will not fuse. Two fused gametes form a zygote, new diploid organism. Many unicellular protists use a zygote as a wintering stage. On spring, zygote splits with meiosis, and four haploid spores start four new organisms which reproduce all summer with mitosis (vegetative reproduction, cloning):
$X+X \rightarrow XX \rightarrow I+I+I+I \rightarrow X \rightarrow I+I \rightarrow ...$
Despite its simplicity, this life cycle has all three possible ways of reproduction: sexual (ploidy doubles: syngamy), asexual (ploidy reduces: meiosis of zygote) and vegetative (ploidy does not change: mitotic divisions). To mark these ways of reproduction, we will use “R!” shortcut for the meiosis, and “Y!” shortcut for syngamy (Figure $1$). It should be noted that before every mitosis (and meiosis), cell DNA goes through duplication (S-stage of the cell cycle).
Figure $1$ The life cycle of unicellular eukaryote. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/04%3A_Multicellularity_the_Cell_Cycle__the_Life_Cycle/4.02%3A_Syngamy_and_Meiosis.txt |
Origin of Death
Cells do not always part after mitosis, but sometimes stay together to form multicellular organisms. This increases their size, and hence provides a defense against predators. Unfortunately, it is not possible simply to increase the size of cell because the really big cell will have less surface (in relation to the volume), therefore it will have multiple difficulties with photosynthesis, respiration and other processes which relate with surface of cell. But many cells together will make surface big enough (Figure \(1\)). Multicellular organism has two modes of growth: scaling the body and multiplying cells.
Figure \(1\) Origin of multicellularity. It is not feasible just to enlarge cell, surface is too small. But if cells do not part after mitosis, they might form the body which is big enough to escape from predators. This also provide with new mode of growth and possibility of the division of labor (colored cells).
Multicellularity allows these cells also to divide the labor and cooperate. This is extremely important for the future evolution.
Cells in the multicellular body are not connected forever. Sometimes, one or few cells escape and start a new body. This body will be exact copy (clone) of the previous one (vegetative reproduction). It is also possible that when these “escaped cells” go the different route: they become “sex delegates”, gametes. All gametes want syngamy, and these cells will search for the partner of the same species but with another genotype. In case of heterogamy and oogamy, it is easy to recognize because genders will provide a hint: male will search for the female. In case of isogamy, gametes search for the partner with different surface proteins. After they finally mate, a diploid cell (zygote) appears. Zygote may winter and then divide meiotically. This is the simplest life cycle of multicellular organism (Figure \(2\)), quite similar to the cycle discussed above for unicellular organism.
Figure \(2\) Most ancient life cycle of the multicellular organism. Zygote does not grow, it divides meiotically. Somatic (“grey”) cells are going to die, only germ cells transfer their DNA to future generations.
However, frequently zygote starts to grow and divide mitotically, making the diploid body. There are two reasons to make multicellular body out of zygote without meiosis: (a) because in can and (b) because diploid is better. “It can” because zygote already contains DNA program about how to build multicellular body. Why diploid is better, explained in next section.
If multicellular organism consists of diploid cells (\(2n\)), we will use the neutral term diplont. Multicellular organisms with haploids cells (\(n\)) are haplonts.
“Escaped cells”, “sex delegates”, or mother cells of gametes from the above is a first stage of the division of labor when cells are separating into two types, germ cells and somatic cells. Somatic cells are those which will eventually die, but germ cells are capable of giving offspring. Having germ cells is not absolutely necessary for multicellular organisms, but most of them have well separated germ lines. Thus, origin of death is directly connected with this separation: somatic cells are not needed for future generations. Unicellular organisms are potentially immortal, and same are cancer cells which also escape from organism (but they cannot make the new one).
Life cycle of multicellular organism could be described starting from haplont (Figure \(3\)). When environment conditions are favorable, it has vegetative reproduction. One variant of vegetative reproduction is that cell (mitospore) separates itself from a haplont, then divides into more cells and becomes a new haplont. Sometimes, whole chunks are separated and grow into new haplonts. When conditions change, haplont may start the sexual reproduction: syngamy. In syngamy, one gamete separates from the haplont and unites with a gamete from another haplont. Together, gametes form a zygote. This zygote might go straight to meiosis (as it happens in unicellular eukaryotes) but more frequently, zygote will grow, divide mitotically and finally becomes a diplont. This diplont might be superficially almost identical to haplont but every cell of it contains diploid nucleus (every chromosome has a pair). Diplont (similarly to haplont) may reproduce itself vegetatively (make clones): cell separates itself from a diplont, then divides mitotically into more cells and becomes a new diplont.
The diplont is also capable for asexual reproduction: there could be a cell separates itself from a diplont and divides with meiosis creating four spores, each of them will grow into haplont.
Figure \(3\) General life cycle. Haploid part is on the left, diploid on the right, syngamy on the top, meiosis on the bottom. "M" letter is used to label mitosis.
Sporic, Zygotic and Gametic Life Cycles
The life cycle described above is the sporic life cycle (Figure \(4\)). Organisms with sporic life cycle have both diplont and haplont, equally or unequally developed.
Figure \(4\) Sporic life cycle. Overview. Haploid part is on the left, diploid on the right, syngamy on the top, meiosis on the bottom.
In all, there are three types of life cycles: sporic, zygotic, which is the most similar to unicellular and most primitive; and gametic, which is used by animals and a few protists (Figure \(5\)). The zygotic life cycle starts with syngamy and goes to meiosis. It has no diplont. Gametic life cycle goes from meiosis to syngamy. It has no haplont.
Protists have all three types of life cycles whereas higher groups have only one. Animals exhibit gametic cycle, whereas plants\(_2\) retained the more primitive sporic cycle.
Evolution of Life Cycles
The most striking difference between unicellular and multicellular life cycles is that zygote of multicellular organism may start to make diploid body (diplont) which sometimes is visually almost identical to haplont. This is because in the evolutionary perspective, diplonts are “better” than haplonts. Frequent situation of gene dominance allows only one variant (allele) of the gene to work, that may save organism from lethal mutations. An increased number of genes could help to make more proteins. A third reason is that diplonts’ genomes are more diverse. One gene may be able to withstand one group of conditions, and the other variant may have a different set of possible conditions. Therefore, diplont is able to take advantage of the capabilities of both genetic variants.
Figure \(5\) The evolution of life cycles (green arrows represent five evolutionary transitions) from unicellular zygotic to multicellular gametic through different variants of sporic cycles.
As a consequence, the evolution of life cycles goes from zygotic (similar to unicellular) to the sporic cycle (Figure \(6\)), and then to the more and more expressed domination of diplont, and finally to the complete reduction of haplont, gametic life cycle. It is still an open question how zygotic protists evolved to the sporic side. Most probably, zygote (which is diploid by definition) did not want to divide meiotically. Instead, it grows (which is seen in some protists) and divides mitotically, giving birth to the diplont. This is how first sporic cycle started. The last step of this evolutionary chain was a complete reduction of haplont: after meiosis, spores were replaced with gametes which immediately go to syngamy.
Life Cycle of Vegetabilia
Ancestors of Vegetabilia (plants\(_2\)) were green algae with zygotic life cycle. It could be imagined that their zygote started to grow because these organisms inhabited shallow waters and want their spores to be distributed with a wind. One way for this to happen is to have the spores on the stalk of the plant. This is probably the reason
Figure \(6\) The evolution of life cycles (green arrows represent five evolutionary transi- tions) from unicellular zygotic to multicellular gametic through different variants of sporic cycles.
of zygote growth: primordial diplonts of plants\(_2\) were simply sporangia, structures bearing spores. Then the benefits of diploid condition described above started to appear, and these primitive plants went onto the road of haplont reduction. However, some Vegetabilia (liverworts, mosses and hornworts), still have haplont domination. This is probably because their haplonts are poikilohydric (it is explained in next chapters), adaptation which is beneficial for small plants.
Life cycle of plants\(_2\) is sporic, but the science tradition uses plant-related names for the stages. The cycle (Figure \(7\)) begins with a diplont called a sporophyte, which produces spores. Sporophyte bears a sporangium, inside which mother cell of spores uses meiosis to make spores. The spores germinate and grow into haplont called gametophyte. Gametophyte produces gametes, specifically a spermatozoa (or simply “sperms”) and an oocyte (egg cell). These gametes are developed in special organs—gametangia. Gametangium which contains male gametes (sperms) is called antheridium, and female gametangium is archegonium, the last normally contains only one egg cell (oocyte).
By syngamy (oogamy in this case), the two gametes form a zygote. Next, a young sporophyte grows on the gametophyte, and finally, the cycle starts again. Again, sporophyte of Vegetabilia starts its life as a parasite on gametophyte. Even flowering plants have this stage called embryo. Maybe, this is why the gametophyte of plants\(_2\) has never been reduced completely to transform their cycle into gametic. Even in most advanced plant lineages, their male (which makes only sperms) and female gametophytes have minimum 3 and 4 cells, respectively, but not 0!
Figure \(7\) Life cycle of land plants. Red color is used for innovations, comparing with previous (general) life cycle scheme. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/04%3A_Multicellularity_the_Cell_Cycle__the_Life_Cycle/4.04%3A_Life_Cycle_of_the_Multicellular_Eukaryote.txt |
• 5.1: Tissues
Tissue is a union of cells which have common origin, function and similar morphology. Tissues belong to organs: organ is a union of different tissues which have common function(s) and origin. Plants have simple and complex tissues. The simple tissues (tissues with uniform cells) are composed of the same type of cells; complex tissues (tissues with more than one type of cells) are composed of more than one type of cell, these are unique to plants.
• 5.2: Organs and Organ Systems
• 5.3: The Leaf
• 5.4: The Stem
The stem is an axial organ of shoot. It has functions of support, transportation, photosynthesis, and storage. Stem has radial structure, no root hairs and grows continuously.
• 5.5: The Root
Root is a latest evolutionary innovation in the vegetative plant anatomy. Many “primitive” plants (all mosses and even some ferns like Psilotum) do not have roots; some flowering water plants like the> rootless duckweed (Wolffia) or the coontail (Ceratophyllum) have also reduced their roots. However, large homoiohydric plants need the constant supply of water and minerals, and this evolutionary challenge was responded with appearance of the root system.
05: Tissues and Organs - How the Plant is Built
From now on, we will frequently use multiple names of plants\(_2\) group, they are summarized on Figure \(1\), and in more details—on Figure 6.1.1.
Epidermis and Parenchyma
Why did plants go on land? In order to escape competition with other plants for resources like the sun and nutrients, but also to obtain much more sunlight that was otherwise seriously reduced underwater. The move to land also helped plants escape predators. Lastly, plants benefited from this change because they escaped from the temperature-gases conflict: warmer temperatures are good for organisms but significantly decrease the amount of gases diluted in water.
Although this action solved several problems, it also raised new issues that needed to be dealt with. The most important was the risk of drying out. To combat this, plants developed their first tissue: epidermis (complex surface tissue) covered with a cuticle (plastic-like isolation layer) which served a purpose similar to a plastic bag. For the really small (millimeters) plant it is enough because, in accordance to surface / volume law (i.e., when body size grows, body surface grows slower then body volume (and weight)), they have high relative surface, and diffusion can serve for gas exchange. However, bigger plants also need to exchange gases, and they developed stomata which served as a regulated pore system. The remaining cells became second tissue: parenchyma (tissue or cell type of spherical, roughly connected living cells) or ground tissue (same as parenchyma (see) but only applied for tissue), or main tissue).
Another response (Figure \(3\)) for drying was a development of poikilohydricity (see below), the ability to hibernate in (almost) dried condition. As hibernation is generally dangerous since it requires “system restart”, that evolutionary route did not become the main. Tissue is a union of cells which have common origin, function and similar morphology. Tissues belong to organs: organ is a union of different tissues which have common function(s) and origin. Plants have simple and complex tissues. The simple tissues (tissues with uniform cells) are composed of the same type of cells; complex tissues (tissues with more than one type of cells) are composed of more than one type of cell, these are unique to plants.
Parenchyma (Figure \(4\)) are spherical, elongated cells with a thin primary cell wall. It is a main component of young plant organs. The basic functions of parenchyma are photosynthesis and storage. Parenchyma cells are widespread in plant body. They fill the leaf, frequent in stem cortex and pith and is a component of complex vascular tissues (see below). Contrary to parenchyma (which is a simple tissue), epidermis is a complex tissue composed of epidermal and stomata cells. Its main functions are transpiration, gas exchange and defense.
As it seen here, plants acquired tissues in a way radically different from animals (Figure \(2\)): while plants regulate gas and water exchange in response to terrestrial environment, animals actively hunt for food (using kinoblast tissues) and then digest it (with pagocytoblast tissue).
Supportive Tissues: Building Skyscrapers
When more and more plants began to move from the water to the land, competition once again became a problem (Figure \(3\)). To solve this, plants followed “Manhattan solution”: they grew vertically in order to be able to escape competition for the sunlight and therefore must develop supportive tissues.
Collenchyma (Figure \(4\)) is living supportive tissue that has elongated cells and a thick primary cell wall. Its main function is the mechanical support of young stems and leaves via turgor.
Sclerenchyma (Figure \(4\)) is a dead supportive tissue that consists of long fibers or short, crystal-like cells. Each cell has a thick secondary wall that is rich in lignin. Its main function is a support of older plant organs, and also hardening different parts of plants (for example, make fruit inedible before ripeness so no one will take the fruit before seeds are ready to be distributed). Without sclerenchyma, if a plant isn’t watered, the leaves will droop because the vacuoles will decrease in size which lowers the turgor. Fibers inside phloem (see below) are sometimes regarded as a separate sclerenchyma.
Three times in their evolution plants found the new application for lignin or similar polymers: at first, similar chemicals covered the spore wall which was an adaptation to the spore distribution with wind. Then similar chemicals were used to make cuticle, “epidermal plastic bag” to prevent transpiration outside of stomata. Finally, with acquiring of sclerenchyma, plants found how to use dead cells with completely lignified cell walls.
By the way, stomata likely had a similar fate, they historically appeared on sporangia to help them dry faster and release spores effectively. Regulation of transpiration is their second function.
Cell types and tissues
“Parenchyma” and “sclerenchyma” terms are freShoot systemquently used in two ways: first, to name tissues (or even classes of tissues) which occur in multiple places of the plant body, and second, to name the cell types which are components of tissues. Therefore, it is possible to say “parenchyma of stem”, “parenchyma of stem pith”, “parenchyma of xylem” and even “leaf mesophyll is a parenchyma”.
Meristems: the Construction Sites
Plant growth requires centers of development which are meristemssites of cell division. Apical meristems are centers of plant development located on the very ends of roots (RAMroot apical meristem) and stems (SAMstem apical meristem). They produce intermediate meristems (like procambiumintermediate meristem developing into cortex, pith and procambium) which form all primary tissuestissues originated from RAM or SAM (optionally through intermediate meristems). The lateral meristemcambium, meristem appearing sideways or cambium originates from the procambium which in turn originates from apical meristems. It usually arises between two vascular tissues and its main functions are thickening and producing secondary vascular tissuessecondary phloem and secondary xylem (Figure \(5\)).
Other meristems include: intercalary which elongate stems from the “middle”, marginal which are located on margins which are responsible for leaf development and repair meristems arising around wounds, they also control vegetative reproduction.
Vascular Tissues
Bigger plants escaped from competition and performed effective metabolism. However, with all the growth the plants went through, their size became too big for slow symplastic plasmodesmata connections. Another, filter paper-like apoplastic transport was also not powerful enough. The solution was to develop vascular tissues, xylem and phloem (Figure \(6\), Figure 5.5.1).
The main functions of xylem are the transportation of water and mechanical support. The xylem tissue transporting water may be found either in a vascular bundle or a vascular cylinder. The three types of xylem cells are tracheary elements (these include tracheids
and vessel member), fibers, and parenchyma. Xylem elements, except for the parenchyma, are rich in lignin and are main components of wood. Tracheids are closed on both ends and connected with pits whereas vessel members are more or less open and connects via perforations. Tracheids, vessel members and fibers are dead cells. Xylem parenchyma, on the other hand, is alive.
Pits of tracheids consist of a pit membrane and the torus in a center, there are no openings. The presence of tracheids and/or vessel elements has evolutionary significance. Vessels (made of vessel members) are more effective; consequently, more “primitive” plants have more tracheids whereas more “advanced” have more vessel members. As an example, gymnosperms have only tracheids while most flowering plants have tracheids and vessel members. Individual development also mimics this evolutionary trend. Younger flowering plants have more tracheids whereas mature plants have more vessel members. Primary xylem mostly has tracheids and vessels with scalariform perforations whereas secondary xylem (which originates from cambium) consists mostly of vessels with open perforations. The common name for secondary xylem is wood.
It is a mistake to think that tracheids are better than vessels. In fact, the main problem is frequently not too slow but too fast water transport. Tracheids have an advanced connection system (called torus) which has the ability to close pore if the water pressure is too high and therefore more controllable. Leaking would be less dangerous in tracheids. And in water-poor environments (like taiga in winter), plants with tracheids will have the advantage. Contrary, having vessels is like to have race car for ordinary life; only flowering plants “learned” how to use them effectively.
Dead cells are useful but hard to control. However, if xylem transport needs to be decreased, there is a way. Xylem parenchyma cells will make tyloses“stoppers” for tracheary elements made by parenchyma cells (“stoppers”) which will grow into dead tracheary elements and stop water if needed. Many broadleaved trees use tyloses to lower xylem transport before the winter.
The phloem tissue transporting sugars generally occurs adjacent, or right next to, the xylem, with the xylem facing the inner part of the plant and the phloem facing the outer part of the plant. The main functions of the phloem are the transportation of sugars and mechanical support. The four types of phloem cells are: sieve tube cells , companion cells, fibers (the only dead cells in phloem), and parenchyma. Sieve tube cells of flowering plants have cytoplasm flowing through perforations (sieve plates) between cells but do not contain nuclei. Companion cells will make proteins for them. However, in gymnosperms and more “primitive” plants there are no companion cells at all, so sieve tube cells do contain nuclei. This is comparable to red blood cells in vertebrates: while mammals have them anucleate, erythrocytes of other vertebrates contain nucleus. The secondary phloem generally has more fibers than the primary phloem.
This small table summarizes differences between xylem and phloem:
Xylem Phloem
Contains mostly Dead cells Living cells
Transports Water Sugar
Direction Up Down
Biomass Big Small
Periderm
*Peridermperidermsecondary dermal tissue is a secondary dermal tissue which arises inside the stem ground tissue, closer to the surface. Like the other dermal tissue (epidermis), it is a complex tissue. It includes three layers (starting from surface): phellemexternal layer of periderm, cork (cork), phellogencork cambium, lateral meristem making periderm (cork cambium) and phelloderminternal layer of periderm (Figure \(7\)). Phellem consists of large dead cells with secondary walls saturated with suberin, and is the main, thickest component of periderm. Phellogen is a lateral meristem, like cambium; it often arises fragmentarily (and also temporarily) and does not cover the whole stem under-surface. But when phellem starts to grow, all peripheral tissues (like epidermis) will be separated from water transport and eventually die. Phellogen makes phellem towards the surface, and phelloderm towards the next layer (phloem). Phelloderm is a minute tissue, and does not play significant role in the periderm.
In older plants, phellogen arises deeper, sometimes inside phloem and separates outer layers of phloem from vascular cylinder. All this mixture of tissues (phellogen, phellem, phelloderm, epidermis and upper layers of phloem) considered as a bark.
Absorption Tissues
Poikilohydric plants that do not save water plants do not save water and they can survive even complete desiccation because their cells will hibernate. An example of a poikilohydric plants would be mosses. Homoiohydric plants that save water plants (which are majority of plants\(_2\)), however, do save water. They try to support the water content and do not survive complete desiccation. An example of a homoiohydric plant would be any “typical” plant, saying, corn. Somehow similar traits are comparable in poikilothermic animals, such as reptiles, and homoiothermic animals, such as birds and mammals, except in reference to body heat rather than water conservation.
Absorption tissues are always simple, primary tissues. Most important of them is rhizodermis(rhizoderm), or root hairs, which originates from protoderm (proto-epidermis), but its lifespan is much shorter than of epidermis. There are other absorption tissues, for example, velamen, which originates from the root cortex and consists of large, empty, easy to get wet dead cells.
Other Tissues
Secretory tissues spread across the plant body, concentrating in leaves and young stems. These tissues may secrete latex, volatile oils, mucus and other chemicals. Its functions can be attraction or dis-attraction, communication or defense, and many others.
In addition to tissues, plant body may contain idioblasts, cells which are quite dissimilar from surrounding cells. Idioblasts used for accumulation of unusual (and possibly dangerous) compounds like myrosinase, protein splitting glucosinolates into sugars and toxic isothiocyanate (mustard oil). We use mustard oil as a spice but for the plant, it works like a binary chemical weapon against insect herbivores: when myrosinase-containing idioblasts are damaged, mustard oil kills damaging insects. Among plants, the whole order Brassicales from rosids is capable to produce myrosinase, examples are different cabbages (Brassica spp.), papaya (Carica), horseradish tree (Moringa) and many others. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/05%3A_Tissues_and_Organs_-_How_the_Plant_is_Built/5.01%3A_Tissues.txt |
Vegetabilia (Figure 6.1.1) have three different types of body construction (Figure \(1\)). The most primitive plants have thallus body, more advanced is the shoot (unipolar) plant body, and most land plants have the bipolar plant body. The thallusflat, non-differentiated body plant body is flat, similar to leaf but do not differentiated into particular organs. Most gametophytes (except true mosses) have this type, and also few sporophytes (which mostly are reduced water plants). Shoot (unipolar) plant body consists only of branching shoots, roots are absent. This is typical to all Bryophyta sporophytes, mosses (Bryopsida) gametophytes, and also to sporophytes of Psilotopsida (whisk ferns). Finally, bipolar plant body present has both shoots and roots (Figure 5.3.1). Most bipolar plants have shoots consist of stems and leaves, but this is not an absolute requirement since young plant stems are normally green and can do photosynthesis.
Typical organs of bipolar plant are stems (axial aerial organs with continuous growth), leaves (flat lateral organ with restricted growth), roots (axial soil organ modified for absorption) and floral units (FU) which are elements of the generative system (fructifications) such as a pine cone or any flower.
Buds, fruits, seeds and specific to seedlings hypocotyl and epicotyl are non-organs for different reasons: buds are just young shoos, fruit is the ripe flower, hypocotyl is a part of stem between first leaves of the seedling (cotyledons) and root (i.e., stem/root transition place), epicotylfirst internode of the stem is first internode of stem (Figure \(2\)), and finally, seed is a chimeric structure with three genotypes so it is impossible to call it “organ”.
Root, stem, leaf and FU are four basic plant organs (Figure \(3\)) which in bipolar plant could be grouped in root and shoot system; the latter is frequently split into generative shoot system (bearing FU), and vegetative shoot system (without FU).
Vegetative shoot system usually consists of main and secondary shoots; shoots contain terminal buds, axillary (lateral) buds, stem (nodes and internodes) and leaves. We will start from leaves.
5.03: The Leaf
The first and ultimate goal of every plant is photosythesis. If a plant is multicellular, it usually develops relatively large, flat structures which goal is to catch sun rays. Terrestrial plants are no exception; most probably, they started to build their body with organs similar to present day leaves.
A leaf is lateral photosynthetic organ of shoot with restricted growth. Its functions are photosynthesis, respiration, transpiration, and synthesis
of secondary chemicals. Features of a leaf (i.e., characters help to distinguish it) include having a bud in the axil, not growing by apex, not producing new leaves or shoots, and having hierarchal morphology (see below).
Morphology of the Leaf
Morphology means external, well visible structural features whereas anatomy needs tools like a scalpel and/or microscope to study needs tools like a microscope and/or scalpel. Leaves are very important in plant morphology. The ability to describe the leaf is a must even for novices in botany.
In all, plants are fractal organisms, like Sierpinski triange (Figure \(3\)). All fractals are self-similar (Figure \(4\)), and plants are no exception. Self-similarity, or “Russian doll effect” means that almost every part of plant may be a part of the bigger complex, this bigger one—the part of even bigger system, and so on. This is what we see in leaves as levels of hierarchy. *Simple leavessimple leafleaf with one level of hierarchy have just one level of hierarchy whereas compound leaves have two or more levels of hierarchy. *Compound leavescompound leavesleaves with two or more level of hierarchy are sometimes mixed with branches but there are many other characteristics which allow to distinguish them (Figure \(2\)).
To describe leaves, one should always note the level of hierarchy like “on the first level of hierarchy, the shape is ..., on the second level of hierarchy, the shape is ...” As it was mentioned above, leaf hierarchy is similar to Russian dolls: every smaller doll has a bigger doll (next hierarchy level) outside. For example, if the leaf is compound (consists of multiple leaflets), the overall shape of it could be, saying, round (circular) but the shape of individual leaflet of the very same leaf could be ovate (Figure \(5\)). As a result, the description will say that on first level of hierarchy the leaf is ovate, and on the third level—circular.
There are three types of leaf characters: general, terminal, and repetitive. General characters are applicable only to the leaf as a whole are only applicable to the whole leaf. Terminal characters are applicable only to the leaf terminals (leaflets) are only applicable to the terminal leaflets. Terminals are the end parts of leaves, they do not split in smaller terminals; clover leaf, for example, has 3 terminals. Lastly, repetitive characters repeat on each level of leaf hierarchy. General and terminal characters do not depend on hierarchy. Repetitive characters are applicable to the leaf parts on each level of hierarchy may be different on each step of hierarchy.
General characters of leaf include stipules and other structures located near leaf base (Figure \(6\)): sheath (typical for grasses and other liliids) and ocrea (typical for buckwheat family, Polygonaceae).
Repetitive characters are the shape of the leaf (Figure \(7\)), leaf dissection, and whether the blade is stalked (has petiole) or not.
Terminal characters are applicable only to terminal leaflets of leaves. These characters (Figure \(9\)) are the shape of the leaf blade base, the leaf tip, the type of margin, the surface, and the venation. The base of the leaf blade could be rounded, truncate (straight), cuneate, and cordate. The leaf apex could be rounded, mucronate, acute, obtuse, and acuminate. Leaf margin variants are entire (smooth) and toothed: dentate, serrate, double serrate and crenate.
Leaf veins are vascular bundles coming to the leaf from stem. Frequently, there is a main vein and lateral veins (veins of second order). There are multiple classifications of leaf venation; and example is shown on the Figure \(10\).
Note that in dichotomous venation, each vein divides into two similar parts which is known as dichotomous branching. The example of dichotomous venation is the leaf of maidenhair tree, ginkgo (Ginkgo biloba). Another frequently segregated type of venation is parallellodromous, but in essence, this is acrodromous venation in linear leaves (for example, leaves of grasses) where most of veins are almost parallel.
To characterize the whole leaf, one might use the following plan:
1. General characters (leaf as a whole):
(a) stipules (present / absent, deciduous / not, how many, size, shape);
(b) base (sheath / no sheath, ocrea / no ocrea)
2. First level of hierarchy: repetitive characters:
(a) symmetry (symmetrical / asymmetrical);
(b)shape;
(c) dissection;
(d) petiole (presence and length)
3. Second level of hierarchy
4. Third level of hierarchy, and so on
5. Terminal characters (leaflets):
(a) base of leaf blade (rounded, truncate, cuneate, cordate);
(b) apex (rounded, mucronate, acute, obtuse, acuminate);
(c) margin (whole, dentate, serrate, double serrate, crenate );
(d) surfaces (color, hairs etc.);
(e) venation (apo-, hypho-, acro-, ptero-, actinodromous)
Heterophyllyh refers to a plant having more than one kind of leaf. A plant can have both juvenile leaves and adult leaves, water leaves and air leaves, or sun leaves and shade leaves. A leaf mosaics refers to the distribution of leaves in a single plane perpendicular to light rays, this provides the least amount of shading for each leaf.
Leaves have seasonal lives; they arise from the SAM through leaf primordia, and grow via marginal meristems. The old leaves separate from the plant with an abscission zone.
The famous poet and writer Johann Wolfgang Goethe is also considered a founder of plant morphology. He is invented an idea of a “primordial plant” which he called “Urpflanze” where all organs were modifications of several primordial ones. In accordance to Goethe’s ideas, plant morphology considers that many visible plant parts are just modifications of basic plant organs.
Modifications of the leaf include spines or scales for defense, tendrilsorgan modifications using for climbing for support, traps, “sticky tapes”, or urns for interactions (in that case, catching insects), plantlets for expansion, and succulent leaves for storage. Plantlets are little mini plants that grow on the main plant and then fall off and grow into new plants; the most known example is Kalanchoë (“mother of thousands”) which frequently uses plantlets to reproduce. Plants that have insect traps of various kinds are called carnivorous plants (in fact, they are still photoautotrophs and use insect bodied only as fertilizer). Several types of these are the cobra lily (Darlingtonia), various pitcher plants (Nepenthes, Cephalotus, Sarracenia), the butterwort (Utricularia), the sundew (Drosera), and the best known, the Venus flytrap (Dionaea).
Anatomy of the Leaf
Anatomically, leaves consist of epidermis with stomata, mesophyll (kind of parenchyma) and vascular bundles, or veins (Figure \(12\)). The mesophyll, in turn, has palisade and spongy variants. Palisade mesophyll is located in the upper layer and serves to decrease the intensity of sunlight for the spongy mesophyll, and also catches slanted sun rays. The palisade mesophyll consists of long, thin, tightly arranged cells with chloroplasts mostly along the sides. The spongy mesophyll are roughly packed, they are rounded and have multiple chloroplasts (Figure \(11\)).
When a typical stem vascular bundle (which has xylem under phloem) enters the leaf, xylem usually faces upwards, whereas phloem faces downwards. Bundles of C\(_4\)-plants have additional bundle sheath cells in their vascular bundles.
The epidermis includes typical epidermal cells, stomata surrounded with guard cells (also optionally with subsidiary cells), and trichomes. Almost all epidermal cells are covered with waterproof cuticle, rich of lignin and waxes.
The stomata assists in gas exchange, cooling and water transpiration. There are two guard cells paired together on each side of the stoma. These guard cells are kidney beans shaped and have a thicker cell wall in the middle. The thicker cell wall on the inside makes use of the so-called “bacon effect” (when bacon slice curved on the
frying pan) because thinner part of the cell wall is more flexible and therefore bends easier. The same curving effect might be seen in blowing air balloon with the piece of scotch on one side. The opening of the stoma starts from K\(^+\) accumulation, then osmosis inflates guard cells, and finally the uneven cell wall facilitates the opening of stoma. The stoma closes when the potassium ions exit the cell and water amount decreases in its vacuoles (Fig [STOMA]).
In most cases, the lower epidermis contains more stomata than the upper epidermis because the bottom of the leaf is cooler and transpiration there is safer. A similar logic is applicable to trichomes (hairs): they are also more frequent on the lower side of the leaf.
Ecological Forms of Plants
When plants adapt to the particular environment conditions, leaves usually respond first. Conversely, one can estimate the ecology of plant simply looking on its leaves.
In regards to water, there are four main types of plants: xerophytes, mesophytes, hygrophytes, and hydrophytes. Xerophytes are adapted to the scarce water (Figure \(12\)), they could be sclerophytes (usually with prickly and/or rich of sclerenchyma leaves) and succulents (with water-accumulating stems or leaves). Mesophytes are typical plants which adapt to regular water. Hygrophytes live in constantly wet environment, their leaves adapted to high transpiration and sometimes even to guttation (excretion of water drops). Hydrophytes grow in water, their leaves are frequently highly dissected to access more gases dissolved in water, and their leaf petioles and stems have air canals to supply underwater organs with gases.
In regards to light, plants could be sciophytes or heliophytes. Sciophytes prefer the shade to sunlight, their leaves contain mostly spongy mesophyll. Heliophytes prefer the full sun and therefore have leaves filled with palisade mesophyll. The intermediate group are “partial shade” plants.
Halophytes, nitrate halophytes, oxylophytes, and calciphytes are ecological groups adapted to the over-presence of particular chemicals. Halophyte plants are frequent, they accumulate (and look similarly to succulents), excrete or avoid (which looks like sclerophyte) sodium chloride (NaCl). They grow in salty places: sea shores, salt deserts and solonets prairies. Nitrate halophyte plants grow on soils rich in NaNO\(_3\). Oxylophytes grow in acidic soils, whereas calciphytesplants adapted to over-presence of CaCO\(_3\) grow in basic, chalk soils rich in CaCO\(_3\).
Leaves will also reflect adaptations to the substrate, ecological forms named psammophytes (grow on sand), petrophytes (grow on rocks), and rheophytes (grow in fast springs). The latter plants frequently have serious simplifications in their body plan, their leaves and stems are often reduced to form a thallus-like body.
Parasitic plants could be classified in mycoparasites, hemiparasites, and phytoparasites. Mycoparasitic plants feed on soil fungi, phytoparasitic plants are either plant root parasites or plant stem parasites lacking chlorophyll and photosynthesis. Hemiparasitic plants are those which still have chloroplasts but take the significant part of water and even organic compounds from the host plant (like mistletoe, Viscum). | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/05%3A_Tissues_and_Organs_-_How_the_Plant_is_Built/5.02%3A_Organs_and_Organ_Systems.txt |
The stem is an axial organ of shoot. It has functions of support, transportation, photosynthesis, and storage. Stem has radial structure, no root hairs and grows continuously.
Morphology of the Stem
Stem morphology is simple. Its components are nodes (places where leaves are/were attached) and internodes, long or short (in the last case, plant sometimes appears to be stemless, rosette-like).Stems are different by the type of phyllotaxis. The phyllotaxis refers to the arrangement of leaves. If there is one leaf per node, it is a spiral (alternate) arrangement. Two leaves per node means opposite arrangement: two leaves per node arrangement. Opposite leaves can be all in the same plane or each pair can rotate at 90$^\circ$. If there are more than two leaves per node, it is a whorled arrangement, and each whorl can also rotate. Each type of spiral phyllotaxis has its own angle of divergence. Multiple types of spiral leaf arrangement mostly follow the Fibonacci sequence:
$\frac{1}{2}, \frac{1}{3}, \frac{2}{5}, \frac{3}{8}, \frac{5}{13}, \frac{8}{21}, ...$
This sequence of numbers made with simple rule: in the every following fraction, the numerator and denominator are sums of two previous numerators and denominators, respectively. The sequence looks fairly theoretical but amazingly, it is fully applicable to plant science, namely to different types of spiral phyllotaxis (Figure $2$).
To determine formula of spiral phyllotaxis, one needs to start with arbitrary leaf (or leaf scar) and then find the next (upper) one which is directed the same way, lays on the same virtual line. Then, the imaginary spiral should be drawn trough basements from the started leaf to the corresponding upper leaf. This spiral should go through all intermediary leaves, there might be one, two or more intermediary leaves. Also, the spiral will go at least one time around the stem. (Instead of the imaginary spiral, it is sensible to use a thin thread). One needs to count all leaves in the spiral except the first, and also count number of rotations. The number of leaves counted will be the denominator of the formula, and the number of rotations is the numerator. This is how Fibonacci numbers appear in plant morphology.
These phyllotaxis formulas are relatively stable and sometimes even taxon-specific. For example, grasses (Gramineae) have $\frac{1}{2}$ phyllotaxis, sedges (Carex) $\frac{1}{3}$, many Rosaceae (like apple, Malus or cherry, Prunus) have $\frac{2}{5}$, willows frequently have $\frac{3}{8}$, et cetera. It is still not absolutely clear why the spiral phyllotaxis is under such a theoretical mathematical rule. The most feasible hypothesis emphasizes mathematical problem of circle packing and the competition between leaf primordia around SAM.
Anatomy of the Primary Stem
Plant evolution resulted first in the primary stems with no lateral meristems and secondary tissues. Only long after plants “learned” how to thicken their stems.
Development of stem starts from stem apical meristem (SAM) on the top of plant. The SAM produces three primary meristems: procambium, protoderm, and ground meristem. Protoderm cells differentiate into epidermal cells. The ground meristem differentiates into the cortexexternal layer of primary stem or root and pithcentral layer of primary stem or root. The procambium raises between the cortex and the pith. It forms vascular bundles or vascular cylinder.(Figure $2$).
The outer layers of the procambium form the primary phloem. The inner layers become the primary xylem. The middle layer can be entirely spent or will make cambium for the secondary thickening. At times, the layers of the outside of the procambium can form a pericycle. Sometimes the innermost layer of the cortex can form an endodermis (endoderm) (Figure $3$), and outermost layer makes the exodermis (exoderm). All these layers are some kind of the “border control” between functionally different layers of stem. Another frequent variant is the development of collenchyma in the cortex adjacent to epidermis.
Vascular bundles connect leaves and stems. In many plants, they form a ring on the cross-section of the stem. Parenchyma (ground tissue) between vascular bundles typically belongs to both cortex and pith. Another variant is a vascular cylinder, structure which fully encircles the stem. Liliid (monocot) stems generally have dispersed vascular bundles. These three variants are steles, overall configurations of the primary vascular system of the plant stem (Figure 5.5.1). The most frequent kinds of steles are eustele (vascular bundles in a ring), solenostele (vascular cylinder) and ataktostele (dispersed vascular bundles).
All these types were probably originated from protostele, configuration where central xylem is surrounded with phloem and no pith is present (Figure 5.5.2). While the protostele was typical for many prehistoric plants, now only some lycophytes (Huperzia) have protostele in stems.
Saying that, it is important to note that roots of most plants have vascular tissues arranged similarly to protostele. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/05%3A_Tissues_and_Organs_-_How_the_Plant_is_Built/5.04%3A_The_Stem.txt |
Root is a latest evolutionary innovation in the vegetative plant anatomy. Many “primitive” plants (all mosses and even some ferns like Psilotum) do not have roots; some flowering water plants like the> rootless duckweed (Wolffia) or the coontail (Ceratophyllum) have also reduced their roots. However, large homoiohydric plants need the constant supply of water and minerals, and this evolutionary challenge was responded with appearance of the root system.
The Root in an axial organ of plant with geotropic growth. One of root functions is to supply anchorage of the plant body in soil or on various surfaces. Other functions include water and mineral absorption and transport, food storage, and communication with other plants.
Morphology of the Root
There are two types of root systems. The first is a fibrous root system which has multiple big roots that branch and form a dense mass which does not have a visible primary root (“grass-like”). The other is the tap root system which has one main root that has branching into lateral roots (“carrot-like”).
Along with having different systems, there are different types of roots: primary root originated from the root of the seedling, secondary (lateral) roots originate from the primary roots, and adventitious roots originate on stems (sometimes also on leaves), the example are prop roots of screw pine (Pandanus).
Roots employ many different modifications which help to protect, interact and storage. For example, roots of parasitic plants are modified into haustoria which sink themselves into the vascular tissue of a host plant and live off of the host plant’s water and nutrients.
Roots of mangroves (plants growing in ocean coastal swamps) are frequently modified into supportive aerial roots (“legs”). Since these swamp plants need oxygen to allow cell respiration in underground parts, there are pneumatophores, specialized roots which grow upward (!) and passively catch the air via multiple pores. Plants which grow on sand (psammophytes, see above) have another problem: their substrate constantly disappears. To avoid this, plants developed contractile roots which may shorten and pull plant body deeper into the sand.
Some orchid roots are green and photosynthetic (Figure $3$)! However, as a rule, root is the heterotrophic organ, because root cells have no access to the light.
Root nodules present on the roots of nitrogen-fixing plants, they contain bacteria capable to deoxidize athmospheric nitrogen into ammonia: N$_2$ $\rightarrow$ NH$_3$. Root nodules contain also hemoglobin-like proteins which facilitate nitrogen fixation by keeping oxygen concentration low. Nitrogen-fixing plants are especially frequent among faboid rosids: legumes (Leguminosae family) and many other genera (like alder, Alnus, or Shepherdia, buffaloberry) have root nodules with bacteria. Some other plants (mosquito fern, Azolla and dinosaur plant, Gunnera) employ cyanobacteria for the same purpose.
Mycorrhiza is a root modification started when fungus penetrates root and makes it more efficient in mineral and water absorption: it will exchange these for organic compounds. In addition to mycorrhizal fungi, endophytic fungi inhabit other plant organs and tissues.
Anatomy of the Root
On the longitudinal section of young growing root, there are different horizontal layers, zones: root cap covering division zone, elongation zone, absorption zone, and maturation zone (Figure $4$). The root cap protects the root apical meristem (RAM), which is a group of small regularly shaped cells. A small, centrally located part of the RAM is the quiescent center where initial cells divide and produce all other cells of root. Root cap is responsible for the geotropic growth, if the root tip comes into contact with a barrier, root cap will feel it and will grow on a different direction to go around it.
The elongation zone is where the cells start to elongate, giving it length. The absorption zone where the rhizodermis tissue (root hairs) develops and where water and nutrients are absorbed and brought into the plant. Within the maturation zone, root hairs degrade, many cells start to acquire secondary walls and lateral roots develop (Figure $4$).
On the cross-section of the root made within absorption zone, the first tissue is the rhizodermis, which is also known as the root epidermis, then cortex, which segregates external exodermis and internal endodermis one-cellular layers, and vascular cylinder (Figure $5$ ). Typically, roots have no pith. In some cases (for example, in orchids), cortex may give multi-layered velamen (see above), another absorption tissue.
Vascular cylinder is located in the center of the root, it contains the pericycle which is made of mostly parenchyma and bordering endodermis. Pericycle cells may be used for storage, they contribute to the vascular cambium, and initiate the development of lateral roots. Consequently, lateral roots are developing endogenously and break tissues located outside, like aliens in the famous movie. Root phloem is arranged in
several strands whereas xylem typically has a radial, sometimes star-shaped structure with few rays (Figure $6$). In the last case, phloem strands are located between rays of xylem.
Root tissues develop in the way similar to stem, RAM gave rise to ground meristem, procambium, and the protoderm, which in turn make all primary tissues mentioned above. Later, pericycle develops into lateral roots or the vascular cambium which in turn produces into the secondary xylem and phloem. The secondary root is similar to secondary stem (see below).
Water and Sugar Transportation in Plants
Plants need water to supply photosynthesis (the oxygen is from water!), to cool down via transpiration, and to utilize diluted microelements. Dead velamen (paper-like), rhizoids (hair-like), and living rhizodermis (rhizoderm) are responsible for water uptake.
In rhizodermis, root hairs increase the surface area where the plant has to absorb the nutrients and water. To take water, hair cells increase concentration of organic chemicals (the process which needs ATP) and then use osmosis. There are two ways that water transport may go: apoplastic or symplastic. Apoplastic transport moves water through the cell walls of cortex: from the rhizodermis to the endodermis. Endodermis cell walls bear Casparian strips (rich of hydrophobic suberin and lignin) which prevent the water from passing through the cell wall and force symplastic transport (Figure $7$) through cytoplasms and plasmodesmata. Symplastic transport there is directed to the center of root only and requires ATP to be spend.
By pumping water inside vascular cylinder and not letting it back, endodermis cells create the root pressurepressure force made solely by roots (Figure $8$). It is easy to observe on tall herbaceous plants cut near the ground: drops of water will immediately appear on the cutting. Inside tracheary elements of xylem, water moves with the root pressure, capillary force and the sucking pressure of transpiration. The latter means that water column does not want to break and if water disappears from the top (stomata on leaves), it will move water inside plant. The main direction of water movement is from roots to leaves, i.e. upwards.
Products of photosynthesis (sugars) are moving inside living cells of phloem; these cells (sieve tubes) use only symplastic transport to distribute glucose and other organic compounds among all organs of plants. In fact, phloem transports these components in all directions: to the flowers (usually upwards), and at the same time to the roots (usually downwards). | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/05%3A_Tissues_and_Organs_-_How_the_Plant_is_Built/5.05%3A_The_Root.txt |
When plants developed basic tissues and organs and thus became mature enough to survive on land, they started to increase in their diversity. All plants studied in this and following chapters belong to plants\(_2\), or kingdom Vegetabilia which is split into three phyla (Figure 6.1.1): Bryophyta (mosses and relatives), Pteridophyta (ferns and allies), and Spermatophyta (seed plants). The most striking differences between these phyla lay in the organization of their life cycles.
Land plants have a sporic life-cycle (Figure 4.4.7) that begins with a diplont (sporophyte); the mother cell of spores goes through the meiosis and produces haploid spores. These spores develop into haplont which produces female and male gametangia (gamete “homes”). Female is called archegonium, the male—antheridium; the archegonium produces oocyte which is fertilized by the antheridium’s spermatozoon in the process of oogamy. When this fertilization happens, it forms a diploid zygote which then matures into a young sporophyte growing on a gametophyte. This kind of same species parasitism is almost unique in the living world. Only viviparous animals (like mammals with their pregnancy) could be compared with land plants.
• 6.1: Bryophyta - the Mosses
Bryophyta has approximately 20,000 species. They do not have roots, but have long dead cells capable of water absorbency via apoplastic transport, these cells are called rhizoid cells. Their sporophyte is reduced to sporogon, which is simply a sporangium with setamosses: stalk of the sporogon (see) (stalk), and is usually parasitic. Gametophyte of bryophytes starts its development from a protonema, thread of cells.
• 6.2: Pteridophyta - the Ferns
Pteridophyta, ferns and allies, have approximately 12,000 species and six classes. They have a sporic life cycle with sporophyte predominance whereas their gametophytes are often reduced to prothallium, small hornwort-like plant. Another frequent variant is the underground, mycoparasitic gametophyte. Pteridophyta (with one exception) have true roots. Most of them have vascular tissues and are homoiohydric. This is why seed plants together with ferns have a name vascular plants.
06: Growing Diversity of Plants
Bryophyta has gametophyte predominance while Pteridophyta and Spermatophyta both have sporophyte predominance (and the main difference between Pteridophyta and Spermatophyta is that Spermatophyta has seeds). Bryophyta has approximately 20,000 species. They do not have roots, but have long dead cells capable of water absorbency via apoplastic transport, these cells are called rhizoid cells. Their sporophyte is reduced to sporogon, which is simply a sporangium with setamosses: stalk of the sporogon (see) (stalk), and is usually parasitic. Gametophyte of bryophytes starts its development from a protonema, thread of cells. Bryophyta are poikilohydric; they go through dehydration or extremely low water concentration without any serious physiological damage to the plant.
Life cycle of mosses is similar to the general life cycle of land plants described above. They begin with a gametophyte with an archegonia and antheridia. The antheridium produces biflagellate spermatozoa which fertilizes the egg and produces diploid zygote; zygote grows into a sporogon and its cells (mother cells of spores) go through meiosis which produces haploid spores. Spores will be distributed with the wind, land on the substrate and germinate into protonema stage which then develops into a green, well-developed gametophyte. Most of moss gametophytes have a shoot body that consists of a stem and leaves (but no roots) while others have a thallus body, which is a flat, leaf-like, and undifferentiated structure.
There are three main groups, also known as subphyla, of Bryophyta: Hepaticae (liverworts), Bryophytina (true mosses), and Anthocerotophytina (hornworts).
• Hepaticae are phylogenetically closest to green algae. Their thallus typically has dorsal and ventral parts, and the sporogon is bag-like. Inside the sporangium, there is no central column (columella) but elaters are present, which are cells that loosen spores. One of the most widespread liverwort is Marchantia, it is commonly found in wet shady places. It became a frequent weed in greenhouses.
• Bryophytina consists of multiple classes (Figure \(2\)), the most important are Sphagnopsida—peat mosses, Polytrichopsida—hair cap mosses, and Bryopsida—green mosses. Bryophytina have a radially structured shoot-like body with a stem and thin leaves. Their sporogon is long and has columella, but does not have elaters. Sporogons of true mosses are usually supplied with peristomemosses: attachment to moss sporangium, helps to distribute spores, structure which helps in spore distribution. Some advanced true mosses (hair cap moss, Polytrichum) have tall gametophyte with proto-vascular tissues, while others (stinkmoss, Splachnum) employ insects for the distribution of spores. Peat moss (Sphagnum) is probably the most economically important genus of Bryophyta.
• Anthocerotophytina (Figure \(3\)) evolutionary are closests to the next phylum, Pteridophyta (ferns and allies). Hornworts have a flattened thallus body, their long photosynthetic sporogon has columella and elaters. The presence of stomata on sporogons and the ability of some hornwort sporogons to branch and sometimes even live independently from the gametophyte provide a support for the advanced position of this group. Hornworts are rare and quite small (first millimeters in size), and like liverworts, they prefer shady and wet places.
Mosses have become known as the “evolutionary dead end” because their poikilohydric gametophyte requires water for fertilization and does not have a root system; this restricts the size and requires dense growing. However, if the sexual organs are near the soil surface, then the parasitic sporogon would not grow tall enough, and consequently would not be able to effectively distribute spores with the wind.
Three natural forces “tear” the body of moss: wind and light require plant to be taller whereas water requires it to be smaller (Figure \(4\)). Mosses did not resolve this conflict.
The only way to fix the situation properly would be to make the sporophyte taller, independently growing and therefore and reduce dominance of the gametophyte. This is what ferns (Figure \(5\)) did. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/06%3A_Growing_Diversity_of_Plants/6.01%3A_Bryophyta_-_the_Mosses.txt |
Pteridophyta, ferns and allies, have approximately 12,000 species and six classes (Figure \(1\)). They have a sporic life cycle with sporophyte predominance whereas their gametophytes are often reduced to prothallium, small hornwort-like plant. Another frequent variant is the underground, mycoparasitic gametophyte. Pteridophyta (with one exception) have true roots. Most of them have vascular tissues and are homoiohydric. This is why seed plants together with ferns have a name vascular plants. Pteridophyta sporophytes always start their life from an embryo located on the gametophyte. While Pteridophyta have true xylem and phloem, they do not have developed secondary thickening.
Most ancient pteridophytes appeared in Silurian period, they were rhyniophytes. Rhyniophyles had well-developed aboveground gametophytes and relatively short, dichotomously branched leafless sporophytes. The next important steps were formation of leaves and further reduction of gametophytes.
Diversity of pteridophytes
Lycopodiopsida, or lycophytes have at least four genera and more than 1,200 species. Lycophytes belong to microphyllous lineage of pteridohytes. This means that their leaves originated from the emergences of the stem surface, and therefore are more similar to moss leaves than any other leaves of pteridophytes and seed plants. Lycophyte sporangia are associated with leaves and often form strobilus which is a condensation of sporangia-bearing leaves (sporophylls when they are leaf-like or sporangiophores when they are divergent). Their spermatozoon usually has 2 flagella (like mosses) but are sometimes also multiflagellate (like spermatozoa of other ferns). Lycophytes used to be the dominant plants of Carboniferous tropical swamp forests and their remains became coal. Contemporary lycophytes are much smaller but still thrive in wet and warm places. More basal lycophytes (clubmosses Huperzia and Lycopodium) have equal spores and underground gametophytes, whereas more advanced Selaginella (spikemoss) and Isoëtes (quillwort) are both heterosporous (see below) with reduced aboveground gametophytes. Quillwort is a direct descendant of giant Carboniferous lycophyte trees, and despite being an underwater hydrophyte, it still retains the unusual secondary thickening of stem. Many spike mosses are poikilohydric (another similarity with mosses).
Equisetopsida (horsetails) is a small group with one genus, Equisetum, and has about 30 different herbaceous species that typically live in moist habitats. The leaves of these plants are reduced into scales, and the stems are segmented and also photosynthetic; there is also an underground rhizome. The stem epidermis contains silica which makes it have an abrasive surface, and because of this, American pioneers would use this plant to scour pots and pans. This is how it received the nickname “scouring rush.” The stem has multiple canals, this is somehow similar to stems of grasses. The sporangia are associated with hexangular stalked sporangiophores; there are also elaters which are not separate cells but parts of the spore wall. Gametophytes are typically minute and dioecious, but the plants themselves are homosporous: smaller suppressed gametophytes develop only antheridia while larger gametophytes develop only archegonia.
Psilotopsida (whisk ferns) is a small tropical group which consists of only two genera, Psilotum and Tmesipteris, with only seven different species. They are herbaceous plants that grow as epiphytes. Whisk ferns are homosporous, and their sporangia are fused into synangiaadnate sporangia. Psilotopsida have protostele like the some lycophytes, and long-lived underground gametophytes; they also have multiflagellate spermatozoa similar to all other ferns. Both Psilotum and Tmesipteris lack roots; in addition, Psilotum also lacks leaves.
Ophioglossopsida (tongue ferns) is a small group that consists of approximately 75 species, and are closest relatives to whisk ferns. Ophioglossopsida have an underground rhizome (sometimes with traces of secondary thickening) with aboveground bisected leaves: one half of each leaf is the leaf blade while the other half becomes the sporophyll. The gametophytes also grow underground. Ophioglossum vulgatum, known also as the adder’s tongue fern, has chromosome number \(2n=\)1,360 which is the largest chromosome number ever!
Marattiopsida (giant ferns) are tropical plants, with several genera and about 100 species. These are similar to true ferns and have compound leaves that are coiled when young. They are also the biggest ferns, as one leaf can be six meters in length. They have short stems, and leaves with stipules. Their sporangia have multi-layer walls and are fused into synangia (not like true ferns). At the same time, they are located on the bottom surface of leaves (like in true ferns). Gametophytes are relatively large (1–2 cm), photosynthetic, and typically live for a long time. These ferns were important in the Carboniferous swamp forests.
Pteridopsida (true ferns) have more than 10,000 species and make up the majority of living monilophytes (all classes of Pteridophyta except lycophytes). Their leaves are called fronds because of apical growth; young leaves are coiled into fiddleheads (Figure \(2\)). True ferns are megaphyllous: their leaves originated from flattened branches. True ferns have unique sporangia: leptosporangia. Leptosporangia originate from a single cell in a leaf, they have long, thin stalks, and the wall of one cell layer; they also open actively: when sporangium ripens (dries), the row of cells with thickened walls (annulus) will shrink slower than surrounding cells and finally would break and release all spores at once. Leptosporangia are also grouped in clusters called sori which are often covered with umbrella- or pocket-like indusia. Gametophytes of Pteridopsida are minute and grow aboveground. Some genera of true ferns (like mosquito fern Azolla, water shamrock Marsilea and several others) are heterosporous.
True ferns are highly competitive even to angiosperms. In spite of their “primitive” life cycle, they have multiple advantages: abilities to photosynthesize in deep shade (they are not obliged to grow fast), to survive high humidity, and to make billions of reproductive units (spores). Ferns do not need to spend their resources on flowers and fruits, and are also less vulnerable to vertebrate herbivores and insect pests, probably because they do not employ them as pollinators and, therefore, can poison tissues against all animals.
Heterospory: Next step on land
Vertebrate animals became fully terrestrial (amphibians became first reptiles) only when their fertilization became completely independent from water. Plants started to perform the similar “evolutionary efforts” even earlier, but while reptiles actively approach the sexual partner, plants cannot do the same because their tissues and organs evolved for completely different purposes. Instead of the active sex, plants use “carpet bombing” with spores; this was invented to increase the chance that two spores land nearby and the distance between sperm and egg cell will be minimal.
However, since simple increase in the number of spores is a great waste of resources, plants minimized spore size; this will also allow for the longer distance of dispersal. On the other hand, some spores must remain large because embryo (if fertilization occurs) will need the support from the feeding gametophyte. Consequently, plants ended up with division of labor: numerous, minuscule male spores which grow into male gametophytes with antheridia only, and few large female spores which make female gametophytes producing only archegonia (Figure \(3\)).
This heterosporic cycle makes fertilization less dependent on water and more dependent on spore distribution and gametophyte features (Figure \(4\)). It also allows for numerous improvements in future.
Division of labor allows resources to be used more efficiently and also restricts self-fertilization. In the plant evolution, there was a high need for heterospory because it independently arose in several groups of pteridophytes and even among mosses. In the extreme cases of heterospory (Figure \(5\)), a female spore does not leave the mother plant and germinate there, “waiting” for the fertilization from the male gametophyte developed nearby; in fact, this is incipient pollination, the step towards the seed.
Heterosporous plants produce one female spore, megaspore, which is rich in nutrients; megaspores are not widely dispersed, but the female gametophyte that comes of it provides nutrition and protection for the zygote, embryo, and young sporophyte. Heterosporic life cycle (Figure \(6\)) starts with a male gametophyte and a female gametophyte, both of which produce gametes. Once fertilization occurs, a zygote develops into sporophyte. The sporophyte will then produce two different sporangia types: female megasporangia and male microsporgangia. Meiosis in megasporangium will frequently result in one female spore, megaspore (similar to the meiosis in the ovaries of vertebrate animals), whereas in the microsporangium, meiosis and subsequent mitoses will make numerous microspores; both the megaspore and microspores will develop into gametophytes and the cycle will repeat.
In all, heterospory allows for separation between male and female haploid lineages. Male gametophytes become so small that they could easily be transported as a whole. Whole male gametophytes start to be a moving stage—this is origin of pollination. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/06%3A_Growing_Diversity_of_Plants/6.02%3A_Pteridophyta_-_the_Ferns.txt |
Competition over resources (primarily water and sun light) always drove plant evolution. The most logical way to escape competition was to enlarge the body. But if only primary tissues are available, this growth is strictly limited. Without secondary thickening, the trunk will easily break under the weight of growing crown, and the plant will die. This is easy to see in plants which still dare to develop the tree-like habit without secondary growth: tree ferns and palms. In addition, tree ferns have no bark which limits their distribution to the really wet places. On the other hand, thickening of stem will allow for branching, and branching allow for even bigger aboveground body. But then, new problems associated with both size and life cycle will pose another great challenge.
• 7.1: Secondary Stem
In many seed plants, secondary growth begins in their first year within the stem and continues on for many more years. These plants are classified as woody. They develop secondary tissues like periderm and wood, and even tertiary structures like bark.
• 7.2: Branching Shoot
Secondary stem allows for extensive branching. In seed plants, branching is based on the axial buds. These buds are located in axils of leaves and develop into secondary shoots. There are two main types of branching: monopodial and sympodial
• 7.3: Life Forms
Thickening and branching change the appearance of plant. The most ancient classification employ both branching and thickening and divide plants into trees, shrubs and herbs. This approach was the first classification of life forms. Life forms tell not about evolution, but about how plant lives. We still use this classification. With some modifications, it plays a significant role in gardening.
• 7.4: Modified Shoot
Like leaves and roots, shoots and stems also have modifications. Some examples are rhizomes, stolons, tubers, bulbs, corms, thorns, spines, cladophylls, and stem traps. Rhizomes (example: ginger, Zingiber) are underground stems that burrow into the ground just below the soil surface, and usually tend to have small, scale-like leaves that are not photosynthetic. Buds from the axils of the leaves make new branches that will grow to become aboveground shoots.
• 7.5: Origin of the Seed
When plants developed the secondary growth, the almost unlimited perspectives opened for enlarging their body. However, these giants faced a new problem.
• 7.6: Spermatophyta - Seed Plants
Seed plants consist of approximately 1,000 species of non-angiosperms (gymnosperms) and about 250,000 species of angiosperms. They have a sporic life-cycle with sporophyte predominance, and seeds. The gametophyte is reduced to cells inside the ovule or pollen grain. Males have a minimum number of cells being three and females being four. The antheridia are absent and in flowering plants (Angiospermae) and Gnetopsida the archegonia are also reduced.
Thumbnail: A female Coulter Pine (Pinus coulteri) cone. Image used with permission (Cc By 2.5; Geographer).
07: The Origin of Trees and Seeds
In many seed plants, secondary growth begins in their first year within the stem and continues on for many more years. These plants are classified as woody. They develop secondary tissues like periderm and wood, and even tertiary structures like bark.
The first step in producing secondary phloem and xylem (other names are metaphloem and metaxylem) is to form the vascular cambium, which involves cell division inside the vascular bundles and the parenchyma that are between the bundles (Figure \(1\)). The vascular cambium divides in two directions. The cells that are formed to the outside become the secondary phloem, and those formed to the inside are the secondary xylem (Figure \(3\)). After several years, central pith disappears under the pressure of growing wood, and only traces of primary xylem (protoxymem) can be seen under the thick secondary xylem. Altogether, these tissues (pith + primary xylem + secondary xylem) are wood (Figure \(2\)).
The secondary phloem forms outside of the vascular cambium, and traces of primary phloem (protophloem) are visible above it. It is rich in fibers, and unlike the wood, it does not form annual rings.
Most of cambium cells are fusiform initials forming axial vessel elements, while some cambium cells are ray initialscambium cells which make rays and they form rays: combinations of parenchyma cells and tracheids transporting water, minerals and sugars (because it is dark inside the stem and only respiration is possible) horizontally. Rays are visible best on the tangential section of the stem (when section plane is tangent to the stem surface); two other possible sections (radial and transverse) show axial components of the stem better. In the secondary phloem, rays are sometimes dilated (wedge-shaped).
The cambium usually does not work evenly all year round. In temperate climates, a ring forms for each growing season and makes it possible to determine the age by counting the growth rings. This is because at the end of season cambium makes much smaller (“darker”) tracheary elements. Trees growing in climates without well-expressed seasons will not make annual rings. To tell the age of a tree, researchers observe the number and thickness of annual rings that are formed. This is called dendrochronology.
Some trees (like oaks, Quercus) have large vessel elements are found primarily in the wood formed early in the season (early wood); this pattern is known as ring porous. Large vessel elements of other trees (like elm, Ulmus) occur more evenly in both early and late wood. This pattern is known as diffuse porous wood: with large vessel elements in both early and late wood.
Vesselless wood of conifers is of a simpler structure with relatively few cell types. There are simple rays and frequently resin ducts; resin is secreted by specialized cells.
In the tree trunk, the lighter wood near the periphery is called sapwood and has functioning xylem where most of the water and minerals are transported. Darker wood closer to the center is called heartwood and is a non-functional, darkly colored xylem (Figure \(4\)). Tracheary elements are dead cells and to block them, plants uses tylosesvessel element “stoppers” which also help control winter functioning of vessels. A tylose forms when a cell wall of parenchyma grows through a pit or opening into the tracheary element; they look like bubbles.
Most liliids (for example, palms) do not have lateral meristems and true wood. Some thickening does occur in a palm but this happens at the base of the tree, as a result of adventitious roots growing. Palms may also have diffuse secondary growth which is division and enlargement of some parenchyma cells. These processes do not compensate the overall growth of plant, and palms frequently are thicker on the top than on the bottom. Few other liliids (like dragon blood tree, Dracaena) have anomalous secondary growth which employs cambium but this cambium does not form the stable ring.
Constantly thickening stem requires constantly growing “new clothes”, secondary dermal tissue, periderm. Periderm is a part of bark. Bark is everything outside vascular cambium. It is unique structure which is sometimes called “tertiary tissue” because it consists of primary and secondary tissues together:
• \(\mbox{trunk} = \mbox{wood} + \mbox{vascular cambium (``cambium'')} + \mbox{bark}\)
• \(\mbox{wood} = \mbox{secondary xylem} + \mbox{primary xylem} + \mbox{[pith]}\)\(^{[1]}\)
• \(\mbox{bark} = \mbox{bast (primary + secondary phloem)} + \mbox{periderm} + \mbox{[cortex]} + \mbox{[epidermis]}\)
• \(\mbox{periderm} = \mbox{[phelloderm]} + \mbox{cork cambium (phellogen)} + \mbox{cork (phellem)}\)
Each year, a new layer of phellogen (cork cambium) appears from the parenchyma cells of the secondary phloem which makes bark multi-layered and uneven. On the surface of a young stem, one may see lenticels, openings in phellem layer which supply the internals of the stem with oxygen; together with rays, lenticels work as ventilation shafts. To produce lenticels, some phellogen cells divide and grow much faster which will finally break the periderm open.
Apart from the lenticels, older or winter stems have leaf scars with leaf traces on their surface. The first are places where leaf petiole was attached, and the second are places where vascular bundles entered the leaf.
The secondary structure of root reminds the secondary structure of stem, and with time, these two organs become anatomically similar. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/07%3A_The_Origin_of_Trees_and_Seeds/7.01%3A_Secondary_Stem.txt |
Secondary stem allows for extensive branching. In seed plants, branching is based on the axial buds. These buds are located in axils of leaves and develop into secondary shoots. There are two main types of branching: monopodial and sympodial (Figure 7.3.1).
• Monopodial branching is when the buds do not degrade and all the shoots continue to grow.
• Sympodial branching is when the terminal buds do degrade (make FU and/or die out) and the lateral shoot closest to the terminal bud now becomes the terminal shoot and continues the vertical growth. This happens because the terminal SAM suppresses the downstream meristems by producing the auxin hormone (apical dominance). Apical dominance is a basis of multiple gardening trimming techniques.
Monopodial branching creates the conical (spruce-like) crown whereas sympodial branching will create crowns of many different shapes. Monopodial growth is considered to be more primitive. Some monopodial trees may even die if the terminal bud is damaged. Even more ancestral mode of branching is dichotomous, when every branch splits into two; this is frequent in lycopods and some other Pteridophyta.
7.03: Life Forms
Thickening and branching change the appearance of plant. The most ancient classification employ both branching and thickening and divide plants into trees, shrubs and herbs. This approach was the first classification of life forms. Life forms tell not about evolution, but about how plant lives. We still use this classification. With some modifications, it plays a significant role in gardening:
• Vines Climbing woody and herbaceous plants
• Trees Woody plants with one long-lived trunk
• Shrubs Woody plants with multiple trunks
• Herbs Herbaceous plants, with no or little secondary xylem (wood). Sometimes, divided further into annuals (live one season), biennials (two seasons) and perennials.
This classification system has many downfalls. What is, for example, the raspberry? It has woody stems but each of them lives only two years, similar to biennial herbs. Or what is duckweed? These small, water-floating plants with ovate non-differentiated bodies are hard to call “herbs”.
As one can see, the actual diversity of plant lifestyles is much wider than the classification above.
Architectural Models Approach
During the winter, it is easy to see that some tree crowns have similar principles of organization. In the winter-less climates, the diversity of these structures is even higher. On the base of branching (monopodial or sympodial), location of FU, and direction of growth (plagiotropic, horizontal or orthotropic, vertical), multiple architectural models were described for trees. Each model was named after a famous botanist such as Thomlinson, Corner, Attims, and others. In temperate regions, one of the most widespread models is Attims (irregular sympodial growth): birches (Betula) and alders (Alnus) grow in accordance with that model (Figure \(2\)). In tropical regions, many plants (like palms and cycads) have single thick trunks crowned with large leaves, this is Corner model (Figure 7.4.1).
7.04: Modified Shoot
Like leaves and roots, shoots and stems also have modifications. Some examples are rhizomes, stolons, tubers, bulbs, corms, thorns, spines, cladophylls, and stem traps. Rhizomes (example: ginger, Zingiber) are underground stems that burrow into the ground just below the soil surface, and usually tend to have small, scale-like leaves that are not photosynthetic. Buds from the axils of the leaves make new branches that will grow to become aboveground shoots.
Stolons (runners) are aboveground horizontal shoots, which sprout and produce a new plants (example: strawberry, Fragaria). Tubers (example: potatoes, Solanum) are enlarged portions of rhizomes. The “eyes” of potato are actually lateral buds and the tuber body is comprised of many parenchyma cells that contain amyloplasts with starch. Corms and bulbs are shoot structures that are used for storage. A corm (example: crocus, Crocus) is a short, thick underground storage stem with thin scaly leaves. A bulb (example: onion, Allium) differs from a corm in the fact that it stores its nutrients in its fleshy leaves (Figure \(2\)).
Thorns (example: hawthorn, Crataegus) are defensive shoots that help to protect the plant from predators. Spines are not modified stems, but rather modified, reduced leaves or stipules, or bud scales (example: almost all cacti, Cactaceae family). Prickles (example: rose, Rosa) are modified surface tissues of stem.
Cladophylls (examples: Christmas cactus, Schlumbergera; ribbon plant, Homalocladium) are leaf-like, flattened shoots. Phyllodes are actually leaf modifications (example: Australian acacias, Acacia) they visually similar to cladophylls but originated from flattened leaf petioles. Shoot insect traps are used by some carnivorous plants, such as bladderwort (Utricularia). The following table emphasizes the diversity of organ modifications:
Leaf Stem shoot
Absorption Absorption leaves (bromeliads) Rhizoids Default
Defense Spines, scales Thorns, prickles Spines
Expansion Plantlets Rhizomes, stolons, runners Adventive buds
Interactions Traps, sticky epidermis, urns, colored leaves Traps, insect nests Haustoria, mycorrhizae, root nodules, nematode traps, insect nests
Photosynthesis Default, phyllodes Cladophylls Green roots (orchids)
Storage Succulent leaves, pitchers Bulbs, corms, tubers Storage roots
Support Tendrils, false stems, floats, suckers Default, tendrils Buttress, aerial and contractile roots, suckers
Please note that superficially similar structures (e.g., shoot and leaf tendrils) might have different origin.
Raunkiaer’s Approach
Christen Raunkiaer used a different approach to classify life forms which is useful to characterize the whole floras (all plant species growing on some territory), especially temperate floras. He broke plants down into six categories: epiphytes, phanerophytes, chamaephytes, hemicryptophytes, cryptophytes and therophytes.
Epiphytes do not touch soil (they are aerial plants), phanerophytes have their winter buds exposed, chamaephytes “put” their winter buds under the snow, winter buds of hemicryptophytes on the soil surface, cryptophytes in the soil and/or under water, and therophytes do not have winter buds, they go through winter as seeds or vegetative fragments (Figure \(4\)). Typically, northern floras have more plants of last categories whereas first categories will dominate southern floras. Note that Raunkiaer “bud exposure” is not far from the hardiness in the dynamic approach explained below.
Dynamic Approach
There are many life forms classifications. This is because life forms represent numerous secondary patterns in plan diversity, along with the main pattern which taxonomy wants to describe.
Dynamic life forms classification uses the fact that in nature, there are no strict borders between different life forms. If we supply the pole to some shrubs, they may start to climb and therefore become vines. In colder regions, trees frequently lose their trunks due to low temperatures and form multiple short-living trunks: they become shrubs. Conversely, in tropics, many plants which are herbs in temperate regions, will have time to develop secondary tissues and may even become tree-like.
Dynamic approach uses three categories: hardiness, woodiness, and slenderness (Figure \(5\)). Hardiness is a sensitivity of their exposed parts to all negative influences (cold, heat, pests etc.) This is reflected in the level of plant exposure, plants which are hardy will expose themselves much better. Woodiness is the ability to make dead tissues, both primary and secondary (reflected in the percentage of cells with secondary walls). High woodiness means that plants will be able to support themselves without problems. Slenderness is an ability to grow in length (reflected in the proportion of linear, longer than wide, stems). Low slenderness results in rosette-like plants. Combining these three categories in different proportions, one may receive all possible life forms of plants.
These three categories could be used as variables of the 3D morphospace. Every numbered corner in the morphospace diagram (Figure \(5\)) represents one extreme life form:
1. Reduced floating annuals like duckweed (Lemna). Please note that zero hardiness is impossible; duckweed hardiness is just low.
2. Short annual herbs like marigold (Tagetes); they accumulate wood if warm season is long enough.
3. Bulb perennials like autumn crocus (Colchicum).
4. Australian “grass trees” (Xanthorrhea) with almost no stem but long life.
5. Herbaceous vines like hops (Humulus).
6. Monocarpic tree-like plants like mezcal agave (Agave).
7. Perennial ground-cover herbaceous plants like wild ginger (Asarum).
8. Trees like redwood (Sequoia).
What is even more important, all possible positions on the “surface” and inside this cube also represent life forms. For example, the dot marked with “B” are slender, woody but only partly hardy plants. The partial hardiness means that vertical axes will frequently die, and then new slender woody axes develop from scratch. Woody wines and creeping bushes will correspond well with this description. As you see, this morphospace not only classifies existing plants but also could predict possible life forms. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/07%3A_The_Origin_of_Trees_and_Seeds/7.02%3A_Branching_Shoot.txt |
When plants developed the secondary growth, the almost unlimited perspectives opened for enlarging their body. However, these giants faced a new problem.
Big animals like elephants, lions, and whales tend to produce minimal number of offspring but increase the child care to ensure survival. This is called K-strategy, this is opposite to r-strategy usually smaller creatures which employs big numbers of offspring, and most of them will not survive (Figure \(1\)).
Analogously, bigger plants would need to do the same as K-strategic animals: make few daughter plants but defend and supply them with all needs until they mature. However, big secondary thickening spore plants were not capable of family planning; they still made billions of spores and then left them to fend for themselves. Naturally, only few from these billions would survive to become fertilized.
Spore reproduction is cheap and efficient but as birth control is not available, results are unpredictable. Even worse, these spore tree forests were not at all stable: in accidentally good conditions, many spores would survive and make sporophytes which start to grow simultaneously and then suppress each other and even die from over-population. But if the environmental conditions are bad, then none of the gametophytes will survive so there would be no new saplings to replace the old trees.
It is similar to the so-called “dinosaur problem”. This situation arose when giant Mesozoic reptiles also lost the control for their offspring: their egg size was limited due to physical restrictions, therefore, young dinosaurs were so much smaller than adults; then the only possible strategy was to leave them alone (Figure \(2\)). As a result, at the end of Mesozoic dinosaurs either decreased in size (became birds), or went extinct.
Plants, however, kept their size and survived. This is because they developed the seed (Figure \(3\)). A seed is the result of enforced control of the sporophyte over the gametophyte. The idea of a seed is to hide most of the heterosporous life cycle inside mother plant (Figure \(3\)). In seed plants, everything happens directly on the mother sporophyte: growing of gametophytes, syngamy, and growing of daughter sporophyte. Consequently, the female spore (megaspore) never leaves the sporangium. It germinates inside, waits for fertilization and then the zygote grows into and embryo, still inside the same sporangium.
What will finally leave the mother plant is the whole female sporangium with gametophyte and embryo on it. This is the seedchimeric structure with mother (seed coat), daughter (embryo) and endosperm genotypes. It can be defined as chimeric structure with three genotypes: seed coat (mother plant megasporangium, \(2n\)), endosperm (female gametophyte, \(n\)), and daughter sporophyte (embryo, \(2n\)).
It should be noted here that flowering plants have endosperm of different origin; it is called endosperm\(_2\) and usually is triploid (\(3n\)) whereas female gametophyte endosperm is haploid (\(n\)) endosperm\(_1\)haploid nutrition tissue originated from female gametophyte. The other note is that apart from seed coat (which originates from integumentextra cover of megasporangium(s), megasporangium extra cover(s)), mother sporophyte also gives nucelluswall of megasporangium (wall of megasporangium) which sometimes is used as a feeding tissue for the embryo. This last tissue is called perispermnutrition tissue originated from nucellus (see).
One problem is still left. How will sperms reach female gametophyte and egg cell? The target is now high above the ground, on a branch of the giant tree. The only possible solution is pollination. Pollination is the distribution of the whole male gametophytes which are called pollen grains. Plants have no legs so they always need a third party in their sex, this is mostly wind or insects. A pollen grain is not a spore, mother sporophyte cares about male lineage too, and male spore grows into very small male gametophyte. It contains multiple haploid cells; some of which are sperms.
The lesser problem is: How would these sperms will swim to the egg cell? Some seed plants will excrete the drop of liquid from the top of the ovule (integument(s) + megasporangium), whereas the other, more advanced way is to grow a sperm delivery tool, the pollen tube (Figure \(4\)) made from one of the pollen grain cells. Fertilization with pollen tube is often called siphonogamy.
Consequently, seed plants with the pollen tube do not have flagella even on male gametes; these cells are spermatia: aflagellate, non-motile male gametes. (Below, we will continue to call all male gametes “sperms”). Pollen tube also allows only two male gametes per gametophyte: in living world, male gametes are usually competing for fertilization—this selects the best genotypes; whereas in higher seed plants, competition is between pollen tubes. Haploid pollen tube grows inside alien tissue of diploid sporophyte, so this growth is extremely slow in many seed plants. However, angiosperms made their pollen tubes grow fast.
With all these revolutionary adaptations, seed plants were first to colonize really dry places, and, in turn, allowed all other life to survive in arid climates.
The cycle of a seed plant (Figure \(4\)) begins with a sporophyte (\(2n\)) and has both the female and male organs where some cells undergo meiosis. Inside the ovule (which is the megasporangium with extra covers), female gametophyte (\(n\), future endosperm\(_1\)) produces the egg cells. Male gametophytes (pollen grains) ripen in the pollen sacseed plants: microsporangium which is the microsporangium. The pollen sac sends out the pollen grains which meet up with the ovule. The pollen grain then releases the sperms which fertilize the egg cell, and a zygote is formed. The zygote grows into embryo (which uses endosperm as a feeding tissue) and then into the sporophyte.
Several plant lineages met this “seed challenge”, there were seed lycophytes and also seed “horsetails”. However, seed ferns made it first and became ancestors of seed plants.
Seed Structure and Germination
Seeds are diverse. For example, in an onion (Allium), a seed (Figure \(6\)) has endosperm, one cotyledonembryonic leaf (embryonic leaf), radicle (embryonic root), and the lateral embryonic bud (plumula).
Beans (Phaseolus) and other Leguminosae are examples of seeds without endosperm—actually, it was there, but growing embryo usually eats it out completely. These seeds have two large cotyledons. Grass (Gramineae) seeds contain several specific organs, namely coleoptile, coleorhiza, and scutellum. The scutellum is an enlarged cotyledon, coleoptile is the bud cover, and coleorhiza covers the embryonic root, radicle (Figure \(7\)). Onion and grasses are monocots with lateral embryonic bud. Other seed plants have a terminal embryonic bud and two or multiple cotyledons. Pine (Pinus) is an example of a plant that has multiple (five or more) cotyledons. Some plants like orchids (Orchidaceae) do not have developed embryo and even endosperm in seeds, their germination depends on a presence of symbiotic (mycorrhizal) fungus.
The first step in germination and starts with the uptake of water, also known as imbition. After imbition, enzymes are activated that start to break down starch into sugars consumed by embryo. The first indication that germination has begun is a swelling in the radicle. In onion and pea (Pisum), a structure that looks like a hook goes up through the soil and expose cotyledons and both hypocotyl and epicotyl (first internode). In beans, grasses, and palms, only epicotyl is exposed aboveground whereas cotyledons and hypocotyl remain underground. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/07%3A_The_Origin_of_Trees_and_Seeds/7.05%3A_Origin_of_the_Seed.txt |
Seed plants consist of approximately 1,000 species of non-angiosperms (gymnosperms) and about 250,000 species of angiosperms. They have a sporic life-cycle with sporophyte predominance, and seeds. The gametophyte is reduced to cells inside the ovule or pollen grain. Males have a minimum number of cells being three and females being four. The antheridia are absent and in flowering plants (Angiospermae) and Gnetopsida the archegonia are also reduced. The sporophyte will always start as an embryo located inside the nutrition tissue, endosperm\(_1\) which is the female gametophyte or in endosperm\(_2\) (see the next chapter). Spermatophyta have axillary buds (buds in leaf axils). Like ferns, they are megaphyllous and homoiohydric, and have a secondary thickening. Higher groups of seed plants lost flagellate spermatozoa and developed pollen tubes. The classes of Spermatophyta are Ginkgoopsida, Cycadopsida, Pinopsida, Gnetopsida, and Angiospermae.
Ginkgoopsida is just one species; ginkgo or maidenhair tree (Ginkgo biloba). This plant is long extinct in the wild but is grown on Chinese temple grounds as a decorative tree. Ginkgo is a large tree bearing distinctive triangle-shaped leaf with dichotomous venation. This plant is also dioecious (as an exception among plants, Ginkgo has sexual chromosomes like birds and mammals) and the pollen is transported by wind to female (ovulate) trees. The pollen grains of the ginkgo plants produce two multi-flagellate spermatozoa; the edible seed is fruit-like and becomes ripe after lying on the ground for a long time. Maidenhair tree has symbiotic cyanobacteria in cells. As ginkgo probably went through the population bottleneck, there are very few, almost no, phytophagous insects that can damage ginkgo leaves. The only fungus which is capable to eat them, Bartheletia, is also a living fossil.
Cycadopsida—cycads is a class with few genera and about 300 species that grow mostly in tropics. Only one species grows naturally in the United States, Zamia pumila, and can be found in Florida and Georgia. Cycads are palm-like plants with large, pinnate leaves. Their wood is rich of parenchyma since stem has anomalous secondary thickening. They are all dioecious and its cone is large and protected by prickles and woody plates. The ovules of these plants are attached to modified leaves (megasporophylls) that are gathered in upright cones. Like ginkgo, they have multi-flagellate spermatozoa, archegonia and large oocyte. Cycad seeds are distributed by animals. Life cycle is extremely slow.
Pinopsida—conifers are the most widely known and economically important among gymnosperms. Conifers consist of approximately 630 species. Most of them are temperate evergreen trees, but some are deciduous, such as larch (Larix). The stem has a large amount of xylem, a small cork, and minute pith. The ovules are attached to specialized leaves, seed scales, and are compacted in cones with bract scales (Figure \(1\)). Some conifers, like junipers (Juniperus) and yews (Taxus), lack woody cones; these plants have fleshy scales. Seeds are distributed by wind and animals.
In all, conifer life cycle takes up to two years. Conifers do not have flagellate spermatozoa; their non-motile male gametes (spermatia) move inside long, fast-growing pollen tube. Among families of conifers, Pinaceae (pine family) have resin and needle-like leaves; Pinus have them in shortened shoots, brachyblasts, and their large cones have woody scales. Cupressaceae (cypress family) do not have resin, produce small cones that have a fused bract and seed scales, have dimorphic leaves, and some of their genera (like “living fossil” Metasequoia from China) are deciduous in an unusual way: they drop whole branches, not individual leaves.
Gnetopsida—gnetophytes are sometimes called chlamydosperms. They are a small class with only three genera that are not at all similar: Ephedra, Welwitschia, and Gnetum. While these plants morphologically remind of angiosperms, they are molecularly related more to other gymnosperms. Ephedra are horsetail-like desert leafless shrubs, Gnetum are tropical trees, and Welwitschia are plants which have a life form that is really hard to tell (Figure \(2\)).
Ephedra has archegonia, but in Gnetum and Welwitschia they are reduced. On the other hand, Ephedra and Gnetum have double fertilizationthe process when two brother male gametes fertilize two sister female cells: both male nuclei fuse with cells of the one female gametophyte (endosperm\(_1\)): with egg cell and another haploid cell, sister to the egg. Double fertilization in gnetophytes results in two competing embryos, and only one of them will survive in future seed.
Both Gnetum and Welwitschia have vessels (like angiosperms). Gnetum also has angiosperm-like opposite leaves with pterodromous venation, like, for example, coffee tree (however, this probably is a result of modification of dichotomous venation). Ovules of chlamydosperms are solitary and covered with an additional outer integument; the male gametes are spermatia moving inside pollen tube.
Welwitschia is probably most outstanding among gnetophytes. There is only one species that occurs in the Namibian desert. The best way to describe this plant is an “overgrown seedling.” It has a small trunk with two wide leaves that have parallelodromous venation. The secondary thickening is anomalous, wood has vessels. Plant is insect-pollinated, and its winged seeds are dispersed by the wind. Fertilization is not double, but, along with pollen tubes, involves the most crazy structures: prothallial tubes which grow from female gametophyte and meet with pollen tubes to make zygote.
Life cycles determine the basic diversity of plants, they designate plant phyla. Let us compare three types of life cycles again (Figure \(3\)) and again (Figure \(4\)). What is visible on all these schemes, as well as on all similar schemes from above, is growing complexity of cycle, growing reduction of haploid stage, and growing self-similarity within the cycle. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/07%3A_The_Origin_of_Trees_and_Seeds/7.06%3A_Spermatophyta_-_Seed_Plants.txt |
Thumbnail: Anagallis arvensis f. azurea. Image used with permission (CC BY-SA 3.0; Lumbar).
08: The Origin of Flowering
Flowering plants (angiosperms, Angiospermae) are sometimes referred to as “Spermatophyta 2.0.”, or “upgraded gymnosperms”. In fact, there is no single character which unequivocally differs flowering plants from other seed plants. Only several characteristics combined together will distinguish angiosperms. Flowering plants have their ovules inside an additional cover: pistil which corresponds with megasporophyll (sporangium-bearing leaf); later, the pistil develops into the fruit. These plants have an almost complete reduction of gametophytes: three or even two cell of the pollen (male gametophyte) and seven (sometimes even four) cells in embryo sac (female gametophyte), there are no archegonia or antheridia. Like gnetophytes, they have double fertilization. The sperms (spermatia) come through the pollen tube (like in conifers and gnetophytes). One sperm fertilizes the egg cell, and the other sperm fertilizes the biggest cell of embryo sac (Figure $1$).
While the first fertilization results in a “normal” diploid zygote which grows into embryo, the second fertilization ignites the process of feeding tissue development. This feeding tissue is endosperm$_2$, frequently triploid ($3n$) since it originates from the sperm and cell with two nuclei and sperm, or diploid ($2n$), if the biggest cell of embryo sac (central cell) had one nucleus only.
Double fertilization may be explained in several ways:
1. the second fertilization results in second, “altruistic” embryo which sacrifices itself to feed the sibling;
2. second fertilization is only a signal which initiates the development of endosperm and it does not really matter which genotype it has;
3. to make a functional nutrition tissue, angiosperms need a polyploid genome whereas its origin is not so important.
Second hypothesis explains well how angiosperms saved time and resources. Third hypothesis is indirectly supported by the fact that in animals, namely two families of scale insects, there is a similar process (zygote descendant joins sister cell of the egg) which resulted in special polyploid bacteriome, tissue rich of symbiotic bacteria.
One way or another, flowering plants abandoned pre-fertilization development of the nutrition tissue, and changed endosperm$_1$ to endosperm$_2$ (Figure $2$).
In the Mesozoic era, gymnosperms were the dominating plants of the tree story. However, in the uderstorey, herbaceous spore plants did not surrender to seed plants and were still dominating. Amazingly, there were almost no herbaceous gymnosperms! The explanation is that gymnosperms, being quite advanced in general, had a slow and ineffective life cycle.
While ferns and mosses have one “gunshot” in their life cycles (this is fertilization, because dissemination of spores is mainly random), seed plants have two: first, they want to pollinate the target plant, and second, they still need to fertilize egg cell. Naturally, keeping these two
“gunshots” is more complicated then keeping one.
Second shot ancestrally uses water, but higher seed plants managed to get rid of it with pollen tube. First shot used wind which is a natural pollination agent. However, more sophisticated pollination (like insect pollination) was hard to achieve, partly because it requires edible parts like nectar or excess pollen.
If gymnosperms were to increase the speed of life cycle, make more sexual structures, grow rapidly, improve vegetative reproduction, make better pollination and seed dispersal, they could win the competition with ferns in the understory. This is exactly what happened with flowering plant ancestors. Flowering plants grow fast and restore missing (eaten) parts with high speed, they parcellate (clone from body parts) easily, they have small and numerous floral units (flowers) which are frequently bisexual but protected from self-pollination and adapted to insect pollination, they guard ovules with pistil wall, their pollen tube grows in hours (not days and weeks), they use fruits to distribute seeds.
Since gymnosperm fertilization occurs after gametophyte development, there is frequently a waste of resources: if fertilization does not occur, then all nutrition tissue (endosperm$_1$) will be lost; such empty seeds are unfortunately not rare among gymnosperms. Fertilization of angiosperms involves the signaling event: when second sperm fertilizes central cell, it “rings a bell” saying that the first fertilization is now completed. Endosperm (endosperm$_2$ in that case) will start to develop only after the fertilization, and resources will not be wasted. This agile life cycle is the main achievement of angiosperms.
There is a growing evidence that these ancestors were paleoherbs, herbaceous plants (and maybe, even water plants like one of the most primitive angiosperms, fossil Archaefructus, or basal extant Ceratophyllum). Right after they won a competition with herbaceous spore plants, they started to conquer the tree storey again, and now, angiosperms dominate the Earth. There are more than 250,000 species of them which is more than any other group of living beings except insects. There are about 300 families and around 40 different orders. The only places that angiosperms do not grow are the open ocean and the central Antarctic.
The life cycle of angiosperm (Figure $3$) begins much like that of other seed plants; however, when it reaches the point of fertilization, it changes. The male gametophytes, pollen grains, produce pollen tubes which rapidly grow to the ovule and deeper, to the embryo sac. The embryo sac typically has seven cells and eight nuclei (two nuclei in the central cell). The first sperm fertilizes the egg and produces the zygote whereas the second sperm fertilizes the central cell and produces the mother cell of the endosperm$_2$:
1. 1st sperm cell (1st spermatium, $n$) + egg cell ($n$) $\rightarrow$ zygote ($2n$)
2. 2nd sperm cell (2nd spermatium, $n$) + central cell ($2n$ or sometimes $n$) $\rightarrow$ mother cell of endosperm$_2$ ($3n$ or sometimes $2n$)
(At the time of fertilization, central cell could be haploid, with one nucleus, or diploid, with two nuclei; this is because it runs mitosis without cytokinesis at the end. Consequently, nucleus of the second sperm fuses with either one or two nuclei and endosperm$_2$ is either diploid or (more often) haploid.)
At the end of life cycle, the flowering plant develops the fruit (Figure 8.2.1). Each part of the fruit is of different origin: fruit skin and wall are from mother plant pistil, seed coat is from mother plan ovule, endosperm$_2$ is a result of second fertilization, and embryo is a daughter plant resulting from the first fertilization.
What is interesting, the embryo of angiosperms is still parasitic: it lives on endosperm which originates from (fertilized, ignited) cell of female gametophyte—in essence, still similar to mosses. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/08%3A_The_Origin_of_Flowering/8.01%3A_Spermatophyta_2.0.txt |
The Flower
A flowercompact generative shoot with sterile, male and female zones, specifically in that order, other flower terms see in the separate glossary in the text (Figure $3$) is a compact generative shoot that is comprised of three zones: sterile (perianth), male (androecium), and female (gynoecium) (Figure $2$). Perianth is typically split into green part (calyx, consists of sepals) and color part (corolla, consists of petals). Sometimes perianth consists of similar parts which are neither sepals nor petals: tepals. This might be seen in the tulip (Tulipa) flower where tepals change their color from green (like in calyx) to red, white or yellow (like in corolla).
The general characters that a flower has are sex, merosity, symmetry, and the position of the gynoecium. Merosity is simply the number of parts in each whorl of a plant structure, whether it is the number of sepals, petals in a corolla, or the number of stamens. The position of the gynoecium refers to whether the ovary is superior or inferior (Figure $6$). Inferior ovary (cucumber, Cucumis, apple Malus or banana Musa) will develop into a fruit where stalk and remnants of perianth are on the opposite ends, whereas superior ovary will make fruit where stalk is placed together with perianth (like in tomatoes, Solanum). More terms are described in the following separate small glossary:
FLOWER PARTS occur in whorls in the following order—sepals, petals, stamens, pistils.
(The only exceptions are flowers of Eupomatia with stamens then perianth, Lacandonia with pistils then stamens, and some monocots like Triglochin, where stamens in several whorls connect with tepals.)
PEDICEL flower stem
RECEPTACLE base of flower where other parts attach
HYPANTHIUM cup-shaped receptacle (Figure $2$)
PERIANTH = CALYX + COROLLA
SEPALS small and green, collectively called the CALYX, formula: K
PETALS often large and showy, collectively called the COROLLA, formula: C
TEPALS used when sepals and petals are not distinguishable, they form SIMPLE PERIANTH, formula: P
ANDROECIUM collective term for stamens: formula: A
STAMEN = FILAMENT + ANTHER
ANTHER structure containing pollen grains
FILAMENT structure connecting anther to receptacle
GYNOECIUM collective term for pistils/carpels, formula: G. Gynoecium can be composed of:
1. A single CARPEL = simple PISTIL, this is MONOMERY
2. Two or more fused CARPELS = compound PISTIL, this is SYNCARPY
3. Two or more unfused CARPELS = two or more simple PISTILS, this is APOCARPY
(Note that variant #4, several compound pistils, does not exist in nature.)
To determine the number of CARPELS in a compound PISTIL, count LOCULES, points of placentation, number of STYLES, STIGMA and OVARY lobes.
Figure $3$ Most important parts of the flower.
PISTIL Collective term for carpel(s). The terms CARPEL and PISTIL are equivalent when there is no fusion, if fusion occurs then you have 2 or more CARPELS united into one PISTIL.
CARPEL structure enclosing ovules, may correspond with locules or placentas
OVARY basal position of pistil where OVULES are located. The ovary develops into the fruit; OVULES develop into seeds after fertilization.
LOCULE chamber containg OVULES
PLACENTA place of attachment of OVULE(S) within ovary
STIGMA receptive surface for pollen
STYLE structure connecting ovary and stigma
FLOWER Floral unit with sterile, male and female zones
ACTINOMORPHIC FLOWER A flower having multiple planes of symmetry, formula: $\ast$
ZYGOMORPHIC FLOWER A flower having only one plane of symmetry, formula: $\uparrow$
PERFECT FLOWER A flower having both sexes
MALE / FEMALE FLOWER A flower having one sex, formula: ♂ / ♀ (Figure $5$)
MONOECIOUS PLANTS A plant with unisexual flowers with both sexes on the same plant
DIOECIOUS PLANTS A plant with unisexual flowers with one sex on each plant, in effect, male and female plants
SUPERIOR OVARY most of the flower is attached below the ovary, formula: $G_{\underline{\dots}}$
INFERIOR OVARY most of the flower is attached on the top of ovary, formula: $G_{\overline{\dots}}$
(Inferior ovary only corresponds with monomeric or syncarpous flowers.)
WHORL flower parts attached to one node
Flower formula and diagram
Since there are so many terms about flowers, and at the same time, flower structure and diversity always were of immense importance in botany, two specific ways were developed to make flower description more compact. First is a flower formula. This is an approach where every part of flower is designated with a specific letter, numbers of parts with digits, and some other features (whorls, fusion, position) with other signs:
$\ast K_{4}C_{4}A_{2+4}G_{\underline{(2)}}$: flower actinomorphic, with four sepals, four petals and six stamens in two whorls, ovary superior, with two fused carpels
$\uparrow K_{(5)}[C_{(1,2,2)}A_{2,2}]G_{\underline{(2\times2)}}$: flower zygomorphic, with five fused sepals, five unequal fused petals, two-paired stamens attached to petals, superior ovary with two subdivided carpels
$\ast K_{(5)}C_{(5)}[A_{5}G_{\underline{(3)}}]$: actinomorphic flower with five fused sepals and five fused petals, five stamens attached to pistil, ovary inferior, with three fused carpels
The following signs are used to enrich formulas:
PLUS “+” is used to show different whorls; minus “$-$” shows variation; “$\vee$” = “or
BRACKETS “[]” and “()” show fusion
COMMA “,” shows inequality of flower parts in one whorl
MULTIPLICATION “$\times$” shows splitting
INFINITY “$\infty$” shows indefinite number of more than 12 parts
Flower diagram is a graphical way of flower description. This diagram is a kind of cross-section of the flower. Frequently, the structure of pistil is not shown on the diagram. Also, diagrams sometimes contain signs for the description of main stem (axis) and flower-related leaf (bract). The best way to show how to draw diagram is also graphical (Figure $7$); formula of the flower shown there is $\ast K_{5}C_{5}A_{5}G_{\underline{(5)}}$.
ABC model
All parts of flower have a specific genetic developmental origin explained in the ABC model (Figure $8$). There are three classes of genes with expression which overlaps as concentric rings, and these genes determine which cells develop into particular organ of the flower. If there are A and C genes expressed, cells will make sepals and pistils. In areas where A and B are active, petals will form; areas where B and C are active are the sites where stamens will appear. A will make a sepal, C will “create” a carpel:
• A alone $\rightarrow$ calyx
• A + B $\rightarrow$ corolla
• C + B $\rightarrow$ androecium
• C alone $\rightarrow$ gynoecium
Origin of flower
An example of a primitive magnoliid flower would be Archaefructus which is a fossil water plant from the lower Cretaceous time period in China. Its fructifications (flower units, FU) were very primitive and did not yet form a compacted flower, instead, there were multiple free carpels, and paired stamens (Figure $9$).
Another ancestral flowering plant is Amborella,a small forest shrub of New Caledonia (Figure $10$), which is an island in the Pacific Ocean.
Amborella has irregular flowers, a stylar canal, unusual 5-celled embryo sacs that have one central cell, and only four other cells (egg cell and its “sisters”). A stylar canal is a canal that leads to the ovary that the pollen tubes pass through so these plants are not completely “angiospermic”, this represents one of the stages of the origin of pistil (Figure $11$).
The Inflorescence
Inflorescence is an isolated generative shoot (shoot bearing FU). Together, inflorescences make generative shoot system. Its diverse structure is of not lesser importance than the structure of vegetative shoot system.
The vast diversity of inflorescences can be split into four groups, or “models” (Figure $12$). Sole flower is sometimes considered as a “Model 0”.
Two models are most widespread. Model I inflorescences are based on the racemebasic monopodially branched inflorescence (Model I) (monopodially branched generative shoot). They are simple or double and mostly monopodial (Figure $14$).
Model II inflorescences (Figure $13$) bear or consist of closed (sympodially branched) units. The most complete but more rare variant is thyrsus, whereas reduced variants (monochasia and dichasia) are more frequent.
Pollination
Pollination could be of two types: self- and cross-pollination. Cross-pollination can happen in both abiotic and biotic ways. Abiotic would be represented by gravity, wind, or water; biotic would be performed by agents like insects, birds, bats, or in some cases tree mammals like possums. Wind-pollination is seen as being wasteful and unintelligent due to the fact that the plant needs to produce so much more pollen without any precise targeting.
Adaptation to the particular pollination agent results in different pollination syndromes. For example, cup-shaped flowers are usually pollinated with massive animals like beetles and even bats. Funnel-shaped flowers as well as labiate flowers (with lips), are adapted to flies and bees. Flowers with long spurs attract butterflies and birds (like hummingbirds or sugarbirds).
Self-pollination often exists like a “plan B”, in case cross-pollination is, for some reason, impossible. Sometimes, self-pollinated flowers even do not open; these flowers are called cleistogamous.
If pollination needs to be avoided, apomixis will prevent it. Apomixis requires reproductive organs, but there is no fertilization. One type of apomixis is apospory when an embryo develops from the maternal diploid tissue when an embryo develops from the maternal diploid tissue, but does not go through the meiosis stage. In this process, asexual reproduction will have become vegetative. Another type of apomixis would be apogamy (parthenogenesis) when embryo develops from an unfertilized gamete after diploidization has occurred. Here, vegetative reproduction evolved from sexual reproduction.
The Fruit
A fruit is defined as ripened ovary, flower, or whole inflorescence. The origins of the fruit coat and the pericarp (Figure $15$) which is comprised of the exocarp, mesocarp, and endocarp, are mostly from the wall of the pistil.
Fruits can be simple, multiple, or compound. *Simple fruitssimple fruitfruit originated mostly from one pistil come from a single pistil (like cherry, Prunus). *Multiple fruitsmultiple fruitfruit originated from many pistils are formed from many pistils of the same flower (strawberry, Fragaria). A compound fruitfruit originated from the whole inflorescence: infrutescence (infructescense) would be a pineapple (Ananas) or fig (Ficus) which comes from multiple flowers (inflorescence).
Fruits can be dry or fleshy. An example of dry fruit is a nut like peanut (Arachis) or walnut (Juglans). Examples of fleshy fruits include apples (Malus) or oranges (Citrus).
Fruits also delegate dispersal function to their different parts. *Dehiscent fruitsdehiscentfruits which open (like canola, Brassica) open and delegate dispersal to individual seeds.
Indehiscent fruits (like papaya, Carica) will not open and will be dispersal units (diaspores) themselves.
Schizocarp fruits (like in spurge, Euphorbia or maple, Acer) are in between: they do not open but break into several parts, and each of them contains one seed inside. For example, maple fruit consists of two “wings”, each of them contains the part of fruit and one seed.
In addition, simple fruits could be monomerous (1-seeded) like nut or achene (sunflower, Helianthus), or bear multiple seeds (like follicle in tulip, Tulipa).
All these different variants have their own names partly described in the following table:
Type Consistency Opening Example(s)
Simple Fleshy Indehiscent Drupe, Berry, Hesperidium, Pome
Simple Dry Dehiscent Capsule, Legume (pod), Silique (Figure 8.3.1)
Simple Dry Schizocarpic Regma, Samara, Shizocarp
Simple Dry Indehiscent Caryopsis (grain), Nut (incl. acorn), Achene
Multiple Fleshy Indehiscent Multiple drupe
Multiple Dry Dehiscent Follicle
Multiple Dry Indehiscent Multiple nut
Compound Fleshy Indehiscent Compound berry
Compound Dry Indehiscent Compound nut | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/08%3A_The_Origin_of_Flowering/8.02%3A_The_Flower_and_the_Fruit.txt |
Angiosperms is a giant (quarter of million species) class with four subclasses (Figure $1$):
• Magnoliidae being the most primitive with flowers of numerous free parts (like water lily, Nymphaea, fossil Archaefructus and Amborella);
• Liliidae or monocots are grasses, palms, true lilies and many others with trimerous flowers;
• Rosidae with pentamerous or tetramerous flowers and free petals;
• Asteridae most advanced, bear flowers with fused petals and reduced number of carpels.
Rosids and asterids each comprise about 1/3 of angiosperm diversity.
Among the numerous taxonomic groups described by scientists in the last 300 years, families of flowering plants hold the distinct place. They were established in collaborative efforts of French botanists, namely Michel Adanson and Antoine
Jussieu. Adanson based his research on methods which are now frequently called “bioinformatics” and therefore was long ahead of his time. Jussieu proved Adanson’s ideas by establishing the living garden where plants were arranged by these families. At first, families were not accepted by “fathers of botany” like Carolus Linnaeus. But with time, more and more facts were accumulated which support the ideas enclosed in the families differentiation. The most amazing was almost absolute support of plant families concepts with new molecular methods. Many groups which looked stable (like orders of birds and mammals) appeared less robust than plant families. This is why plant families are so important.
Practically, families provide a great help in knowing plants. For example, the flora of whole North America has 20,000 species of plants. It is almost impossible to remember them all. However, there are only 200 plant families in North America. Therefore, knowing the family saves lots of time and efforts in plant determination.
Several plant families are especially important since they play a big role in economics, form widespread types of vegetation, or are simply extremely rich in species. Three of these families will be characterized below. Characterization of family should follows the plan below:
1. Meta-information: name, position in classification, number of species, distribution
2. Ecological preferences
3. Morphology and anatomy of stem, leaf and root
4. Generative organs from inflorescence to fruit, including flower diagrams and formulas. Seed.
5. Representatives and their importance
Leguminosae, or Fabaceae—legume family
Belong to rosids (Rosidae). Up to 17,000 species, third largest angiosperm family after Compositae (aster family) and Orchidaceae (orchids). Widely distributed throughout the world, but preferably in tropics. Have root nodules with nitrogen-fixing bacteria. Leaves alternate, pinnately compound (once or twice), with stipules.
Three subfamilies (Caesalpinioideae, Mimosoideae, Papilionoideae) often treated as separate families. Sepals 5, united. Petals 5, in Papilionoideae they are free, unequal and have special names: banner, keel and wing (Figure $2$), in Mimosoideae they fuse and form tube. Stamens often 10 with 9 fused and one free stamen; in Mimosoideae, stamens are numerous. Singe pistil with single carpel. Flower formula of Mimosoideae is $\ast K_{(5)}C_{(5)}A_{5-\infty}G_{\underline{1}}$ Papilionoid legumes have formula like $\uparrow K_{(5)}C_{1,2,2}A_{1,[4+5]}G_{\underline{1}}$
Fruit is a legume (pod): dehiscent with one camera; this is different from silique of cabbage family (Cruciferae) which has two cameras (Figure $3$). Mature seeds without endosperm.
Representatives of Leguminosae:
• Mimosoideae: stamens numerous, petals connected
-Acacia—dominant tree of African and Australian savannas, often with phyllodes
-Mimosa—sensitive plant
• Papilionoideae: stamens 9+1, petals free; this subfamily contains many extremely important food plants with high protein value
-Glycine—soybean
-Arachis—peanut with self-buried fruits
-Phaseolus—bean
-Pisum—pea
Compositae, or Asteraceae—aster family
Belong to asterids (Asteridae). More than 20,000 species—second place in flowering plants. Cosmopolitan, but better represented in temperate and subtropical regions. Prefer open spaces. Herbs, rarely woody plants; store carbohydrates as inulin (not starch), sometimes have resin or laticifers (subfamily Cichorioideae). Leaves are alternate or opposite, without stipules, with pterodromous venation.
Flowers in involucrate heads which mimic one flower (Figure $4$). Calyx reduced to hairs or bristles (pappus), petals fused in tube or ligula (with 5 or 3 teeth). Stamens 5, fused by anthers, pollen lifted up and distributed by outer sides of stigmas, this is secondary pollen presentation (Figure $5$). Pistil has 2 carpels, ovary inferior. Fruit is achene, mature seed has almost no endosperm. Flower formula of the tubular (disk) flower is $\ast K_{\infty}C_{(5)}A_{(5)}G_{\overline{(2)}}$ Ligulate (ray) flower typically has formula like $\uparrow K_{\infty}C_{(3\vee5)}A_{(5)}G_{\overline{(2)}}$
Fruit of aster family is one-seeded achene (it is a frequent mistake to call it “seed”). In achene, walls of inferior ovary are tightly fused with seed coat. Achenes frequently bear diverse dispersal structures: trichomes, teeth, hooks and others.
Oil plants, vegetables, ornamentals and medicinal plants distributed in multiple subfamilies, most important are three:
• Carduoideae: mostly tubular flowers
-Centaurea—knapweed
-Cynara—artichoke
-Carthamus–safflower
• Cichorioideae: mostly 5-toothed ligulate (pseudo-ligulate) flowers + lacticifers with latex
-Taraxacum—dandelion
-Lactuca—lettuce
• Asteroideae: tubular + 3-toothed ligulate flowers
-Helianthus—sunflower (BTW, “canola”, or Brassica napus from Cruciferae is the second main source of vegetable oil)
-Artemisia—sagebrush
-Tagetes—marigold and lots of other ornamentals
Gramineae, or Poaceae—grass family
Belong to liliids (Liliidae, monocots). Approximately 8,000 species distributed throughout the world, but most genera concentrate in tropics. Prefer dry, sunny places. Often form turf (tussocks)—compact structures where old grass stems, rhizomes, roots, and soil parts are intermixed. Grasses form grasslands—specific ecological communities widely represented on Earth (for example, North American prairies are grasslands). Stems of grasses are usually hollow and round. Leaves with sheaths.
Flowers reduced, wind-pollinated, usually bisexual, form complicated spikelets. Each spikelet bears two glumes; each flower has lemma and palea scales (Figure $6$). Perianth is reduced to lodicules. Stamens from 6 to 1 (most often 3), with large anthers. Flower formula is $\uparrow P_{0-3}A_{0-3+2-3}G_{\underline{(2)}}$
Fruit is a caryopsis; it includes flower scales. Seed contains embryo with coleoptile, coleorhiza and scutellum (Figure 7.5.7).
Most primitive grasses are bamboos (Bambusoideae subfamily). There are many other subfamilies. Two are especially economically important:
• Pooid (Pooideae) grasses usually are C$_3$ plants, wheat (Triticum), rice (Oryza), barley (Hordeum) and rye (Secale) belong to this group.
• Panicoid (Panicoideae) grasses are mostly C$_4$ plants like corn (Zea), sorghum (Sorghum) and sugarcane (Saccharum).
| textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/08%3A_The_Origin_of_Flowering/8.03%3A_Three_plant_families_you_wanted_to_know_but_were_too_afraid_to_ask.txt |
Plants are main components of terrestrial ecosystems, they are primary producers, and almost all terrestrial life if based on plants. Consequently, plants will determine how a particular territory might look, which could be, for example, grassland, tundra, or forest. These types of vegetation (i.e., visually different plant communities) will have different occurrence on Earth. Below is the list of the most important types (they also called biomes):
Tundra Small-sized plants adapted to the short season, wet soils and sometimes also permafrost
Taiga Conifer forests
Deciduous forest Broadleaved temperate forests. The other type of deciduous forests are dry forests of tropical climates.
Grassland Prairie (North America), steppe (Eurasia), savanna (Africa and Australia), llanos (north South America), pampas (south South America)
Shrubland Chaparral (North America), maquis (Mediterranean), fynbos (South Africa), bush (Australia)
Desert Different from shrubland by plants staying apart and soil surface visible
Tropical forest Selva, tropical rain forest: humid and warm environment, the peak of Earth biodiversity
Naturally, these biomes are directly related with the climate, mostly with the coldest temperatures and amount of precipitation. If the Earth would be one continent, then these vegetation types will be arranged from a pole to equator exactly in the order from the list above. However, the real picture is more complicated (Figure \(1\).)
Some smaller biomes, especially different kinds of wetlands (like sphagnum bogs or mangroves) are significantly dispersed, sometimes even intra-zonal (occur in different climatic zones).
9.02: Geography of Vegetabilia
While taiga forest looks similar in Alaska (North America) and Patagonia (South America), a closer look will immediately reflect that species, genera and even families of plants are quite different. As an example, both Alaska and Patagonia forests include large conifers, but while in Alaska we frequently see members of Pinaceae family like spruces (Picea) or firs (Abies), in Patagonia these trees are absent and “replaced” with superficially similar trees of Araucariaceae and Podocarpaceae conifers.
Analogously, Arizona desert is similar to African Kalahari but while American deserts are rich with cacti, similarly looking African plants belong to completely different group, succulent spurges (Euphorbia). The effect of these differences on the botanically educated traveler is a bit similar to the nightmare when you first see a familiar thing but approach it—and realize that this is something completely alien and strange.
These floristic differences are due to the various geological and biological histories of these places. Plant biogeography studies them, explains them and creates the floristic kingdoms classification (Figure \(1\)) which takes into account not ecological but taxonomical (phylogenetic) similarities and differences.
There are only five floristic kingdoms:
Holarctic Most of North America and temperate Eurasia. Holarctic kingdom is largest, it covers two continents and most of Northern hemisphere. Typical representatives are pines (Pinus) and oaks (Quercus).
South American From South Florida to Patagonia and Antarctic islands. Aroids (Araceae family) and bromeliads (Bromeliaceae) are very common South American groups.
African Excluding Mediterranean Africa (very north of the continent). African acacias (Senegalia) are common to the most of savannas there.
Sometimes, botanists separate the southern tip of Africa into smallest Cape floristic kingdom which has multiple endemic plant genera (like Berzelia, kolkol) and even whole families.
Indo-Pacific From India to pacific islands including Hawaii. This kingdom is especially rich of orchids (Orchidaceae); tropical pitcher plants (Nepenthes) grow only there.
Australian Australia, Tasmania and New Zealand. Numerous specific plant groups, including Eucalyptus, Banksia and many others.
Every plant group has a specific range—the area of distribution. There are multiple common ranges, e.g., circumpolar (groups distributed across North Pole, both in North America and Eurasia, like spruces, Picea) or Gondwanian (groups distributed in the South Africa, Australia and South America, like protea family, Proteaceae). Sometimes, there are disjunctions (breaks in range); a typical explanation for the disjunction is long-distance dispersal (like for ispaghula, Plantago ovata in California and West Asia) or extinction in the connecting places (like for tulip tree, Liriodendron in China and Atlantic states).
Recently, many plants became invasive after being introduced willingly (e.g., as forage plants) or accidentally (e.g., with seeds of other plants). These plants (like Eurasian spotted knapweed, Centaurea stoebe in North America, or North American box elder, Acer negundo in Eurasia) are often noxious since they tend to destroy the native vegetation.
It is frequently said that humans stated the new epoch of Earth life, homocene—era of Homo sapiens dominance, homogenization and great extinction of the flora and fauna. We need to stop that! | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/09%3A_Plants_and_Earth/9.01%3A_Geography_of_Vegetation.txt |
The goal of taxonomy is to describe diversity, provide an insight to the evolutionary history (phylogeny), help to determine organisms (diagnostics) and allow for taxonomic estimations. The latter means that if we know features of one plant, the taxonomically close one should have similar features. For example, plants from cabbage family (Cruciferae) contain mustard oil (which is responsible for the horseradish taste of many of them). DNA analysis shows that papaya (Carica from Moringaceae family) is taxonomically close to Cruciferae. We may guess that papaya also have mustard oil, and this is true! Papaya seeds have the prominent horseradish taste.
One of the oldest methods of taxonomy is expert-based. Experts produce classifications based of their exclusive knowledge about groups. First taxonomic expert was Carolus Linnaeus (XVIII century). Experts use a variety of methods, including phenetics, cladistics (see below), general evolutionary approach, their ability to reshape available information and their intuition. Their goal is to create the “mind model” of diversity and then convert it to classification, using neighbor groups as a reference (for example, to assign ranks).
10: Methods of Taxonomy and Diagnostics
The more contemporary, much more formalized than expert-based is cladistics. Below, cladistic procedure is explained using artificial example of three organisms. The goal of the analysis is the creation of a phylogeny tree (cladogram) which becomes the basis of classification. Below is a short instruction which explains the basics of the cladistic analysis on the artificial example of several “families” of plants.
1. Start with determining the “players”—all subtaxa from bigger group. In our case, it will be these three “families”:
Alphaceae
Betaceae
Gammaceae
2. Describe these three groups:
Alphaceae: Flowers red, petioles short, leaves whole, spines absent
Betaceae: Flowers red, petioles long, leaves whole, spines absent
Gammaceae: Flowers green, petioles short, leaves dissected, spines present
3. Determine individual characters (we will need at least \(2N+1\) characters where \(N\) is number of studied taxa):
(1) Flower color
(2) Petiole size
(3) Dissection of leaves
(4) Presence of spines
4. Polarize the characters: every character should have at least two character states where “0” is ancestral, plesiomorphic state, and “1” is derived, apomorphic state. To decide which state is plesiomorphic and which is apomorphic, use these kinds of arguments:
(a) Historical evidence (e.g., from fossils)
(b) Developmental evidence
(c) Comparative evidence
5. If this information is absent, find the outgroup which is the most ancestral, most early divergent taxon related to our groups. In our case, we will employ outgroup:
Omegaceae: Flowers green, petioles short, leaves whole, spines absent.
6. Label characters with “1” (apomorphic) or “0” (plesiomorphic):
(1) Flower color green—0; red—1
(2) Petiole size small—0; big—1
(3) Dissection of leaves absent—0; present—1
(4) Absence of spines—0; spines present—1
7. Make character table containing both subtaxa and labeled characters:
(1)
(2)
(3)
(4)
Alphaceae
1
0
0
0
Betaceae
1
1
0
0
Gammaceae
0
0
1
1
(Outgroup, Omegaceae evidently has all zeroes.)
8. Start the tree from outgroup (this step is not absolutely necessary but will make phylogeny more clear):
9. Most ancient ingroup (Alphaceae) is a first branch, label it with bar which shows acquisition of the advanced state of first character (red flower color):
10. Attach more and more sub-taxa. It is possible to do this randomly (like most of phylogeny software), or attach groups to make shortest tree. For example, Betaceae and Gammaceae have equal number of synapomorphies but Betaceae have only one character different from Alphaceae it is sensible to attach it first, and then attach Gammaceae:
This tree has 4 evolutionary events (length \(=4\))
11. If Gammaceae was attached first, then resulted tree will be be one step longer:
There are five evolutionary events; in other words, length of tree \(=5\). (“p” are parallel characters (homoplasies); there might be also reversals (“r”), when apomorphic character disappears).
There could be also tree with length \(=6\), or even more if tree includes character reversals, but all of them will be longer than the first one.
12. Choose the shortest, most parsimonous tree. Second tree has 5 events, first tree has 4 events, others could be only longer. Consequently, we choose the first tree. By the way, many computer programs do not follow the procedure above strictly and simply produce all possible trees, and finally choose the shortest.
13. Use the chosen tree as a source of classification:
Order Alphales
1. Family Alphaceae
2. Family Betaceae
Order Gammales
1. Family Gammaceae
This step is needed only if you wish to convert cladogram into traditional, classification. In fact, cladograms are rank-free and might be used as is.
Cladograms often used as source of time trees which are made with genetic information and information from fossils. If we know the age of taxonomic group, we can use it as more objective replacement of rank.
Ability to review and compare phylogenetic trees requires understanding of several basic rules, for example:
1. Tree edges may be freely rotated in any direction. For example, these trees are same:
2. Direction of branches also does not matter. These trees are same:
It is not always simple to make classification from a tree. On the previous example, we simply designate the whole branch as a taxon (order which contains our three families). There are situations when only middle part of the branch seems to be acceptable as a taxon. In these cases, remaining part is called paraphyletic taxon.
Paraphyletic groups include all immediate ancestors of its members but not all descendants of these ancestors. Good example of paraphyletic taxon are reptiles: when we take mammals and birds from amniote branch, reptiles will be what is left. Gymnosperms (all seed plants without angiosperms) is another example, but in this case some molecular trees show that gymnosperms is also a natural branch (i.e., monophyletic group). Monophyletic groups include all immediate ancestors and all their descendants.
When the group contains taxa from different branches, it is polyphyletic. Polyphyletic groups are not allowed.
Another important distinction between groups of the phylogeny tree is stem and crown groups. All extant members together with their immediate ancestors form a crown of taxon (Figure \(2\)). If one member of crown went extinct, we can estimate that it was somehow similar to other crown members. In other words, if we find a way ho to re-create mammoth, we probably understand how to feed it because it belongs to the Elephantidae family crown. However, if the fossil, extinct members of taxon branch outside of crown (stem groups), there are much less taxonomic estimations. It is hard to guess, for example, how to care for Archaeopteryx “dinosaur bird” because such organisms are not exist now and have no living similarities. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/10%3A_Methods_of_Taxonomy_and_Diagnostics/10.01%3A_Cladistics.txt |
The other way of making classification is even more mathematical. This is phenetics based on multivariate methods of data analysis. One of its methods is cluster analysis which is described below.
1. Contrary to cladistics, phenetics considers characters as all equal and does not employ any evolutionary assumptions.
2. We need to decide which taxa we will need, assess their descriptions, extract characters—all these is similar to cladistics (see above).
3. Character polarization is not needed, character codes may be specified more or less arbitrarily, and there is no need for outgroup.
4. Character table could be the same as in previous example (again, see above).
5. Then, we will need to create the square matrix (or table) of similarity:
Alphaceae Betaceae Gammaceae
Alphaceae 1
Betaceae 0.75 1
Gammaceae 0.25 0 1
Every cell of this matrix contains a value of similarity $K$: $K=\frac{\mbox{number of matching characters}}{\mbox{number of all characters}}$
Please note that there are many more relevant coefficients of similarity but they are out of our scope.
6. Then we need to make the dendrogram which is a tree-like structure. Tradi- tionally, dendrogram is built from bottom to top, from more similar to less similar groups. For example, we may start from connecting the closest taxa, Alphaceae and Betaceae:
7. Then we need to attach other taxa which are closest to previous group:
Sometimes, when we have multiple taxa, we end up with several independent groups (clusters). In that case, different clusters could be connected on the base of average similarity.
8. Betaceae and Alphaceae are closer, so we can unite them in one order:
Order Alphales
1. Family Alphaceae 2. Family Betaceae
Order Gammales
1. Family Gammaceae
10.03: Dichotomous keys
Diagnostics is a practical science which helps to determine living organisms. One of the best way of determining was invented in the end of 18 century by famous French naturalist, Jean-Baptiste Lamarck. He created the dichotomous key (sometimes called descriptive key, or descriptive table). The legend says that when Lamarck demonstrated this key for the first time, he gave it to the random stranger (who had no idea about plants and their names), and plant were determined without problems! How to make such a key? The example is below:
1. We need to start with “players”. In this example, it will be same three plant families:
Alphaceae
Betaceae
Gammaceae
2. Assess descriptions of these three groups (we copy this from the above):
Alphaceae: Flowers red, petioles short, leaves whole, spines absent
Betaceae: Flowers red, petioles long, leaves whole, spines absent
Gammaceae: Flowers green, petioles short, leaves dissected, spines present
3. Start with a character which let to split the list into two nearly equal groups. Then add other character(s). It is always good to use more characters!
1. Petioles long......................................................................................... Betaceae.
-Petioles short ........................................................................................................2.
2. Flowers red, leaves whole, spines absent.......................................... Alphaceae.
Flowers green, leaves dissected, spines present ................................Gammaceae.
As you see here, key consists of steps. Every step has a number and typically two choices. Number is attached to the first choice whereas the second choice is marked with minus “–”. The choice will lead either to the name, or to another step. The choice sentence might contain several phrases, the first is the most important and the last is the least important. | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/10%3A_Methods_of_Taxonomy_and_Diagnostics/10.02%3A_Phenetics.txt |
K-strategy
population growth when there is small number of offspring with high probability to survive
r-strategy
population growth when there is huge number of offspring with low probability to survive
absorption zone
root: zone of root hairs
achene
one-seeded indehiscent dry fruit of Compositae, cypsella
adventitious roots
originate from stem
anatomy
invisible, internal structure which needs tools like a scalpel and/or mi- croscope to study
anomalous secondary growth
when there are multiple, short lived layers of cam- bium
apical meristems
RAM (see) and SAM (see)
apogamy
apomixis (see) when an embryo develops from unfertilized gamete, parthenogenesis
apomixis
making seeds without fertilization
apospory
apomixis (see) when an embryo develops from the maternal diploid tissue
ataktostele
vascular bundles dispersed
bipolar plant body
both root and shoot systems present
botany
the scientific study of plants and plant-like organisms
brachyblasts
shortened shoots of pines, larches and some other Pinaceae conifers
bract scales
sterile bracts under seed scales in conifers
buds
embryonic shoots
bulb
short, thick underground storage shoot with prevalence of leaf tissues
calciphytes
plants adapted to over-presence of \(CaCO_3\)
Casparian strips
part of endodermis cell walls which prevents apoplastic trans- port
central cell
biggest cell of embryo sac, with two (or sometimes one) haploid nuclei
cladophylls
leaf-like, flattened shoots
cleistogamous
self-pollinated flowers which do not open
collenchyma
living supportive tissue
companion cells
nucleate “helpers” to anucleate sieve tube cells
complex tissues
tissues with more than one type of cells
compound fruit
fruit originated from the whole inflorescence: infrutescence
compound leaves
leaves with two or more level of hierarchy roots which pull plant deeper in substrate
contractile roots
roots which pull plant deeper in substrate
corm
short, thick underground storage shoot with prevalence of stem tissues
cortex
external layer of primary stem or root
cotyledon
embryonic leaf
cross-pollination
pollination between genetically different plants
cuticle
plastic-like isolation layer
dehiscent
fruits which open
dichotomous
branching: when terminal bud always divides in two
double fertilization
the process when two brother male gametes fertilize two sis- ter female cells
elongation zone
root: zone of expanding cells
embryo sac
female gametophyte of flowering plants
endodermis
the innermost layer of cortex
endophytic fungi
fungi which grow inside plant body
endosperm\(_1\)
haploid nutrition tissue originated from female gametophyte
endosperm\(_2\)
triploid (sometimes diploid) nutrition tissue originated from second fertilization
epicotyl
first internode of the stem
epidermis
complex surface tissue
eustele
vascular bundles in a ring
exodermis
the outermost layer of cortex
fibers
long and narrow sclerenchyma cells
fibrous root system
no primary root visible
fiddleheads
spiral tops of young fern leaves
floral units (FU)
elements of generative system, fructifications
flower
compact generative shoot with sterile, male and female zones, specifically in that order, other flower terms see in the separate glossary in the text
fronds
leaves of ferns
fruit
ripe floral unit (FU)
fusiform initials
cambium cells which make vessel elements
general characters
in leaf description, characters which are applicable only to the leaf as a whole
generative shoot system
all generative shoots together
ground meristem
primary meristem which makes cortex and pith
ground tissue
same as parenchyma (see) but only applied for tissue
halophytes
plants adapted to over-presence of NaCl
haustoria
sucker roots of parasitic plants
heartwood
non-functional part of wood
heliophytes
plants adapted to full sun
hemiparasites
photosynthetic plants, feeding partly on other plants
heterophylly
situation when one plant has more than one leaf type
heterosporic
with male and female spores
homoiohydric
plants that save water
hydrophytes
plants growing in water and frequently using water for the support
hygrophytes
terrestrial or partly submerged plants adapted to the excess water
hypocotyl
root/stem transitional place
idioblasts
solitary cells dissimilar from surrounding cells
indehiscent
fruits which do not open
indusia
covers of groups of sporangia (sori)
inflorescence
isolated generative shoot
integument
extra cover of megasporangium
intercalary
meristems which grow in two directions
internodes
spaces between nodes
lateral meristem
cambium, meristem appearing sideways
lateral veins
smaller veins, typically branching out of the main vein (see)leaf lateral photosynthetic organ of shoot with restricted growth
leaf primordia
embryonic leaves
leaf scars
marks of leaf petioles
leaf traces
marks of leaf vascular bundles
lenticels
“openings” in bark allowing for gas exchange
leptosporangia
sporangia with 1-celled wall
main vein
central, most visible vascular bundle of leaf (midrib)
marginal
meristems which are located on margins
maturation zone
root: oldest part of root
megaphyllous
with leaves originated from joint branches
megasporangia
female sporangia
megaspore
female spore
megasporophylls
modified leaves with attached megasporangia
meristems
sites of cell division
merosity
multiple of flower parts numbers
mesophyll
photosynthetic parenchyma of leaf
mesophytes
plants adapted to the average water
microspores
male spores
microsporgangia
male sporangia
monilophytes
all Pteridophyta except lycophytes
monopodial
branching: when terminal bud continues to grow every year
morphology
visible, external structure
multiple fruit
fruit originated from many pistils
mycoparasites
plants feeding on soil fungi
mycorrhiza
roots symbiotic with fungi
nodes
place where leaves are attached
nucellus
wall of megasporangium
ocrea
part of the leaf which goes upwards along the stem
opposite
leaf arrangement: two leaves per node
organ
union of different tissues which have common function(s) and origin
orthotropic
growth: vertical
ovule
seed plants: megasporangium with integument
oxylophytes
plants adapted to acidic substrates
palisade mesophyll
mesophyll of elongated, tightly packed cells
parcellate
reproduce vegetatively with easily rooted body parts
parenchyma
tissue or cell type of spherical, roughly connected living cells
perforations
openings
pericarp
most of fruit tissue
pericycle
parenchyma layer just outside of vascular tissues
periderm
secondary dermal tissue
perisperm
nutrition tissue originated from nucellus (see)
peristome
mosses: attachment to moss sporangium, helps to distribute spores
petrophytes
plants adapted to grow on rocky substrates
phellem
external layer of periderm, cork
phelloderm
internal layer of periderm
phellogen
cork cambium, lateral meristem making periderm
phloem
vascular tissue transporting sugars
phyllode
leaf-like petioles
phyllotaxis
leaf arrangement
pistil
cupule, additional cover of ovules
pit
structure connecting tracheids
pith
central layer of primary stem or root
plagiotropic
growth: horizontal
plants
are not animals!
plants\(_1\)
all photosynthetic organisms
plants\(_2\)
kingdom Vegetabilia
pneumatophores
air-catching heliotropic roots
poikilohydric
plants that do not save water
pollen sac
seed plants: microsporangium
pollen tube
fungus-like cell which brings spermatia (see) to egg
pollination
transfer of male gametophytes (pollen grains) from microsporangia (pollen sacs) to megasporangia (ovules) or cupules (pistils)
prickles
modified, prickly stem surface growths
primary meristems
intermediate tissues which start out of apical meristems and make primary tissues
primary root
originates from embryo root
primary stem
stem with primary tissues only
primary tissues
tissues originated from RAM or SAM (optionally through inter- mediate meristems)
procambium
intermediate meristem developing into cortex, pith and procam- bium, primary meristem which makes vascular tissues
protoderm
primary meristem which produce epidermis or rhizodermis
protonema
mosses: embryonic thread of cells
protostele
central xylem surrounded with phloem
psammophytes
plants adapted to grow on sandy substrates
quiescent center
core part of root apical meristem
raceme
basic monopodially branched inflorescence (Model I)
radial
section: cross-section
RAM
root apical meristem
ray initials
cambium cells which make rays
rays
stem: parenchyma cells arranged for horizontal transport
repetitive characters
in leaf description, characters which are applicable to the leaf parts on each level of hierarchy
rheophytes
water plants adapted to fast moving water
rhizodermis
root epidermis, root hairs
rhizoid cells
dead cells accumulating water apoplastically
rhizome
underground horizontal shoot
ring porous
wood: with large vessel elements mostly in early wood
root
an axial organ of plant with geotropic growth
root cap
protects root meristem
root nodules
bulb-like structures which contain nitrogen-fixing bacteria
root pressure
pressure force made solely by roots
SAM
stem apical meristem
sapwood
functional part of wood
schizocarp
fruits which segregate into smaller indehiscent units
sciophytes
plants adapted to shade
sclerenchyma
dead supportive tissue
sclerophytes
plants preventing water loss, they frequently employ sclerenchyma
secondary (lateral) roots
originate from primary root (see)
secondary vascular tissues
secondary phloem and secondary xylem
seed
chimeric structure with mother (seed coat), daughter (embryo) and endosperm genotypes
seed scales
megasporophylls (see) of conifers
seta
mosses: stalk of the sporogon (see)
sheath
part of leaf which surrounds the stem
shoot plant body
unipolar body: no root system, shoots only
sieve tube cells
living cells which transport sugar
simple fruit
fruit originated mostly from one pistil
simple leaf
leaf with one level of hierarchy
simple tissues
tissues with uniform cells
siphonogamy
fertilization with the help of pollen tube
solenostele
vascular bundles in “hollow” cylinder
sori
clusters of sporangia
spermatium
aflagellate, non-motile sperm cell (plural: spermatia)
spines
reduced, prickly leaves
spiral
leaf arrangement, or alternate leaf arrangement: one leaf per node
spongy mesophyll
mesophyll of round, roughly packed cells
sporogon
moss sporophyte
stele
configuration of vascular tissues in stem or root
stem
axial organ of shoot
stipules
small attachments to the leaf; typically, located near the base of petiole
stolon
aboveground horizontal shoot
stomata
(stoma) pores which opened and closed by guard cells
succulents
plants accumulate water
surface / volume law
when body size grows, body surface grows slower then body volume (and weight)
sympodial
branching: when terminal bud degrades every year
synangia
adnate sporangia
tangential
section when plane is tangent to surface
tap root system
primary root well developed
tendrils
organ modifications using for climbing
terminal characters
in leaf description, characters which are applicable only to the leaf terminals (leaflets)
thallus
flat, non-differentiated body
thorns
prickly shoots
thyrsus
basic sympodially branched inflorescence (Model II)
tissue
is a union of cells which have common origin, function and similar morphology
tracheary elements
water-transporting dead cells
tracheids
tracheary elements without perforations (openings)
transverse
section: longitudinal
tuber
enlarged portion of rhizome
tyloses
“stoppers” for tracheary elements made by parenchyma cells, vessel el- ement “stoppers”
vascular bundles
“chords” made of xylem (inner) and phloem (outer) layers
vascular cylinder
“hollow” cylinder made of xylem (inner) and phloem (outer) layers
vascular plants
Pteridophyta + Spermatophyta
vascular tissues
tissues which transport Shoot systemliquids
velamen
absorption tissue made of dead cells
vessel members
tracheary elements with preforations (openings)
wood
secondary xylem, stem: everything deeper than vascular cambium
xerophytes
plants adapted to the scarce water
xylem
vascular tissue transporting water | textbooks/bio/Botany/Introduction_to_Botany_(Shipunov)/10%3A_Methods_of_Taxonomy_and_Diagnostics/10.04%3A_Glossary.txt |
Plants have eukaryote cells. Compared to prokaryote cells, plant cells are larger and they have organelles. They have their DNA contained in a nucleus and photosynthesis occurs in chloroplasts. Like plant cells, animal cells are also eukaryote cells. Unlike animal cells, plant cells have a cell wall. The cell wall is made of cellulose but may be thickened and strengthened in some cells.
A eukaryotic plant cell differs considerably from a prokaryotic cell of a bacteria or archaea. These are much simpler and smaller. Their DNA is found in a single chromosome and is not bound by a membrane. Similarly photosynthetic cyanobacteria do not have chloroplasts but rather photosynthesis occurs within the general cavity of the cell.
1.02: Cell wall
The cell wall is initially deposited on the surface of the middle lamella. This primary cell wall occurs on the surface of all plant cells. It is substantially composed of cellulose molecules bundled together to form fibrils.
The primary cell wall is the only cell wall present in some cells. In other cells a secondary cell wall is deposited inside the primary cell wall. This secondary cell wall may contain lignin. Lignin makes the cell wall rigid and stronger. A cell membrane lies immediately adjacent to the cell wall, on the interior surface, and surrounds the contents of the cell.
To allow communication between cells there are membrane lined pores, or plasmodesmata, which run through the cell walls.
1.03: Cell membrane
Immediately inside the cell wall there is a cell membrane surrounding the contents of the cell. It is made up of a phospholipid bilayer with proteins. The outer surface of the phospholipid layer is attracted by water (hydrophilic) whereas the tail of the phospholipid molecule is repelled by water (hydrophobic). The proteins may be embedded in the membrane or just attached to the surface. Some of the embedded protein molecules pass right through the membrane and are important for transport of substances through the membrane.
Cell Membrane functioning
The cell membrane is important for compartmentalising different parts of the cell to allow metabolic functioning to occur and to control substances in the cell. It allows control of substances entering the cell and it allows the cell to compartmentalise waste into the vacuole. Oil droplets, vesicles from the golgi apparatus and vacuoles just have a single bilipid membrane around them. The nucleus, chloroplasts and mitochondria have a double bilipid membrane around them.
Diffusion
Diffusion is the process of random movement of molecules towards a state of equilibrium; the net movement is always from the direction of greater concentration to lesser concentration and in complex solutions, each substance moves independently of the other. Substances tend to diffuse until they are evenly distributed.
Small, non-polar molecules can pass through the lipid bilayer of a membrane by diffusing through it.
Facilitated diffusion
Facilitated diffusion also involves molecule movement down a concentration gradient until the concentration of molecules are equal on both sides of the membrane. However in this case the solute molecules do not move through the membrane on their own. They combine with a carrier molecule in the membrane which allows the solute molecule to pass through the membrane. No energy is used and they pass through the carrier protein until the concentration is the same on both sides of the membrane.
Active transport
Active transport is different from the other transport processes above in that it involves transport of a solute against a concentration gradient (i.e. from an area of low concentration to one of higher concentration). This process relies on carrier molecules but also requires energy as it forces molecules to move against the concentration gradient. Energy comes from the energy storage molecule ATP and is generated through cellular respiration.
Active transport may also be indirect. In the figure below the sodium ions have been concentrated above the membrane. The sodium ions seek to equilibrate the concentration each side of the membrane but for the sodium ions to travel though the membrane, the protein carrier requires an amino acid be attached and pumped in the opposite direction. Thus actively concentrating the sodium ions then results in transport of the amino acids indirectly as the sodium ions move down the concentration gradient. | textbooks/bio/Botany/Plant_Anatomy_and_Physiology_(Bellairs)/01%3A_Inside_a_Plant_Cell/1.01%3A_Eukaryote_cells.txt |
The nucleus is the control centre of the cell and is often the largest organelle in the cell. It contains about 20% ribonucleic acid (RNA) and 20% deoxyribonucleic acid (DNA). It has four parts: nuclear envelope (membrane), nucleoplasm, nucleolus and chromosomes or chromatin.
The nuclear envelope is a double membrane that surrounds the nucleus. It contains pores that allow rapid communication between the cytoplasm of the cell and the nucleoplasm.
Nucleoplasm is similar to the cytoplasm of the cell but contains more protein macromolecules and appears darker than the cytoplasm.
The nucleolus is a roughly spherical body consisting of a mass of fine threads and particles of RNA, proteins and DNA. Its major role is the synthesis of ribosomal RNA.
1.05: Chromosomes and chromatin
The DNA is usually dispersed in the nucleus as chromatin, but during mitosis and meiosis it becomes condensed and forms into a number of approximately cylindrical structures, the chromosomes.
Chromosomes are the DNA-containing structures of eukaryotic nuclei that form during the process of cell division.
1.06: Chloroplasts
Chloroplasts are large organelles and their function is the formation and storage of carbohydrates from photosynthesis. The chloroplast is bounded by a double membrane.
The matrix of the chloroplast is known as the stroma. Also inside the chloroplast are separate internal membranes that form lamellae or rounded tongue-like thylakoids within the enclosing double membrane. These tongue-like or disk-like thylakoid membranes may be stacked in layers and these are referred to as grana. Grana are joined to each other by other membranes.
There are a range of other organelles which are similar to chloroplasts that are used for storage and pigmentation.
1.07: Mitochondria
Mitochondria are the major site of ATP and energy production in plants and animals. Numbers vary from 20 to 100,000 per cell and they vary in form and activity.
Mitochondria are double-membraned organelles (like the nucleus) so are said to be surrounded by an envelope. The outer membrane (matrix) is very elastic, the inner is folded many times (christae) and protrudes into the internal cavity.
1.08: Endoplasmic reticulum
The endoplasmic reticulum (ER) is a complex system of membranes, tubules, cisternae and vesicles, appearing in two types: smooth and rough ER. Smooth ER is comprised of interconnected vesicles and cisternae that do not contain ribosomes. Smooth ER is involved in sterol biosynthesis, detoxification reactions and fatty acid desaturation. Rough ER membranes are associated with ribosomes attached to the outer surface of the membrane. Rough ER has a role in protein biosynthesis and are the sites where amino acids are assembled in a specific sequence to produce polypeptide chains.
1.09: Ribosomes
Ribosomes occur free in the cytoplasm and also attached to membranes of the ER. Ribosomes contain RNA. They temporarily bind to two other types of RNA molecules (messenger and transfer RNA) when amino acids are assembled to form proteins.
1.10: Golgi apparatus
The golgi apparatus is a stack of smooth cisternae (membrane-bound spaces) piled on each other. These flattened plate-like membrane-bound sacs contain tubules and have vesicles protruding from their margins. Vesicles bud off from the tubules and contain materials for cell wall construction. There is a maturing face and a forming face to the golgi body. New cisternae are added to the forming face and as they mature they move progressively across the stack. At the mature face, cisternae are swollen and secretory vesicles are shed. Once the vesicle detaches from the Golgi body (presumably after reaching a critical size) they move across the cytoplasm to the cell membrane and the material is discharged. The membrane of the vesicle ruptures and becomes continuous with the plasmalemma and the contents are released outside of the cell. Vesicles may also fuse with vacuoles.
1.11: Vacuoles
Vacuoles are used for compartmentalising cellular contents and for controlling some waste products. They are also important for maintaining cell turgor and for cell expansion. The tonoplast is the membrane that surrounds the vacuole and controls movement of substances into and out of the vacuole. | textbooks/bio/Botany/Plant_Anatomy_and_Physiology_(Bellairs)/01%3A_Inside_a_Plant_Cell/1.04%3A_The_nucleus.txt |
The apical meristem produces new cells by cell division. These small squat cells divide and expand in size. They then differentiate into all the various cell types of the plant.
The great variety of cell types in a plant can be divided into three broad tissue systems: the dermal, vascular and ground tissue systems.
2.02: Ground tissues
The main tissue types of the ground tissue system are parenchyma, collenchyma and sclerenchyma. Parenchyma have thin walls of cellulose, whereas collenchyma have cell walls with thickened areas of additional cellulose. Sclerenchyma cells have lignified cell walls. They can be further categorised into narrow long cells (fibers) and cells of various other shapes (sclereids).
Parenchyma
When parenchyma cells are modified to create tissues with air spaces for buoyancy or aeration of tissues, then the tissue is described as aerenchyma rather than parenchyma.
Sclerenchyma
Sclerenchyma cells have lignified cell walls. They can be of two broad types: sclereids and fiber cells.
2.2.3.2 Fibers
Fiber cells are sclerenchyma cells that are long and thin.
2.03: Vascular tissues and cell types
There are two vascular tissues in the vascular tissue system: xylem for water transport and phloem for transport of photosynthates.
Xylem
The xylem is a complex tissue containing a range of cell types including: vessel cells, tracheids, fibers, parenchyma
2.04: Dermal tissues and features
The dermal tissue is largely composed of squat more or less cubic dermal cells, but it also contains specialist guard cells around the stomata, and various trichomes and root hairs.
Cuticle
The cuticle is a layer of cutin and waxes external to and embedded in the cell wall on the exterior surface of the plant on stems and leaves.
2.05: Secondary tissues
Secondary tissues are produced in woody plants. Secondary xylem and secondary phloem are produced from a cylinder of meristematic tissue within the woody stems and roots. This cylinder of meristematic tissue is the vascular cambium. The secondary xylem provides additional structural support and additional water conduction tissue in shrubs and trees. The secondary phloem replaces the primary phloem.
Similarly, as the trunk of a woody plant gets larger, the dermal tissue need to be expanded and replaced. New dermal tissue is produced by the cork cambium, which lies beneath the bark.
3.01: Stems
Stems are produced by the primary apical meristem in but may be increased in girth in woody plants due to secondary growth. Secondary growth is produced by lateral meristems in the woody stems and roots of woody plants.
Secondary xylem and secondary phloem are produced from a cylinder of meristematic tissue within the woody stems and roots. This cylinder of meristematic tissue is the vascular cambium. The secondary xylem provides additional structural support and additional water conduction tissue in shrubs and trees. The secondary phloem replaces the primary phloem.
Similarly, as the trunk of a woody plant gets larger, the dermal tissue need to be expanded and replaced. New dermal tissue is produced by the cork cambium, which lies beneath the bark.
3.02: Leaves
We see a massive amount of variation in the sizes and shapes of leaves. Similarly, the anatomical structure of leaves can vary considerably. Plant leaves may be specialised to maximise light utilisation, to minimise water loss, to facilitate C4 photosynthesis or CAM photosynthesis, to resist damage due to water stress, or to float on water.
3.03: Roots
Though unseen, the roots of a plant also have specialist anatomical features that enable plants to efficiently obtain nutrients and control the substances entering a plant.
Figure 3.9. Diagram of the structures of and areas of a developing root. (Image from: Marsland, Douglas. (1964) Principles of modern biology. Holt, Rinehart and Winston, New York. Digitized Cornell University Library, No known copyright restrictions. Text Sean Bellairs.)
Figure 3.10. The apical meristem and meristematic tissues developing from the apical meristem of the root. (Image Jen Dixon (CC attribute, share alike). Text and arrows Sean Bellairs.)
Figure 3.11. The endodermis (E) in the monocot Smilax. Cells making up the endodermis have walls that are heavily impregnated with suberin, forming the Casparian strip. Suberin is a fatty acid and highly hydrophobic, thus creating a barrier to water and solutes. (Berkshire Community College Bioscience Image Library, public domain; text and arrow Sean Bellairs).
Figure 3.12. The endodermis denoted by the band of the red stained casparian band in Zea mays. The interior of the root is at the top and the casparian band is between the vascular tissue and the cortex. (Image by BlueRidgeKitties (CC attribute, share alike)).
Figure 3.13. Effect of the casparian band on water flow between the cortex and the xylem. In the cortex water and solutes can move symplastically (through the living cells) or apoplastically (through the non-living cellulose cell walls and intercellular spaces. The casparian band forces all water movement into the vascular tissues to move though the cell membranes (Diagram by Sean Bellairs, CC attribute, share alike). | textbooks/bio/Botany/Plant_Anatomy_and_Physiology_(Bellairs)/02%3A_Plant_Cells_and_Meristems/2.01%3A_Development_of_a_plant.txt |
Learning objectives
By the end of this chapter, you will be able to:
• Define horticulture and describe its disciplines and sub-specialities.
• Apply the principles of experimental design to your own experiments in this course and in daily life.
• Use biological language to describe the parts of the above-and below-ground plants parts that contribute to your diet.
In Chapter 1, you’ll discover what horticulture is and how it relates to other disciplines that involve the cultivation of plants, and take a deep dive into the different types of scientific experimentation. Then you’ll explore some of the plant parts that you eat, so you can start thinking about the plants that are all around us and how we use them in our daily lives.
Thumbnail: Plants contribute to our lives in countless ways: from the foods we eat to the clothes we wear, from the structures we build to the flowers we grow in our gardens. David Mark. Pixabay license
01: Plants in our Lives
Learning objectives
By the end of this section you will be able to:
• Define the term horticulture.
• Describe disciplines related to horticulture.
• Describe some of the specialties in the field of horticulture.
Horticulture and related disciplines
Horticulture
Horticulture is the art and science of the development, sustainable production, marketing, and use of high-value, intensively cultivated food and ornamental plants. The word is derived from the Latin words hortus (garden plant) and cultura (tilling the soil). Horticulture includes ornamental and food plants that are grown with intensive and individualized care, and often in a small space rather than in an expansive field.
Horticultural plants overview
Food plants
Flowers, ornamental shrubs, ornamental trees, turfgrass, native grasses, and forbs are all horticultural plants. The plants producing the vegetables and fruits we eat are all horticultural plants.
They all have a fairly high value per acre. They have a high value per acre and, like the ornamental plants, require intensive management.
Agronomy
Agronomy is another term commonly used in reference to food production, and refers to the management of plants grown over large areas with less intensive management than that normally provided to garden plants. Its etymology is from the Greek agros (= field) and nomos (~management). Agronomy fields are larger than gardens, so the plants grown in these fields are less intensively and individually managed than those in most gardens. It is estimated that a single agronomy farm produces food for over 150 people.
Extensive agronomic crop production requires fewer person-hours of management per acre than intensive horticultural production, which requires more person-hours of management. In contrast, agronomy refers to management of field crops such as cereals (e.g. corn, wheat, rice, barley) and legumes (e.g. soybeans, common beans, peanuts, alfalfa) and a few other high-acreage crops, like cotton. These are typically plants that have a low dollar value per acre, and in many cases the crops are used for animal feed rather than for direct human consumption. These are grown over extensive areas with less intensive management, or at least with fewer people per acre involved in managing the crop than would be typical of horticultural crops.
Forestry
Forestry is the science or practice of propagating, planting, managing, and caring for forests, and of harvesting products from them. Forestry, which focuses on trees for building materials, pulp, and paper, is a third type of plant-production system, considered separately from horticulture and agronomy, and is not covered in this course.
Agriculture
Agriculture is the science or practice of farming, including cultivating soil for growing crops and rearing animals to provide food, fiber, and other products. The term is derived from the Latin ager (field) and cultura (tilling the soil). While the Latin root means “field” and implies a larger land area than “garden,” “agriculture” typically encompasses both horticulture and agronomy. For instance, the University of Minnesota College of Food, Agricultural and Natural Resource Sciences (UMN CFANS) includes both the Department of Horticultural Science and the Department of Agronomy and Plant Genetics. There is, however, no hard, distinct line separating horticulture and agriculture. While horticulture deals with plants you might find in a garden, it’s common to find those same plants (like vegetables and fruits) grown in large fields and harvested in volumes sufficient to supply grocery stores. Other ornamental garden plants, such as annual and perennial flowers, ornamental shrubs, and trees, are planted in extensive, designed landscapes. Field corn used for animal feed is considered an agricultural crop, while sweet corn is considered a horticultural crop, yet they are the same species of plant.
Here is a summary of terms:
• Horticulture: Requires intensive management on fewer acres and higher human input per acre, and produces a higher value per acre. Includes ornamental plants and whole foods (like those found in the produce aisle).
• Agronomy: Requires extensive production on more acres with lower human input per acre, and produces a lower value per acre. Includes animal feed and processed food ingredients, (such as oil, protein, sugar, and starch).
• Agriculture encompasses both horticulture and agronomy.
Domesticated plants and wild plants
The plants grown in horticulture and agronomy are usually domesticated rather than wild, meaning that humans have selected them, intentionally or unintentionally, for particular characteristics such as adaptation to cultivation in a garden, large showy flowers, or large, sweet fruits. You will learn about the science of plant improvement and domestication in the section on plant breeding.
Because garden plants are grown in modest-sized spaces, the gardener can provide intensive management such as a complex garden design, special care for the soil and plant health, and regular weed control.
In general, then, “horticulture” refers to domesticated ornamental and food plants that humans grow in modest-sized spaces where they provide intensive management.
Horticulture and plant propagation
Science of plants
Plant science explores how a plant is put together and how its parts work together during a plant’s life cycle — from seed to seed.
Throughout this course, you will study plant structure, growth, and reproduction, applying what you learn to plant propagation practices in the lab portion of this course.
Science in our lives
For many of you, this course might be the only science course you take. The course therefore goes beyond the subject of plants to help you to see the world as a scientist might see it. Science is a systematic enterprise that builds and organizes knowledge in the form of testable explanations based on observations and predictions.
You will learn how to propagate plants, and learn about plant structure and function. But perhaps more importantly, you will learn about science as a way of understanding and appreciating the world around you — in this case, the horticultural world around you.
Review questions
1. What is the difference in meaning between the Latin words hortus and agros?
2. Differentiate among horticulture, agronomy, and agriculture.
3. In general, which would you expect to provide the highest value per hour of human management: horticultural plants like vegetables, or agronomic commodity crops like corn?
Horticulture specialties
Within the industry, and also within universities, horticulture is often subdivided into specialties according to the use of the plant or plant part that is produced. Here are six of these specialties:
• Breeding and genetics: development of new cultivars (cultivated varieties) of plants for production via sexual reproduction.
• Floriculture: production and marketing of plants valued for their flowers and propagated by seed or by cuttings.
• Landscape horticulture: production, marketing, and maintenance of plants used in designed and managed landscapes.
• Olericulture: production and marketing of plants or plant parts valued for culinary use as vegetables.
• Pomology: production and marketing of plants or plant parts valued for their culinary use as fruits including nuts.
• Post-harvest management: development of practices that maintain quality and prevent spoilage of harvested horticultural plants or plant parts during storage and transportation.
Review and looking ahead
Plant propagation refers to plant multiplication, or making many plants from just a few. Two broad categories of multiplication will be addressed in this course:
• Asexual reproduction: ausing new plants to arise from plant parts like leaves, stems, or roots, or from storage organs like tubers or rhizomes.
• Sexual reproduction: making new plants from spores or seeds.
Review questions
1. Name two or three plants you have eaten in the last few days that are studied in pomology.
2. Name two or three plants you have eaten in the last few days that are studied in olericulture. | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/01%3A_Plants_in_our_Lives/1.01%3A_What_is_horticulture.txt |
Learning objectives
By the end of this section you will be able to:
• Describe why science is considered a discipline of philosophy.
• Summarize the four basic types of experiments.
• Apply the principles of experimental design in this course and in your daily life.
Thinking about science
The primary goal of this section is to help you think about the nature of science. You might be taking this course to fulfill an undergraduate requirement for a biology course with a lab. This course fulfills that requirement because we investigate the process behind using science as a way of learning about the natural world around us. If you’re starting down the path to becoming a plant scientist, understanding the nature of science will be essential for you in your career
Regardless of whether you’re going to pursue a career as a scientist, now is a good time reflect on the nature of science, and to understand how scientific thinking can become a strategy for resolving many issues that you confront during daily life.
Watch this video about connecting science and experimentation to real life:
Scientific inquiry
While “science” is a word commonly used in our culture, in popular use it is rarely spoken of as a philosophy. By identifying science as a philosophy we are taking an epistemic view, one focusing on how knowledge is acquired.
At its core, science is a mode of inquiry: a way of acquiring new knowledge about the world around us and a strategy for understanding the inner workings of elements in that world. Scientists believe that if we follow the principles of this philosophy we will continue to expand our knowledge about how things work in the world around us. This systematic approach is called the “scientific method.”
There are two key steps in the scientific method:
• Hypothesis building through reflective observation.
• Hypothesis testing through experimentation.
A “hypothesis” is a question or proposed explanation made on the basis of limited evidence and used as a starting point for experimentation. Experimentation is commonly equated with science—rightly so, because hypotheses evaluated on the basis of evidence generated through experiments. Experimentation, however, isn’t the whole story. Science—including the development and testing of new hypotheses—is also a creative endeavor.
Watch this video about scientific inquiry:
Scientific inquiry has generated a vast body of knowledge about the world around us. Your school science classes might have required you to memorize facts and relationships, and pay attention to detail. Sometimes such memorization leads students to believe that science is just an accumulation of facts rather than the process behind discovering all of that information.
Scientific discovery builds on what is already known. Even the most accomplished scientists initially approach a problem by learning what is already known. Armed with that information, they then apply their own creativity to form new hypotheses about something they have observed, and design experiments to test those hypotheses. They also communicate their results publicly so that others can benefit from their work and have the opportunity to challenge conclusions. In this way, science builds on itself.
The foundational knowledge you learn in science classes prepares you to develop and test hypotheses and to make new discoveries of your own. While a good memory may help you pass a science classes, you will absorb a body of knowledge more effectively when you learn how facts fit and work together in systems rather than learning through the brute force of memorization.
In this section we work from the point of view that science is a way of acquiring knowledge—a mode of inquiry—and that this mode of inquiry follows a process called the scientific method. Those who follow the philosophy of science:
• Use it to understand how the natural world works.
• Start by learning what is already known.
• Carefully observe the subjects of their scientific inquiry and look for details about form, function, and interaction with the environment.
• Develop hypotheses about the inner workings of natural phenomena not yet understood.
• Test their hypotheses by making observations, conducting experiments and collecting and evaluating evidence.
• Communicate with others about their hypotheses, experiments, and the outcomes of their studies so that others can repeat, validate, and build upon their work.
Although science is typically used to understand how the natural world works, it is also regularly applied to the development of new technologies that are based on these natural phenomena and to the solving of problems associated with the natural world.
Putting the scientific method to work
As noted, the scientific method relies on building hypotheses and then testing them through experimentation. In the lab section of this course you will develop hypotheses about the effects of various treatments on propagation success and then conduct experiments to test those hypotheses. Because experimentation is such a key component of the scientific method, we’ll spend time characterizing and examining four types of experimentation and explore whether they are part of the scientific method. While each is valuable when applied in the right circumstances, only one clearly follows each step of the scientific method to uncover new knowledge about the natural world.
Types of experiments
The types of experimentation we will cover are:
• Demonstration
• Evaluation
• Exploration
• Discovery
Demonstration experiments
Demonstration experiments are a classic method used in educational settings to help students learn and understand known relationships already discovered by others. Learners will usually have had prior exposure to the relationships through preliminary observations, lectures, reading, and discussions, and will have some sense of what the experimental outcome might be.
Good demonstration experiments actively involve the learner, who manipulates the experimental materials, applies the treatments, and observes the outcomes, then gathers, analyzes, and interprets the resulting data. Poor demonstration experiments, in contrast, make learners only passive witnesses to something done by an expert at the front of the classroom.
In the plant propagation labs for this course, you will be actively engaged in demonstration experiments. Although you won’t be creating new knowledge, the knowledge will likely be new to you. The hands-on experience of conducting the experiments will help you to learn the concepts more effectively than if you only read a textbook or listened to a lecture. The techniques you learn and use in demonstration experiments often contribute to the learning experience as much as the relationships revealed at the experiment’s conclusion. Employing these techniques will help you gain an understanding of many biological functions, such as the production of adventitious roots and mechanisms for seed dispersal.
While demonstration experiments are valuable for actively learning a body of scientific knowledge previously discovered and communicated by others, the experience is specifically orchestrated for teaching and learning, not for the discovery of new information. Yet since the knowledge is new to the learner, it can still bring the joy of personal discovery and a sense of accomplishment.
In summary, demonstration experiments:
• Are designed for teaching and learning.
• Address relationships that may be new to you, but are otherwise known.
• In their best forms, actively involve the learner.
• May emphasize experimental techniques, in addition to outcomes, as part of the learning experience.
• Are not the types of experiments that are at the core of practicing science as a way to uncover new knowledge.
Evaluation experiments
Evaluation experiments are designed to help us make decisions, and to choose from a number of options. They might, for instance, help us determine the efficacy of a new treatment relative to a known treatment, or decide on further experimentation. An evaluation experiment will highlight a compound, a technique, a piece of equipment, or an organism, and will include a control and/or other alternatives.
Evaluation experiments are common in horticultural and agronomic research, where the purpose of the experiment is to identify, for example, the best cultivar, production method, pest control, fertility regime, or light intensity for growing a crop. Correct experimental design is crucial for assuring that conclusions from the experiment are meaningful and credible.
These experiments are typically used in the development of new technologies to identify the best method for the desired purpose (e.g., which pesticides are effective against the target insect, but not harmful to non-target insects). They are not used to discover new knowledge about how the world works, as they typically don’t advance our understanding of the natural world. The information from an evaluation experiment might, however, point the way to additional experimentation that does help us discover new knowledge. This is particularly true if the outcome of an evaluation experiment is unexpected or novel.
In summary, evaluation experiments:
• Are used to help in decision-making.
• Help users choose a winner or determine efficacy relative to other alternatives.
• Are commonly used when evaluating and recommending horticultural production methods.
• Can be useful in solving problems and developing technologies.
• Require proper experimental design (e.g., comparison to a control) for credibility and meaningfulness.
Exploration experiments
Some scientists specialize in observing and cataloging nature, and some, like members of the group that discovered a new species of hominid, Homo naledi in a South African cave, aggressively search for previously unknown phenomena. In the botanical realm, such scientists study the diversity of organisms within habitats, discover new species, or are in other ways very skilled in “seeing” nature. Explorer-scientists recognize and appreciate detail and can identify the enormous diversity among plants by comparing characteristics that might be overlooked by others. They may also have the capacity to recognize possible interrelationships among organisms and with habitats, making their work particularly important to science. They might notice, for instance, that a particular species of plant is commonly found in wet areas but not in dry, or that a particular vegetable tastes sweeter when grown at higher altitudes than when grown closer to sea level. They don’t confirm the cause of these relationships, but are the first to notice them.
Explorers’ observations are essential to stimulating the development of sound, testable hypotheses. The possible relationships they propose must be tested to determine whether those relationships actually exist, or are artifacts of other effects. Explorers help develop hypotheses, but the work of exploration, cataloging, and seeing possible relationships don’t prove or disprove the hypotheses or necessarily generate new knowledge about relationships. The work does, however, result in new information about the existence of the object or phenomenon itself. An exception is exploration done to test a hypothesis, such as a mission to test the hypothesis that a particular type of ecosystem is required for reproduction of a particular plant species.
Scientists must resist jumping to conclusions based on exploration and observation alone. If you see two people together many times, for example, you might conclude that they are a romantic couple, when in fact they are brother and sister. Relationships hypothesized as a result of exploration and observation must be experimentally tested before they are accepted or rejected.
Exploration experiments uncover new things, many of which can be exciting and eventually change our view of the world. While one of their greatest values is that they lead to the development of new and stronger hypotheses about how the world works, they go so far as to test those hypotheses or fully engage in the cycle of knowledge generation associated with the scientific method. Additional experiments based on this new information are required to put this new information in context and to advance our understanding of how the natural world works.
In summary then, exploration experiments:
• Focus on detailed observation of organisms and habitats.
• Increase our knowledge of the natural world.
• Identify potential relationships that need to be tested.
• Are essential to sound and testable hypothesis-building.
Discovery experiments
Discovery experiments are central to the use of the scientific method in tasks ranging from problem solving to the discovery of new knowledge. They focus on uncovering new relationships and solving problems, follow the scientific method, test hypotheses and their predicted outcomes, and utilize a careful design in order to maintain meaningfulness and credibility.
The similarity between the scientific method and Kolb’s Experiential Learning Cycle is not an accident. The scientific method is a practical strategy based on how we sense and experience the world around us and used to solve problems encountered during those experiences.
The diagram above illustrates a combination of the scientific method and Kolb’s four-step experiential learning, describing a cyclic process for solving problems that can be applied to disciplines as diverse as molecular biology, global warming, and even appliance repair. While you might initially think that appliance repair doesn’t belong in that list, the difference is one of application, not method. Though far removed from the esoteric scientific discoveries we associate with scientific method, appliance repair follows the same steps. Appliances are often, and quite literally, boxes, where you don’t know what is going on inside. But what’s going on inside is knowable, and through that knowledge comes repair.
The learning/problem solving/scientific process could theoretically start anywhere in Kolb’s cycle. But it will likely start with a problem that needs to be solved, something you don’t understand but would like to know more about. You become aware that there is a problem or that you lack understanding because you have an experience where you observe something and then step back and said, “I wonder how that works,” or perhaps, “why is that broken?” Through observation you develop a sufficiently adequate description of the problem to start doing some research on what is already known.
With a good description of the problem in hand, you can begin to review what is known through the work of others, and think about what might be going on in your situation and how your new understanding can be applied to the problem. This is “reflective observation.” It isn’t just sitting back and thinking in a vacuum. You need raw material for your mind to work on, and that only comes through the tough task of gathering and engaging with the background information. There is a very important quiet phase in this process when you let your mind assemble and sort through ideas until alternatives begin to emerge that might lead to a solution. Talking with others and sharing ideas is an important part of this quiet phase.
Sometimes the alternatives are no- brainers (blown fuse?), and sometimes they’re more creative (residue from the wrong detergent gunking up the water level sensor?). Regardless of their simplicity or complexity, these become hypotheses that need to be tested. The hypothesis-building stage includes both a statement of how something works or why it isn’t working, and predictions about what might happen if the hypothesis is true. In appliance repair, for example, the prediction will likely be that the appliance will function normally. In horticultural molecular biology, it might be that you will see accumulation of a particular type of fatty acid in the cotyledons.
You put the hypothesis to the test by designing an experiment that assesses whether your predictions were right. If the outcome doesn’t match your prediction, you reject the hypothesis (the fuse was ok, so that wasn’t the problem). If the outcome does match your prediction, you tentatively accept the hypothesis pending further observation (when the fuse was replaced the washing machine worked again, so it might have been a blown fuse, but on the other hand maybe it was just because the motor had time to cool down). As with evaluation experimentation, experimental design is important in assuring that the conclusions from the experiment are meaningful and credible.
Experimentation leads to new experiences and an incremental increase in knowledge, and then the cycle begins again.
In summary, discovery experiments:
• Focus on uncovering new relationships and solving problems.
• Follow scientific method.
• Test hypotheses and their predicted outcomes.
• Utilize a careful design in order to maintain meaningfulness and credibility.
Summary
Of the four types of experiments, only the discovery experiments are core to the process of science in the narrow sense of being a way of acquiring new knowledge. The other three types of experimentation are still important; demonstration and evaluation experiments are valuable for learning and decision-making and for technology development, and exploration experiments are essential for developing testable hypotheses. But discovery experiments are core to science.
Remember: the methodology of effective washing machine repair, when applied to what is unknown about the physical world, is the methodology of science. It’s not esoteric; it’s good appliance repair.
You might argue that, when applied to a broken washing machine, a discovery experiment results in knowledge that is probably already known by those skilled in appliance repair, so it isn’t really new knowledge about how the world works. That’s a fair criticism. Use of the scientific method can result in new knowledge about how the world works, but whether it uncovers new knowledge depends on the object of experimentation.
Review questions
An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://open.lib.umn.edu/horticulture/?p=94#h5p-3
Experimental design
The methods for designing experiments are carefully studied and often discipline-specific. Methods used in molecular biology, for instance, will be somewhat different from those used in chemistry or in field evaluations of horticultural plants. There are, however, some generalizations we can make about good experimental designs.
Emphasize comparisons
Experiments include more than just one treatment. “Treatment” refers to the factor that you are varying in your experiment—for example, different cultivars of tomato, different fertilizers, or different amounts of light. Experimental designs incorporate comparison of treatments. You usually compare the treatments to one another and often to a control, which is either the application of no treatment or the application of a customary or standard level of treatment.
If you grow a particular type of tomato in your garden, and find that it produces tasty fruit, would you declare it to be the best tomato variety you could grow? Certainly not. You couldn’t even say with certainty that it was the best tomato variety you have ever grown (unless it is the only one you have grown). Next year, however, you could grow that tomato as your control, and grow two other varieties that your neighbors like, and compare fruit quality (appearance, flavor, yield, sugar content). You could then say something definitive about the three tomato varieties because you have compared them to each other after growing them next to each other in the same year and environment.
Replicate treatments
The same treatment is applied to more than one “experimental unit”—the object that receives the treatment. In the example above, the tomato plant is the experimental unit, and you would perhaps plant two or three seedlings of each tomato variety rather than just one. Think of a treatment as something like a fertilizer spread on a patch of land. The patch of land is the experimental unit, while the fertilizer is the treatment.
By applying the treatment to more than one experimental unit you can estimate the variation you get when two experimental units are treated the same, and compare this to the variation when experimental units are given different treatments. If the treatments actually differ in their effectiveness, you would expect the variation between experimental units given different treatments to be much greater than the variation between those given the same treatment. This is one of the fundamental ways in which experiments are statistically analyzed and treatments declared significantly different or not.
Randomize treatments
Once you know how many treatments you are going to apply, and how many replications you want, the product of these two quantities (# treatments × # replications) equals the number of experimental units you need. For instance, if you have three fertilizers you want to test, plus a control, you have four treatments. If you want three replications of each treatment, then you 4 treatments x 3 replications = 12 experimental units or patches of land where you will apply the fertilizers. The treatments will be randomly assigned to each experimental unit (patch of land). This is done using a random number table and is not just haphazard picking. Randomization helps minimize any bias you haven’t recognized in advance and controlled for in other ways.
Review questions
1. What are two types of control treatments?
2. Does increasing the number of replications increase the number of treatments or the number of experimental units?
3. Can you think of an example of how randomization can protect against bias? | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/01%3A_Plants_in_our_Lives/1.02%3A_Science_and_Experimentation.txt |
Learning objectives
By the end of this lesson you will be able to:
• Summarize the various above- and below-ground plant parts that contribute to your diet.
• Use the correct language of biology when identifying parts of plants.
• Appreciate the diversity of edible plant parts.
Above-ground plant parts we eat
Edible leaves and petioles
In this image of an iceberg lettuce cut in half, you can see how the leaf blades are packed and folded together tightly in the lettuce head. Lettuce is an example of a plant shoot with very short internodes on the stem. This results in a compact but leafy plant. Iceberg lettuce is a type of heading lettuce where older leaves envelop newer leaves forming a solid or semi-solid ball or head of lettuce leaves.
Romaine and leaf lettuces exhibit a more open architecture, with the leaves forming a looser head with upright leaves. Romaine lettuce has elongated leaves. There may be some tendency of older leaves to enclose newer leaves, but it is much less pronounced than in iceberg lettuce, and may be absent altogether in some of the garden types. Leaf lettuce lacks the tendency to form heads.
Lettuce leaves generally lack a petiole. The blade narrows a bit, but attaches directly to the node. A leaf lacking a petiole is called a “sessile” leaf. The point of attachment of the leaf to the stem is at a node. If you tear the leaves from a lettuce plant you are left with a short stem made up of many nodes and short internodes.
You can see in the romaine lettuce that its morphology is similar to that of the iceberg lettuce and that it has some tendency to wrap newer leaves within older. However, the nodes are a bit longer than what you see in iceberg lettuce, and that makes the node locations more apparent.
A few examples of leaf parts we eat
An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://open.lib.umn.edu/horticulture/?p=105#h5p-6
Watch this video on edible leaves and petioles:
Modified petioles
Celery is an example of a leaf with a petiole. The parts that you eat are the petioles, while the leaf blades are often not present in the bunch of celery you purchase. If you buy a bunch of celery and pull off the large, outside petioles, inside you will find shorter petioles with the leaf blades still attached.
Celery is a geophyte (covered in a later lesson). Some of the celery petiole — the pale part at the bottom where it attaches to a node on the stem — grows underground. This part is pale because it lacks chlorophyll; the petioles were not exposed to sunlight and chlorophyll failed to develop.
Intentionally covering the petioles to discourage chlorophyll and encourage white, tender stems is called blanching. Blanched celery is more attractive to some cooks and consumers, although it may not be as nutritious.
An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://open.lib.umn.edu/horticulture/?p=105#h5p-7
Edible stems
The photo below shows an asparagus shoot. You can tell it is a shoot by the regular node/internode construction of the stem. Most of the shoot is stem tissue. The triangular growth at each node is colloquially called a “bract” by asparagus growers, but it is actually a very small, scale-like leaf. If the shoots are left unharvested, branches grow from the nodes and then repeatedly branch into soft, feathery green foliage, as shown in the next photo.
Edible inflorescences
Broccoli and cauliflower are eaten as immature inflorescences. The dark green exterior of the broccoli inflorescence is made up of tight flower (or floret) buds that have not yet opened. The term “floret” is often used for the name of a flower born on a complex inflorescence.
Inside the inflorescence, the flower buds are supported by short, thin pedicels. The pedicel is attached to a series of increasingly thick internal stalks which make up the rachis structure of the inflorescence. The rachi all connect to the main stem of the inflorescence, which is the peduncle, and which then attaches to a node on the stem. The peduncle is the bit of the stalk that extends from the node where the inflorescence is attached to where the first rachis branches off. Above that, the central axis of the inflorescence is also called the rachis. An inflorescence can contain many rachi.
These plant parts may look similar, but they’re in different positions in the inflorescence. The terminology is important for distinguishing between parts, making observations, and describing different aspects of the plant, especially for data collection in experiments.
Nasturtiums, shown above, are also an inflorescence. They can be used as a colorful addition to a salad, and have a pleasant spicy flavor. In this case we are eating a single open flower, instead of a mass of immature rachi, pedicels, and florets as we are with broccoli.
It’s important to remember that not all flowers are edible, and some are even poisonous. If you’re interested in edible flowers, you must learn which species are safe to eat and how to identify and prepare them.
Review questions
Cauliflower has very tight flower clusters, but otherwise has a very similar morphology to broccoli. Can you identify the pedicel, rachis, peduncle, and florets?
This Chinese cabbage has a morphology similar to that of romaine lettuce. Can you identify the stem, nodes, and leaf blades?
Fruits
We will deal with fruits in detail later in the course. Just a bit of introductory information: a fruit is a mature ovary that was part of a flower
Sometimes the botanical and culinary definitions conflict with one another. Botanically speaking, for instance, a nut is a fruit, as are a corn kernel, a pumpkin, a tomato, and an orange. As we’ll discuss, you could make a botanical argument that an apple isn’t a true fruit because the juicy part we eat isn’t ovary tissue; the ovary tissue is the core that we throw in the compost.
Below-ground plant parts we eat: Geophytes
Geophytes are plants with underground organs where the plant stores energy or water. Geophytes are often called bulbs, but they are far more diverse than that. Many of these plants protect buds using structures other than bulbs, such as rhizomes or enlarged roots. These modified parts include:
• Bulbs
• Tubers
• Rhizomes
• Roots, including storage and enlarged tap roots
Underground shoots
Bulb – onion
A bulb is a specialized, underground organ with a short, fleshy basal stem enclosed by thick, fleshy scales modified for storage. A true bulb consists of both leaf and stem tissue. The compressed stem, or basal plate, has attached to it a set of modified leaves called scales. These scales serve as the primary storage tissue for carbohydrates, nutrients, and water.
The main stem and apical meristem are protected by the layers of leaves. Axillary buds are born at the junction of the scale and basal plate (leaf and stem). Bulbs with a papery outer covering, like onions, are called tunicated. Plants that produce bulbs without this covering, like lilies, are non-tunicated.
Underground stems
Tuber – potato
A tuber is a thickened, enlarged underground stem typically produced from a swelling of a stolon or rhizome. The stem tissue serves as the primary storage tissue for carbohydrates, nutrients, and water. The potato tuber is a typical example. Potato tubers are born on stolons that emerge from nodes near the soil surface.
It is common garden and agricultural practice to “hill” potatoes (mound loose soil around the base of the main stem of the plant) so the stolon grows into the mound of soil, where the tip swells into a tuber. Unlike a corm, which is also stem tissue, a tuber has no basal plate, but rather is fleshy throughout. The “eyes” of the potato are the meristems or buds from which new, above-ground growth initiates when conditions are favorable. These eyes are found at nodes on the tuber, which indicates that the tuber is shoot tissue rather than root.
Rhizome – ginger
Rhizomes are horizontal-growing underground stems that arise from nodes at or below the soil surface. In plants with fleshy rhizomes, these underground stems store nutrients and swell a bit. The stems are not usually as enlarged as a potato tuber, and the node/internode structure typical of stems is usually more obvious than on a potato. The stem tissue itself is the primary storage tissue, and it grows horizontally in the soil.
Ginger “root” (shown at right) isn’t really a root; it’s a rhizome (modified stem). The nodes and internodes, — found on stems, but not roots — are clearly visible.
Modified roots
Storage roots – sweet potato
Storage roots are enlarged fleshy portions of root tissue, and are are the primary storage tissue. There may be a bit of stem — the crown — attached to these roots, where you will find the buds from which new above-ground growth will initiate.
In plants with storage and fleshy roots, including dahlias and daylilies, it is important to protect the buds on the crown of the root because new shoots originate from there. Roots of some plants can produce shoots directly from the root tissue, Sweet potatoes are propagated this way; roots are cut, new shoots emerge from the cut roots, and these shoots are transplanted into the sweet potato field. Not all plants can produce new shoots from roots.
Tap root – radish, carrot, parsnip, beet, turnip
The swollen primary root is the storage organ. New growth initiates from buds at the crown, which is a small area of stem tissue sitting atop the tap root.
Hypocotyl – radish
The below-ground organ of the Raphinus sativa (radish) is not a root or shoot, but the continued growth of the hypocotyl — the part of the embryo arising from the cotyledonary node (where the cotyledons attach to the beginning of the root), and evident when a seed germinates.
Review questions
1. Compare and contrast a tuber and a storage root. Which one is actually stem tissue?
2. If ginger isn’t a root, what is it and how can you tell?
3. What part of rhubarb and celery do we eat? | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/01%3A_Plants_in_our_Lives/1.03%3A_Plant_Parts_we_Eat.txt |
These are the important terms from this chapter to be sure to know. You might also find these in later chapters.
Chapter 1 flashcards
Agriculture The science or practice of farming, including cultivation of the soil for the growing of crops and the rearing of animals to provide food, wool, and other products.
Agronomy The science and technology of producing and using plants for food, fuel, fiber, and land restoration on an extensive scale. The value per acre is lower than for a typical horticultural crop.
Asexual propagation A form of propagation that results in plants with genetics identical to those of the parent plant.
Bract A modified leaf or scale, usually small, with a flower or flower cluster in its axil.
Bulb A specialized, underground organ with a short, fleshy stem axis (basal plate) enclosed by thick, fleshy scales modified for storage.
Control (in an experiment) Used to verify or regulate a scientific experiment by conducting a parallel experiment or by comparing with another standard.
Demonstration experiment A method for actively learning the body of scientific knowledge that has been previously discovered and communicated by others; specifically orchestrated for teaching and learning, not for the discovery of new information about the world around us.
Discovery experiment A method focused on uncovering new relationships and solving problems, following the scientific method, testing hypotheses and their predicted outcomes, and utilizing a careful design in order to maintain meaningfulness and credibility.
Evaluation experiment A method typically used during the development of new technologies to identify the best products for a desired purpose (e. g., which pesticides are effective against a target insect, but not harmful to non-target insects), but not used to discover new knowledge about how the world works, and thus not typically advancing our understanding of the natural world. Used to pick a winner from among a number of options.
Experimental design The process of planning an experiment to test a hypothesis.
Experimental unit The entity to which a specific treatment combination is applied.
Exploration experiment A method focused on detailed observation of organisms and habitats, used to increase our information about the natural world and to identify potential relationships that need to be tested, and essential to the building of a sound and testable hypothesis.
Floriculture Discipline of horticulture concerned with the production and marketing of plants valued for their flowers.
Forestry The science or practice of propagating, planting, managing, and caring for forests; includes harvesting.
Fruit Ripened ovary together with the seeds within the ovary.
Geophytes Plants with underground organs in which the plant stores energy or water. New growth begins underground, and the function of this growth is the storage of food, nutrients, and water during adverse environmental conditions.
Horticulture The art and science of the development, sustainable production, marketing, and use of high-value, intensively cultivated food and ornamental plants.
Hypothesis Scientific means of forming a question or proposed explanation made on the basis of limited evidence as a starting point for experimentation. In science, a testable statement.
Inflorescence Complete flower structure of a plant; includes the flower, pedicle, rachis, and peduncle.
Internode Stem regions between nodes in plants.
Leaf A usually green, flattened, lateral structure attached to a stem and functioning as a principal organ of photosynthesis and transpiration in most plants.
Leaf blade Broad portion of a leaf; does not include the petiole.
Monocotyledon Seed plant that produces an embryo with a single cotyledon and parallel-veined leaves; includes grasses, lilies, palms, and orchids.
Node Stem region of a plant where one or more leaves attach; location of lateral buds.
Olericulture Discipline of horticulture concerned with the production and marketing of plants or plant parts valued for culinary use as vegetables.
Pedicel Short stalk that holds up the flower.
Peduncle Large, central stalk that attaches the rachi to the stem of the plant.
Petiole Stalk by which most leaves are attached to a stem; part of the leaf structure, not the stem.
Pomology Production and marketing of plants or plant parts valued for their culinary use as fruits, including nuts; propagated by cuttings and grafting (asexual propagation).
Rachis Stalk of a flower that is situated between the peduncle and the pedicel.
Randomization Act of randomly assigning treatments to experimental units using a random number table or computer-generated randomization to help minimize any bias that has not been recognized in advance and controlled for in other ways.
Replication Application of the same treatment to more than one experimental unit.
Rhizome Horizontal stem growing just below the soil surface.
Science Systematic study of the structure and behavior of the physical and natural world through observation and experiment.
Scientific discovery Process of scientific inquiry; builds on what is known by testing hypotheses.
Sessile A leaf that lacks a petiole; called a sessile leaf.
Sexual propagation Form of propagation that results in plants with genetics that differ from those of the parent plants; also called seed propagation.
Stem Supporting and conducting organ, usually developed initially from the epicotyl and growing upward; consists of nodes and internodes.
Treatments Administration or application of agents to a plant to prevent disease or facilitate growth.
Tuber Swollen, underground, modified stems that store food. | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/01%3A_Plants_in_our_Lives/1.04%3A_Terms.txt |
Learning objectives
By the end of this chapter, you will be able to:
• List the seven levels of the plant classification system.
• Recognize the taxonomic diversity of common foods in your diet.
• Summarize the contribution of Linneaus to binomial nomenclature.
• Understand how the two-part scientific naming system works and its applications.
• Describe the differences between epigeal and hypogeal seedling emergence.
This chapter addresses the importance of binomial names, sometimes referred to as scientific names. At a garden center, a plant labeled a bluebill could be Scilla non-scripta, from the monocotyledones, or Mertensia virginica, from the dicotyledones. Two different plants, both from division Anthophyta, but from different Classes. Common names have their place, but they can be ambiguous. Binomial nomenclature is more precise; its use ensures that you’ll get the correct plant and the correct information on how to grow and propagate it. The second section in this chapter addresses seed germination, arguably the most common and important method of propagating plants.
Thumbnail: Garden centers and nurseries tend to use common plant names, but knowing the scientific names will eliminate confusion. “Langley Circle Farm Tour: Cedar Rim Nursery Plants Galore” by Queenie C, CC BY-NC 2.0
02: Taxonomy and Seed Germination
Learning objectives
By the end of this section you will be able to:
• List the seven levels of the plant classification system.
• Recognize the taxonomic diversity of common foods in your diet.
• Summarize the contribution of Linneaus to binomial nomenclature.
• Understand how the two-part scientific naming system works and its applications.
Plant taxonomy
Here are some introductory definitions:
Taxonomy (or systematics): The science of classifying organisms.
Classification: A grouping of plants according to shared qualities or characteristics.
Plant taxonomy: A hierarchical classification system based on morphological (see below) and phylogenetic (see below) similarities among plants.
Nomenclature: A formal system of names attached to taxonomic groupings.
Hierarchy: A system of grouping in which each classification is a subset of a superior grouping, and may contain subordinate categories. As an example: The landmass of the United States (used here as the highest or most inclusive level of classification) is partitioned into states (a middle level of classification). States, in turn, are partitioned into counties (the lowest level in this hierarchy). Counties are subsets of states, which are in turn subsets of the nation. This hierarchical type of grouping system is used in plant taxonomy.
Morphology: The appearance (shape and structure) of a plant. Plant taxonomy is a hierarchy primarily based on grouping together plants that exhibit structural (phenotypic) similarities.
Phylogeny: Ancestral, evolutionary relationships among plants. While plant taxonomy has historically been based on plant morphology, these relationships are currently being verified and expanded using new molecular genetic technologies that uncover genetic similarities through comparisons of shared DNA sequences. In general, plants sharing more DNA are considered more similar from an evolutionary standpoint, and considered to have diverged from each other more recently in evolutionary time than plants that share less DNA.
Taxonomy in the pantry: Classification exercise
To start becoming familiar with taxonomic categories, go to your fridge, cupboard, or pantry and choose a variety of fruits, vegetables, and grains. These might include cans of mushrooms, green peas, black-eyed peas, chickpeas, butter beans, and sweet corn; bags of pine nuts and coconut, and perhaps a banana that was getting a bit too brown.
Think about the many ways in which you could group these foods. You might, for instance, categorize a food by whether it is canned or fresh, by size, manufacturer, or color, or by the meal in which you would typically eat it.
Or you could apply a biological, hierarchical classification system, categorizing them by the morphology and phylogeny of the plant on which they grew. The plant systematics hierarchy we will use in this course is as follows, from highest (most inclusive) to lowest level:
• Kingdom
• Division (or Phylum, although Phylum is more commonly associated with animal taxonomy)
• Class
• Order
• Family
• Genus
• Specific epithet (usually a species name)
Memorize this hierarchy, so it rolls off your tongue like a multiplication table.
Now apply this taxonomic system to your foods. An easy way to do this is to search for each food on the U.S. Department of Agriculture’s site USDA Plants Database. If you type “tomato” into the search bar, select “Common Name” from the dropdown menu, and click “go,” you’ll see all the plants with “tomato” in their common name. Click on Solanum lycopersicum L. (garden tomato) and you’ll get this entry, the description for the common garden tomato. Scroll down to see the “Classification” section, which lists the taxonomic classification and includes Kingdom, Division, Class, Order, Family, Genus, and Specific epithet. Notice that this database has finer divisions of hierarchy than you are required to know, including Subkingdom, Superdivision, and Subclass.
You can use the information in the database to classify your foods. For products with several ingredients, pick one from the ingredient list, such as wheat in crackers or tomato in spaghetti sauce.
While you can sometimes find this info on Wikipedia, be aware that Wikipedia is not always reliable and you’ll want to cross-reference with other sources. If you enter “tomato” into the Wikipedia search bar you’ll get this page. The right sidebar includes the taxonomic classification. “Unranked” is used instead of Division and Class, which means there is some disagreement on whether those names are the correct Division or Class names. You might also see several hierarchical terms listed as “Clade,” rather than the proper terms. If you can’t find complete information on Wikipedia, use the USDA site.
For the foods in our hypothetical pantry — mushrooms, green peas, black-eyed peas, chickpeas, butter beans, sweet corn, pine nuts, coconut, and banana — we can divide them into the following Kingdoms: Plantae and Fungi.
We can separate the products within the Plantae kingdom into two Divisions:
• Pinophyta: the pine nuts, which come from a conifer
• Magnoliophyta: everything else in this kingdom, which come from flowering plants
The cans and bags in the Magnoliophyta division can be separated into these Classes:
• Liliopsida (Monocotyledons — one embryonic leaf in the seed, parallel leaf veins, and petals and sepals in multiples of three): corn, coconut, and banana
• Magnoliopsida (Dicotyledons — two embryonic leaves in seed, and branched leaf veins): green peas, black-eyed peas, chickpeas, and butter beans
In comparison to the other levels, Order is a relatively arbitrary set of classifications that were created in part to make subsequent classifications more manageable. Order will be addressed in the section on phylogeny.
Next, the products can be subdivided by Family.
Depending on details of the particular plant classification system used, there are approximately 230 plant families. Families are often based on types and organization of flower parts and fruit type, including the number of petals, sepals, stamens, and pistils, and the location of the ovary relative to petals. In this website from the University of California Cooperative Extension (optional) the authors identify many of the characteristics used to group plants into families.
Among our food examples, the Family hierarchy includes:
• Arecaceae (coconut, which comes from a palm tree)
• Poaceae (corn, which is a grass)
• Musaceae (banana)
• Fabaceae (the three peas and the butter beans, which are legumes)
Genus and Specific Epithet are the last two classifications. The pairing of genus and specific epithet to name a plant is called binomial nomenclature. Tthe first letter of the genus is capitalized, and the entire binomial is either underlined or written in italics.
Watch this video for an explanation of plant taxonomy.
Review questions
Think about these questions and be able to discuss the answers or know how to find the them using the resources provided:
1. Where are blue spruce trees (a conifer) taxonomically separated from lilies (flowering plants) at the Kingdom or Division level? (Hint: Use the online resources that were provided in this section.)
2. Are lilies (monocots) separated from beans (dicots) at the Class or Order level?
3. At which taxonomic level are flowering plants separated into different classifications based on flower and fruit characteristics?
Example taxonomy tree
Now that you have the names for each of your plants, you can organize them into a taxonomic tree that more clearly shows their relationships to one another. Below is an example tree based on some of the foods found in our hypothetical pantry:
Now, try it yourself. Determine which plants you want to use, look them up on the USDA Plants Database, write down the Kingdom, Division, Class, and so on for each, and begin constructing the tree to show relationships and points of divergence. In this example, the mushrooms diverge from everything else at the Kingdom level, pine nuts diverge from the other three at the Division level, corn is in a different Class than pea and chickpea, and pea and chickpea diverge at Genus.
The point of this exercise is for you to understand that relationships among plants are known, and are categorized in a sophisticated taxonomic system. Some of the plants we commonly eat have close relationships, like the various plants in the Solenaceae family (tomato, eggplant, potato), but others are much more distant.
Linneaus and plant taxonomy
Binomial nomenclature
Carolus Linnaeus (1707–1778), a Swedish professor, is widely recognized for developing the binomial nomenclature for plants. Binomial nomenclature is a scientific classification in which each organism is given two names. In his 1753 book Species Plantarum (kinds of plants), Linnaeus employed this system to describe a great number of plants using Latin polynomials. The first word of the polynomial became the genus, and a marginal note describing the plant became the specific epithet. Several years ago we celebrated Linnaeus’ 300th birthday, and you can find a long set of links about him from a simple Google search.
A proper binomial, in addition to the Genus and specific epithet, also includes the initials of the naming authority — the person who proposed the accepted name. Previous naming authorities might also be listed in parentheses. For example:
• Phaseolus vulgaris L. — common bean. The “L” stands for Linnaeus.
• Phaseolus acutifolius A. Gray — tepary bean. The authority for this one is A. Gray.
Interspecific hybrids (hybrids formed from crossing two different species) may be designated with an “x” separating the two constituent species; the “x” can be read as shorthand for “crossed with” — for example, Phaseolus vulgaris L. x Phaseolus acutifolius A. Gray. They might also be given a new name incorporating an “x” to show that the plant is the result of an interspecific cross: Fragaria chiloensis x Fragaria virginiana = Fragaria x ananassa (cultivated strawberry)
Notice, from these examples of interspecific crosses, that the ability to cross and to have fertile offspring isn’t a firm definition of species. It is generally true that breeding is restricted to within-species boundaries, but there are exceptions.
While some plant names have been updated to reflect the most recent knowledge about their morphology and phylogeny, their older names might still be in common use in some settings. Coleus, for example, has the following binomials, all for the same plant:
• Ocimum scutellarioides L.
• Plectranthus scutellarioides (L.) R. Br. (Notice that “L” is now in parentheses, showing that Linneaus was the earliest naming authority, but that his original name for the plant has now been superseded.)
• Coleus scutellarioides (L.) Benth.
• Coleus blumei Benth.
Important notes about binomial naming conventions:
• The Genus is always capitalized and either italicized or underlined.
• The specific epithet is lowercase and either italicized or underlined.
• The naming authority is capitalized and often abbreviated; if the species has been renamed, the first authority is in parentheses.
• An “x” between the Genus and specific epithet denotes an interspecific cross.
• A “x” before the Genus denotes an intergeneric cross.
Future of plant taxonomy and systematics
Taxonomy might first seem an old and dull science, sorting plants into a database using a system developed by someone born more than 300 years ago. But plant exploration experiments and the discovery of previously unknown species can take researchers to the far corners of the world, and taxonomy is important in classifying and naming these new discoveries. Also, for already discovered species, there is continual discussion about the real relationships among these plants and others and whether currently classified plants should be reclassified based on new information. With advances in molecular genetics through techniques that reveal a plant’s DNA sequence, for example, taxonomy is moving more and more toward a phylogenetic basis, based on evolutionary relationships established through DNA similarities and differences instead of solely on morphological characteristics (features about the plant that you can see).
• Traditional taxonomy relies on morphological phenotype (the appearance of the plant).
• Molecular taxonomy relies on genotype (the particular combination of alleles of each gene in the organism).
For more information, check out this Wikipedia article about molecular phylogenetics.
The Angiosperm Phylogeny Group (APG) is a group of taxonomists who are working together to modify flowering plant taxonomy using molecular systematics. The APG’s work is focused at the taxonomic level of Order and, to some extent, Family. While Order has long been a fairly arbitrary categorization, it may now be based more on molecular relationships.
The utility of classification goes beyond the satisfaction of good organization. Classification can inform us of new or lesser-studied plants that share valuable characteristics with plants already familiar to us. Now we have tools and knowledge that give us increasing control over the transfer of DNA among plants. Plant breeders can use insights from taxonomists to identify DNA sequences in related plants that might provide new sources of resistance to disease and insects, or new quality attributes, if transferred to food crops.
Review questions
An interactive H5P element has been excluded from this version of the text. You can view it online here:
https://open.lib.umn.edu/horticulture/?p=141#h5p-5 | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/02%3A_Taxonomy_and_Seed_Germination/2.01%3A_Plant_Taxonomy.txt |
Learning objectives
By the end of this section you will be able to:
• Describe the differences between epigeal and hypogeal seedling emergence.
• Understand the terms that are used to describe different parts of the seedling as it emerges.
Seeds and their importance
A seed, in botanical terms, is an embryonic plant enclosed inside its seed coat. Typically, the seed also has stored energy (proteins and carbohydrates) that are used by the seed during germination to establish itself when environmental conditions are favorable for growth. The stored energy is what makes seeds valuable for humans, too. Seeds are important in our daily lives because they feed us (food), feed livestock (aka, feed), and provide us with fuel and fiber for personal, home, and industrial purposes.
Seeds are by far the most common mode by which plants reproduce, and most people are familiar with their role in plant propagation and reproduction. The evolutionary advantage of reproduction by seed is the mixing of genetic material through meiotic recombination and the transfer of gametes (pollen) from one parent to another. This mixing of male and female parent genetics results in seeds, and thus seedlings, that are unique from one another and from the parents. The seeds may be dispersed locally or distributed far away through many mechanisms, such as wind, animals, insects, and water. Seedlings will germinate and grow, and those that are most fit in the environment will reproduce and pass on their genes to the next generation. This ability of plants to adapt to local environments and to pass on their genes is evolution in action, as new variations and even new species emerge and disappear from the landscape.
One advantage of seed production is that plants generally produce copious amounts of seed. Each seed may have slightly different germination requirements, a reflection of the diversity resulting from sexual recombination and an evolutionary strategy that allows seeds to germinate at different times. Seeds are able to remain dormant until the conditions are suitable for plant growth and survival, and have mechanisms that prevent germination before winter, during droughts, or in low-light environments. Some weedy species are excellent at interpreting these signals and may lie dormant for years in the soil “seed bank,” only germinating when the seed has been exposed.
Seedling emergence
Most seeds have a very slow metabolism when they are mature, which puts them in a state of quiescence: alive, but not growing and not physiologically active. At germination, the seed’s metabolic pathways are activated, leading to embryo growth and emergence of a new seedling. Germination begins with activation by water uptake. We call this imbibition, and sometimes the seed or fruit requires special treatment for water to get into the seed and start this process. We often use the emergence of the radicle (the embryonic root) from the seed coat as a measure of successful germination. Water uptake alone is not an indication that the seed is alive and growing, despite the expansion of seed tissues.
Cell division is taking place in the epicotyl, and the hypocotyl and the shoot and root are beginning to break through the seed coat. The new plant is beginning to grow and emerge from the soil.
Two types of seedling emergence
Epigeal and hypogeal
Epigeal and hypogeal are terms used to describe the position of the cotyledonary node during germination, indicating whether the node is above or below ground once the seedling has become established.
Epi means above while Hypo means below. The location of the cotyledonary node following seedling emergence is a characteristic used as a first step to differentiate plant species. The position of the cotyledon is affected by the rapidity of cell division in the hypocotyl region of the plant during germination and early seedling growth. The epicotyl is the embryonic shoot region above the attachment point of the cotyledons, and the hypocotyl the embryonic region below the cotyledon attachment point and extending down to where the root begins.
Epigeal
In this type of seedling emergence, cell division in the hypocotyl is initially more active and rapid than cell division in epicotyl. The actively dividing meristem in the hypocotyl causes cell growth and elongation that pushes some of the hypocotyl, as well as the cotyledonary node and epicotyl, above the soil surface. The cotyledonary node is above the ground — epigeal. The drawing shows four stages in the emergence of a pinto bean (Phaseolus vulgaris L.) which exhibits epigeal germination.
This video shows germination of a bean seed over a 10-day time span.
Hypogeal
In this type of seedling emergence, the apical meristem at the tip of the epicotyl is more active than the hypocotyl. This cell division and elongation pushes the epicotyl above the soil while the cotyledons and all of the hypocotyl remain below the soil surface. The cotyledonary node is below the ground — it is hypogeal. The example above is a pea (Pisum sativum L.) which exhibits hypogeal germination.
This video shows hypogeal germination of pea, where the cotyledonary node stays below the soil, and this video shows epigeal germination of bean, where the cotyledonary node is pushed above the soil.
Review questions
• Does “epi” mean above or below? Above or below what?
• Diagram the seedling with the following: hypocotyl, cotyledons, epicotyl, and leaves.
2.03: Terms
Here are the terms from this week’s lessons that you will need to be familiar with for your assignments and for the quiz.
Chapter 2 flashcards
Binomial nomenclature System of naming in which two terms are used to denote a species of living organism, the first indicating the Genus and the second the Specific Epithet.
Class Taxonomic rank below Division and above Order.
Cotyledonary node Food storage structure used in germination.
Dicotyledon Seed plant that produces an embryo with paired cotyledons, floral organs arranged in cycles of four or five, and leaves with net-like veins.
Division Highest taxonomic category, consisting of one or more related classes, and corresponding approximately to a Phylum in zoological classification.
Emergence Germination, when the embryo becomes active and the radicle grows through the seed coat.
Epicotyl Portion of the stem of a seedling or embryo located between the cotyledons and the first true leaves.
Epigeal Type of seedling emergence where cell division in the hypocotyl is initially more active and rapid than cell division in the epicotyl. Cotyledons are brought above the soil surface as the hypocotyl expands.
Family Taxonomic rank below Order and above Genus.
Genotype Genetic composition of an organism.
Genus Group of species possessing fundamental traits in common but differing in other lesser characteristics; taxonomic rank below Family and above Specific Epithet.
Hierarchy System of grouping where each classification is a subset of a superior grouping, and may contain subordinate categories.
Hypocotyl Embryonic shoot below the cotyledons.
Hypogeal Type of seedling emergence where the cotyledons remain below the surface of the ground.
Nomenclature Formal system of names attached to the taxonomic groupings.
Order Taxonomic rank below Class and above Family.
Phenotype Physical appearance of an organism.
Phylum Taxonomic rank below Kingdom and above Class; used in zoological classification.
Radicle Embryonic root that breaks through the seed coat during germination and develops into the seedling’s root system.
Seed Ripened ovule containing a seed covering, food storage, and an embryo.
Seed coat Outer layer of the seed.
Seed germination Activation of metabolic pathways of the embryo leading to the emergence of a new seedling.
Specific epithet Uncapitalized Latin adjective or noun that follows a capitalized Genus name in binomial nomenclature and serves to distinguish a species from others in the same genus, as saccharum in Acer saccharum (sugar maple).
Taxonomy Science of classifying organisms. | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/02%3A_Taxonomy_and_Seed_Germination/2.02%3A_Introduction_to_Seed_Germination.txt |
Learning objectives
• Identify the unique features that distinguish shoots, leaves, and roots.
• Describe ways in which stolons and rhizomes are modified stems.
• Identify the types and parts of the major shoots, leaves, and roots.
The organization of the plant is not unlike that of our own bodies. At the simplest level, cells are organized into tissues; these form organs that make up the plant body. At each level of this organization are specializations for the specific functions that occur during the plant’s life cycle. In this chapter, you’ll explore the structures and functions of leaves, shoots, and roots.
Thumbnail: Each part of a plant — from tiny root hairs to the concealed buds — contributes uniquely to the overall growth of the plant. Pixabay. Pixabay license
03: How Plants Grow Part 1
Learning objectives
By the end of this lesson you will be able to:
• Identify the parts of the angiosperm leaf.
• Describe some of the ways in which leaf parts differ from plant to plant.
• Recognize the basic patterns of leaf shape and orientation of the veins in the leaves.
Leaves
Leaves are shoot structures that attach to stems and branches at nodes. Leaves are made up of cells that usually contain a high concentration of chloroplasts (cell organelles unique to plants) and are specialized sites for photosynthesis. We will explore photosynthesis in greater detail later; for now, remember that photosynthesis is the process of capturing light energy and converting it into chemical energy that can be stored in plants (like starch and sugar). In some plants, leaves may be modified for nutrient storage (as with onions, where the bulb is made up of fleshy leaves), or for support (as with peas, where some leaves are modified into tendrils that wrap around a trellis).
Leaves are also the surface where water that has moved from the soil into the roots and up through the plant finally evaporates back into the atmosphere in a process called transpiration.
Angiosperms, which are flowering plants whose seeds develop inside an ovary, tend to have flattened leaves. Many perennial angiosperms (flowering plants that can grow for many years) have leaves that senesce, or die, at the end of each growing season and are replaced at the beginning of the next growing season. Gymnosperms, plants whose seeds are produced without the protection of an ovary, tend to have needle-like leaves. Perennial gymnosperms tend to hang on to their leaves for a number of years. This saves energy, since the plant doesn’t need to grow a whole set of new leaves every year. The needle-like form helps retain moisture in harsh, dry climates, including those that are very cold and dry.
Leaf parts and venation
Angiosperm leaves typically have a blade or lamina, a flattened part with high chloroplast concentration. They may also have a petiole, the stalk that attaches the blade to the stem at a node. Stipules, small leaf-like bracts at the point of attachment of the petiole to the stem, may also be present. Some leaves have no petiole at all, and are termed sessile.
In contrast to the blade-petiole structure, grasses have a sheath-type structure in which the blade attaches to an envelope of leaf tissue that wraps around the shoot of the plant and then attaches to a lower node on the stem.
Leaf blades also have characteristic patterns of venation. In grasses, the veins lie parallel to each other and to the long edges of the leaf. We call this parallel venation, and it is typical of monocots. Most other angiosperms have a strong major midrib with veins branching from the midrib, smaller veins branching from those, and so on to form a netted venation throughout the leaf. This type of venation is typical of dicots.
Leaves may also have a palmate venation where several veins radiate from the point where the petiole attaches to the blade. Ginkgo tree leaves have palmate venation. The veins fork, then travel a bit, then fork again, travel, fork, and so on until the veins reach the margin (edge) of the leaf. Sugar maple leaves have a classic palmate venation with five lobes.
Watch this video on leaf veins:
Leaf segmentation
Simple leaves
Simple leaves have uninterrupted leaf margins. The leaf may have lobes like the oak leaf, but the blade has one continuous margin. The venation differs in the two examples below. The oak leaf is pinnate, with a major vein heading down the midrib of the leaf. The maple leaf is palmate, with major veins that radiate from the point of attachment to the petiole.
Compound leaves
The sumac leaf is a good example of how a compound leaf has a blade that is completely interrupted and segmented into separate leaflets. What you see in the picture — the entire thing — is one leaf. The leaf is divided or segmented into leaflets.
The petiole extends from the point of attachment at the node to the first leaflet. The central axis from that point on — from the first leaflet to the tip of the leaf — is called the rachis.
Virginia creeper is an example of a palmately compound leaf. The stalk that connects the leaflet to the top of the petiole is called the petiolule. In this case there is no rachis; all leaflets are attached directly to the top of the petiole.
Below is a compound leaf with three leaflets, called a trifoliate leaf. Soybean, clover, and dry bean all have trifoliate leaves. In contrast to the palmately compound leaf above, there is a rachis to which the central leaflet is attached.
To tell whether a leaf is simple or compound, ook for attachment to a node. If the point of attachment doesn’t appear to be a node, it is likely a leaflet attached to the rachis of a compound leaf.
Watch this video on compound leaves:
Additional optional reading
For more information about leaves, explore this Wikipedia page, starting about halfway down at the heading “Morphology (large-scale features)” and continuing through “Veins.”
Review questions
• What advantage do angiosperm leaves have because they are flattened?
• What advantage do gymnosperm leaves have because they are needle-like?
• What is the difference between a simple leaf and a compound leaf?
• Is a petiolule found in a compound or simple leaf? To what structure does it attach?
• What is the difference between a leaf with palmate venation and a palmately compound leaf?
• Draw and label a picture of a leaf with these parts: rachis, petiole, petiolule, and leaflet. | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/03%3A_How_Plants_Grow_Part_1/3.01%3A_Leaves.txt |
Learning objectives
By the end of this lesson you will be able to:
• Identify unique external features of shoots that distinguish them from roots.
• Locate the regions of origin for stems, branches, leaves, and inflorescences.
• Locate the regions of origin for stolons and rhizomes.
• Describe ways in which stolons and rhizomes are anomalies.
Shoots: Not only what’s above the soil
While it’s generally true that the shoot of a plant is the part above the soil, there are exceptions; these will be explored below.
A shoot is made up of a central axis called the stem, and components that grow from specific places on that stem. The stem can be tall and thick in diameter, like in a sunflower, or quite compact and compressed, like in an onion, where the stem may never get above the soil surface. The stem can be rigid like a corn stalk or floppy like a watermelon vine. In each case, the stem is the central axis to which the other shoot components attach. The stem doesn’t need to be upright; it can grow horizontally.
Watch this video to see examples and parts of shoots:
Nodes and internodes
The distinguishing external feature of a stem, and of the branches that arise from the stem, is its repeated node – internode – node – internode construction. A node is the place of origin on the stem for branches, leaves, and inflorescences. Sometimes the node is slightly swollen and obvious, other times not; it depends on the type of plant. Located at the nodes are buds (a colloquial term; later we’ll call them meristems) made up of cells that, given the correct biochemical signal, will rapidly divide and grow into branches, leaves, or inflorescences. More than one bud can grow from a node, so a node can support several structures.
In another chapter we will see how the plant stem has internal bundles of “pipes” that make up the vascular system through which water, nutrients, sugars, and other plant metabolites flow. At the nodes, some of these pipes diverge from the main bundle to provide nutrients, water, sugars, and other metabolites to the branches, leaves, and inflorescences that form at the node.
Between nodes are stretches of stem called internodes. One architectural function of the internode is to spatially orient the leaves, branches, and inflorescences. Long internodes, for example, will spread the leaves out along a stem so that they aren’t shading each other as much as if the internodes were short. Nodes also help with leaf orientation.
The location of nodes determines whether the leaves are located, which is called leaf arrangement, and leaf arrangement is a characteristic of a particular type of plant.
• Alternate — the leaves are attached at nodes on alternate sides as they go up the stem.
• Opposite — the leaves grow directly opposite each other on the stem.
• Whorled — the leaves are oriented in a whorled formation in which their point of attachment appears to spiral up the stem.
Nodes are important because they are where leaves, branches, and inflorescences originate; the internodes are important because their length has a profound impact on plant architecture.
With inflorescences, it can be difficult to tell where the stem stops and the inflorescence begins. One difference is that the stem has nodes and internodes, while the inflorescence does not.
What about vines?
Watch this video showing shoots, nodes, and internodes on vines.
What about grasses?
Take a look at this video to see node/internode structure on grasses. (Note: You can ignore the mention of a Wednesday class. This video is also used in an in-person class.)
What about trees?
In this video, you’ll see nodes and internodes on trees.
More about meristems
Watch this video to take a closer look at meristems.
The tip of the stem is called the apex, and the bud at the tip is called the apical bud, or apical meristem. In the image below, a bud has formed at the apex of the stem. This bud contains a meristem that will “break” or become active next spring and result in early season stem growth.
The crotch formed between the leaf petiole (the stalk that attaches the leaf blade to the shoot stem) and the stem or branch is called the leaf axil, and the buds in that crotch are called axillary buds or axillary meristems. You can see two sets of axillary meristems in the image. If pruned above the axillary buds, the plant will grow from these nodes. Removing the apical meristem is one way to encourage branching. If you’ve ever grown basil, you know that snipping or pinching leaves off right above a node encourages more leaves to grow from that node. This function also gives plants a way to respond to feeding damage or injury by having dormant buds that can grow when prompted.
Review questions
• Looking a photo of a plant, can you identify the stem, nodes, and internodes?
• Can you recognize different types of leaf arrangements on different plants you see?
• Buds at the nodes can develop into one or more of three different structures. What are these three structures?
• What type of buds are found in the crotch between the leaf petiole and the stem?
Stolons and rhizomes
Stolons
Some types of plants produce branches from nodes on the stem that are very close to, or right at, the soil surface. These branches, which have long internodes and lie on the surface of the soil, are called stolons. Not all plants produce stolons, but strawberry is a common example of a plant that does. The “runners” that extend out from the mature strawberry plant are in fact stolons. Stolons have the same typical repeating node/internode structure of a stem, but unlike other branches of the plant, at the nodes of the stolon, adventitious roots can form. Adventitious roots are roots that emerge from the stem rather than from roots. Even though they emerge from the stem above ground, they still act like roots. They anchor the stolon to the ground and absorb water and nutrients for the plant’s use. Leaves, and even branches, can also form from the stolon nodes.
One of the main purposes of stolons is to propagate a plant. The mature strawberry plant sends out a stolon and a new plantlet forms at the stolon node. Once the plantlet is rootedm you can cut the stolon internode between the plantlet and the main stem and transplant the plantlet. For instance, you can start a new patch of strawberry plants by cutting off these plantlets and planting them in a bed.
Potato is another plant that produces stolons; in this case the stolons are often below ground rather than above the soil. Potato tubers (the part that we eat) are formed from swellings of these stolons. When we grow potatoes we mechanically hill soil up around the potato stem during the growing season to cover the developing tubers, preventing them from turning green and bitter from exposure to sunlight.
Rhizomes
Rhizomes are another type of stem tissue originating from a node. In this case it is typically a node that is below the surface of the soil. A rhizome also grows horizontally and has nodes and internodes, but unlike stolons, it is underground. The ginger in the produce section of the grocery story is misnamed ginger “root,” but is actually a rhizome, and you can tell that this is stem tissue because it has nodes and internodes. The nodes are the faint, slightly raised rings around the circumference of the rhizome. If you see nodes and internodes on a plant part, the tissue is stem tissue and not root tissue, even if it is underground.
Rhizomes and stolons are the exceptions to the general notion that shoot tissue is above the soil surface. They are branches, complete with nodes and internodes, but are underground (rhizomes) or near the soil surface (stolons). They are stem tissue.
Turfgrass provides an example of rhizomes, stolons, and another structure typically associated with plants in the grass family called tillers. Here is an optional reading about those structures in turfgrass.
This video describes and shows an example of rhizomes.
Review questions
• What is the term for a horizontally growing stem that is near to or on the soil surface, and that can form adventitious roots at its nodes?
• What is the term for an underground, horizontally growing stem?
• What is one of the main purposes of stolons?
• What type of tissue are rhizomes, stolons, and tubers? Stem tissue or root tissue? | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/03%3A_How_Plants_Grow_Part_1/3.02%3A_Shoots.txt |
Learning objectives
By the end of this lesson you will be able to:
• Locate and identify characteristics of the primary root, lateral or secondary roots, and root hairs.
• Distinguish two major types of root systems and how they develop.
Roots
The general perception is that roots are the parts of the plant that are found in the soil. While this is typically true, there are exceptions, just as there are with the notion that all shoots are above ground. To recognize roots, we’ll look at more than whether or not they are in the soil.
Unlike stems and branches, roots don’t have a node/internode pattern of construction. There are no nodes, no internodes, no leaves, and no branching from regular spots, as you find with stems and branches. Roots do have structures but, in contrast to stems and branches, these structures emerge irregularly from the root according to where they are needed, and to some extent according to inherited tendencies, rather than emerging at specific zones the way leaves, branches, and inflorescences emerge from nodes on the stem.
Watch this video for a short intro to roots.
Purposes of roots
Anchorage
Roots keep the plant moored to the soil in a particular place. This “anchorage” not only facilitates other functions for the plant, but provides a benefit for the soil. An extensive root system helps hold the soil in place so that it is less likely to be eroded by wind or rain. Where there are roots the soil tends to be retained. No roots, and the soil easily gets washed or blown away. On the flip side, if conditions are poor the plant can’t pull up roots and move somewhere else where prospects for growth are better.
Support
The roots, particularly the tap root that we examine below, provides the foundation for upright growth.
Absorption
Roots are the structure of the plant that absorb water and soluble nutrients..
Symbiotic interaction with other organisms
Roots of plants from the taxonomic family Fabaceae — which are commonly called legumes, and include plants like peas, beans, clover, and locust trees — can form a symbiotic relationship with Rhizobia bacteria. This results in nitrogen fixation, which allows for the conversion of nitrogen from the atmosphere into nitrogen compounds that the plant can use to produce proteins and other building-block molecules. For nitrogen fixation to occur, rhizobia require a plant host; they cannot independently fix nitrogen. These bacteria fix nitrogen after becoming established inside root nodules of plants in the Fabaceae family.
Roots also develop associations with Mycorrhizal fungi. In contrast to the Rhizobia bacteria, which only symbiotically interact with a narrow range of plants, Mycorrhizae (mycorrhizae is the plural of mycorrhiza) are fungi that grow in association with roots of a wide range of plants — perhaps most plants. The mycorrhizae help acquire phosphorus from the soil and make it available to the plants’ roots. Mycorrhiza may also enhance water uptake.
Watch this video about symbiotic relationships between roots and soil organisms.
Nutrient storage
Roots of some plants can swell and store high-energy compounds like starch and sugar. Examples include carrots, beets, sweet potato — but not white potato. Roots also store some protein and other nutrients, but the focus is typically on high-energy carbohydrates.
Review questions
• What external features clearly differentiate roots from stems?
• What purposes do roots serve beyond absorption of water and nutrients?
• What are two examples of living organisms that symbiotically interact with roots? How do they differ in terms of the plants they infect and the benefits they provide?
Root systems
A plant’s root originates in the embryo formed within the seed. The section of the embryo that is root tissue is called the radicle (note the spelling). At the tip or apex of the radicle is a region of rapid cell division and growth called an apical meristem (you may recall that shoots have an apical meristem too). As a result of the apical meristem’s rapid cell division, the radicle grows down into the soil. The root that forms from the embryonic radicle is called the primary root. This sketch of half of a peanut seed shows the radicle that is part of the embryo inside the seed. The plumule is the embryonic shoot.
Shortly after germination and establishment of the seedling, plants generally develop one of two types of root systems: tap root or fibrous root.
Watch this video to see the differences between tap roots and fibrous roots.
Tap root systems
The tap root is persistent, meaning that it is retained throughout the life of the plant; it is also defined as a strong primary root that grows downward into the soil. This tap or primary root is the central axis off of which lateral or secondary roots branch in irregular patterns in response to the availability of high-quality soil — soil with adequate moisture, nutrients, and favorable soil structure (proper particle aggregation and pore space that fosters gas exchange and moisture retention).
Lateral or secondary roots typically grow relatively parallel to the soil surface, while the primary or tap root grows perpendicular to the soil surface. Tertiary roots branch off of secondary roots, again in response to nutrient and moisture availability.
A tap root system provides strong leverage and anchorage in the soil. If firmly connected to an upright stem, the tap root can resist uprooting by wind whipping at the shoot and herbivores yanking on the leaves and branches. Both the pigweed and the velvetleaf pictured here are tall, upright plants. The strong taproot helps provide the underground leverage to hold those plants upright.
Fibrous root systems
Fibrous root systems begin the same as tap root systems…with a radicle growing from the seed. However, after a period of early growth, the radicle or primary root stops growing (or slows its growth) and roots begin to form from the stem tissue that is underground, but just above the primary root. These roots emerging from stem tissue are adventitious roots — indicating that the roots emerge from the main stem.
In beans there are two types of adventitious roots. The roots that emerge from the region just above where the main stem stops and the root begins are called basal roots (basal because they are at the base of the main stem). The roots that emerge above these basal roots are called hypocotyl roots. As we’ll see in a later chapter, the portion of the stem just above the root-shoot transition zone is called the hypocotyl. Adventitious roots that contribute to the fibrous root system stay close to the soil surface. Fibrous root systems are excellent at holding soil in place because they are thin, extensive, and weblike. This is why various types of grasses, which have fibrous root systems, are planted in areas that are subject to erosion from flowing water following rains. The fibrous root systems of the grasses, once established, hang on to the soil particles like a web of very thin, interlaced fingers.
The kidney bean root system pictured above has been growing for a few weeks. You can identify the soil line on the stem by where the stem coloration transitions from green to cream or buff color. The root doesn’t start immediately after the stem enters the soil. Instead, the stem continues underground for about an inch. Notice the point where the width of the stem drastically reduces; this is where the primary root tissue starts. Again, the primary root traces directly back to the radicle, which is part of the embryo in the seed. Just above where the root starts are the basal roots, and above these are the hypocotyl roots. As noted above, basal and hypocotyl roots are adventitious roots, as they emerge from the stem.
In this picture of Echinopogon ovatus, known as hedgehog grass in its native Australia, you can see the rhizome or underground stem that is typical of spreading grasses. Note the nodes on the rhizome, which indicate that it is shoot tissue, not root tissue. Also note that the roots emerging from these nodes. The roots are adventitious because they emerge from shoot tissue rather than from the primary root (which disintegrates early in the growth of grasses). Shoot tissue often also emerges from these nodes.
Both tap root systems and fibrous root systems rely on root hairs to gather moisture and nutrients. Root hairs are extensions of the outer layer of cells (called the epidermis) of young roots. Root hairs live for only a few weeks, deteriorate, and are then replaced by fresh root hairs.
Corn (below) provides another example of adventitious roots. In this case, the roots are formed from shoot tissue above the soil and then angle down toward the soil. These are the “brace” or "prop" roots of corn. Sometimes they reach the ground, and other times they hang in the air. The roots that reach the soil branch extensively and are important for moisture and nutrient absorption. Below is a photo of the adventitious brace roots of Prunella vulgaris.
Review questions
• What is the difference between a tap root system and a fibrous root system?
• From what cells on young roots do root hairs form?
• What is the radicle? Does it persist in all mature plants? | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/03%3A_How_Plants_Grow_Part_1/3.03%3A_Roots.txt |
Here are the terms from this chapter that you will need to be familiar with.
Chapter 3 flashcards
Adventitious Tissue arising from an organ other than expected.
Adventitious roots Roots that emerge from the stem rather than roots.
Alternate leaves Leaves are attached on alternate sides as they go up the stem.
Apex Tip of the stem.
Apical bud Bud located on the tip of the stem.
Apical meristem Group of more or less continually dividing cells located at the tip of a shoot or root.
Axil Upper angle between a lateral structure and the stem to which it is attached.
Axillary bud Bud borne in the axil of a stem.
Axillary meristem Group of more or less continually dividing cells located at the axils of a stem.
Basal root Root that emerges from the region just above where the main stem stops and the root begins.
Bract Leaf attached to the terminal node, which is part of the inflorescence rather than the stem. It may also be found at the base of each pedicel.
Branch Vegetative growth coming from a node on the main stem.
Bud Immature vegetative or floral shoot or both, often covered by scales; also called a meristem.
Chlorophyll Green photosynthetic pigment found in plants, algae, and cyanobacteria that captures light for photosynthesis.
Compound leaf Leaf with a blade margin that is completely interrupted and segmented into separate leaflets.
Fibrous root Root system where the radicle grows and then rapidly slows or completely halts in growth. Once this happens, roots will emerge above the radicle and from the stem tissue located below the soil.
Hypocotyl roots Roots that emerge above the basal roots.
Internode Stem regions between nodes in plants.
Lamina Another name for a leaf blade.
Lateral or secondary roots Roots that extend horizontally from the primary root and serve to anchor the plant securely into the soil. This branching of roots also contributes to water uptake, and facilitates the extraction of nutrients required for the growth and development of the plant.
Leaf A usually green, flattened, lateral structure attached to a stem and functioning as a principal organ of photosynthesis and transpiration in most plants.
Leaf axil Upper angle between a leaf petiole and the stem to which it is attached.
Leaf blade Broad portion of a leaf; does not include the petiole.
Leaf margin Edge of the leaf blade.
Leaf primordia Young leaves, recently formed by the shoot apical meristem, located at the tip of a shoot.
Leaf scar Mark indicating the former place of attachment of petiole or leaf base.
Leaf sheath Structure where the blade attaches to an envelope of leaf tissue that wraps around the shoot of the plant and attaches to a lower node on the stem.
Leaflet Small leaf-like structure that is found on compound leaves. Multiple leaflets make up a single compound leaf.
Lenticel Small opening in the cork of woody stems that allows for gas exchange.
Meristem Group of continuously dividing cells; also called a bud.
Midrib Main vein, generally in the center of the leaf, from which secondary veins emerge.
Node Stem region of a plant where one or more leaves attach; location of lateral buds.
Opposite leaves Leaves that grow directly opposite each other on the stem.
Palmate venation Where several veins radiate from the point where the petiole attaches to the blade. The veins fork, travel a bit, fork again, travel, fork, and so on until they reach the margin of the leaf.
Palmately compound leaf Compound leaf where the petiolules of the leaflets connect directly to the petiole (no rachis).
Parallel venation Distribution or arrangement of a system of veins in a leaf blade in a non-intersecting network. The veins are parallel to each other and the long edge of the leaf.
Petiole Stalk by which most leaves are attached to a stem; part of the leaf structure, not the stem.
Petiolule Stalk that connects the leaflet to the top of the petiole.
Pinnate venation Type of webbed venation where there is a strong midrib and the secondary veins fan out opposite one other.
Pinnately compound leaf Compound leaf where the leaflets are arranged opposite one another on the rachis.
Primary meristem Apical meristems on the shoot and root apices in plants that produce plant primary tissues.
Primary root Root that forms from the embryonic radicle.
Prop root Adventitious root that arises from the stem, penetrates the soil, and helps support the stem, as in corn.
Radicle Embryonic root that breaks through the seed coat during germination and develops into the seedling’s root system.
Rhizome Horizontal stem growing just below the soil surface.
Root Organ that anchors the plant into the soil, takes up water and nutrients, and stores food.
Root hair Thin, hairlike outgrowth of an epidermal cell of a plant root that absorbs water and minerals from the soil. Root hairs live for only a few weeks, deteriorate, and are then replaced by fresh root hairs.
Sessile When a leaf lacks a petiole; called a sessile leaf.
Shoot Made up of a central axis (stem) with a repeating pattern of nodes and internodes.
Simple leaf Leaf with an uninterrupted blade margin.
Stem Supporting and conducting organ usually developed initially from the epicotyl and growing upward, and consisting of nodes and internodes.
Stipule Usually a pair of appendages located at the base of a leaf but may be fused into a ring around the stem; variable in size, shape, and texture; serves for protection or to attract pollinators.
Stolon Stem with long internodes that grows along the surface of the ground.
Storage root Root that is modified for storage of nutrients, such as carrots and beets.
Tap root Main root of a plant, usually stouter than the lateral roots and growing straight downward from the stem.
Terminal bud Bud located at the apex of a stem.
Trifoliate leaf Compound leaf with three leaflets that attach to a rachis.
Tuber Swollen, underground, modified stems that store food.
Venation Pattern of veins on a leaf.
Whorled leaves Leaves oriented in a whorled formation in which their point of attachment appears to spiral up the stem. | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/03%3A_How_Plants_Grow_Part_1/3.04%3A_Terms.txt |
Learning objectives
• Recognize the general patterns of plant growth and the diversity of flowers found in angiosperms.
• Distinguish the two types of growth patterns found in angiosperms — determinate and indeterminate.
• Compare the diversity and types of compound inflorescences.
In this chapter we explore the two main types of plant growth, determinant and indeterminate, and the vast diversity in form and number of inflorescences. As you learn the vocabulary, think about why each plant has these growth forms. A species with more flowers and seeds, for example, may be a better fit in its environment than a plant with a small number of flowers, but larger and more robust seeds.
Thumbnail: Salvia farinacea (Blue Sage). guzhengmanCC BY-NC-SA 2.0
04: How Plants Grow Part 2
Learning objectives
By the end of this lesson you will be able to:
• Recognize the general patterns of plant growth and the diversity of flowers found in angiosperms.
• Recognize the two types of growth patterns found in angiosperms — indeterminate and determinate.
• Identify the names of parts of simple and compound inflorescences.
• Recognize the diversity of arrangements of these parts.
Vegetative and reproductive growth patterns
Annual plants are produced from seed in the spring and die at the end of the growing season. These plants typically have a vegetative phase early in their lifespan, followed by a reproductive phase.
During the vegetative phase, stem growth takes place through the addition of new cells — including new nodes and internodes — by the apical meristem (the growing point or bud at the tip of the stem) and through elongation of those new cells. Leaves and branches then emerge at the nodes.
Eventually, and typically at very specific and predictable times, hormonal signals within the plant that are triggered by external agents such as night length or sustained temperatures stimulate the formation of reproductive buds or meristems at nodes. These reproductive meristems give rise to inflorescences. The appearance of these inflorescences signals the transition of the plant from vegetative to reproductive stages.
Determinate growth
In some plants, the apical meristem itself transforms into a reproductive meristem and produces an inflorescence at the end of the stem, called a terminal inflorescence. This determinate growth is beneficial in ornamental plants because it places flowers at the ends of the stems and branches, where they are clearly displayed and showy. Next time you walk past a bed of flowering plants, look at where the flowers are held on the plant. In most cases, they will be at the tip of the stems and branches and positioned on the outer periphery of the plant.
Determinate plants are also popular in agriculture because the plant produces all or most of its flowers at about the same time. The fruits ripen synchronously and can be harvested during a narrow window of time rather than ripening at various times during the season, which would stretch harvest out over many weeks. Corn is an obvious example, with the tassel at the top of the plant being a terminal male inflorescence and the corn ear a terminal female inflorescence. This type of growth pattern is called determinate because once the apical meristem of the plant transforms into a reproductive meristem, the number of nodes on that stem has been determined and will not increase. The stem may increase a bit in length through the elongation of the cells in the internodes, but no additional nodes will be formed.
Indeterminate growth
In other plants, the apical meristem remains a vegetative meristem that is capable of forming new nodes and internodes throughout the season. Once the hormonal signals are right, reproductive axillary meristems at the nodes below the apical meristem produce inflorescences. Even though the reproductive phase has begun, the plant can still grow new nodes and internodes from the apical meristems on stem and branches. As the season progresses and as new nodes are formed by the apical meristem, these nodes also mature to support the formation of more reproductive meristems and the growth of inflorescences.
This type of growth is called indeterminate since the number of nodes on the stem and branches is not determined, and more can be added throughout the year. For ornamental plants, indeterminate growth can mean highly desirable season-long flowering by an individual plant. For food plants, it means that fruits ripen at different times and so are available for a longer period of time through the year (many tomato cultivars are indeterminate). This may not be favored in large agricultural operations where the preference is for the efficiency of one simultaneous and large harvest, but it is great for gardeners who like small amounts of their produce to ripen throughout the season.
Inflorescences
The inflorescence is the flowering structure of the plant. Some inflorescences are very simple and support only one flower. These are called solitary or sole flower inflorescences, and the stalk attaching the flower to the node from which it grew is called the peduncle.
Other inflorescences can support multiple flowers and display complex branching patterns.
The drawing to the right depicts a hypothetical inflorescence that supports multiple flowers. Toward the bottom are the last two nodes of the stem. The next-to-last node supports a leaf, and the terminal node supports an inflorescence and a leaf. Since that leaf is associated with the inflorescence, rather than emerging from a stem node, botanists call it a “bract,” even though it may look like a smaller version of the plant’s other leaves. Since the terminal node transforms to be reproductive, this plant must have determinate growth.
The stem-like part of the inflorescence between the point where it emerges from the terminal node of the stem and the point where the branches of the inflorescence begin is called the peduncle. The central axis of the inflorescence, starting at the point where the first inflorescence branch is attached, is called the rachis. The rachis may subdivide one or more times, and these subdivisions are considered part of the rachis. Finally, there is a short stalk connecting the flower to the rachis; this is called the pedicel.
This type of inflorescence, with peduncle, pedicel, and single-flower structure, is called a simple inflorescence. An inflorescence with a group of flowers is called a compound inflorescence. A type of compound inflorescence with multiple flowers originating from a common point is an umbel. The illustration below shows a simple umbel compared to a compound umbel. On the left, in the simple umbel, the pedicels radiate out from a central point at the end of the peduncle and attach to a single flower. On the right, in the compound umbel, rachi radiate out from the end of the peduncle, and an umbel is attached to the end of the rachis.
Inflorescences can be amazingly complex structures. This site about inflorescences will help you recognize some of the possible arrangements and perhaps start looking for this complexity when you are out among plants.
Review questions
• Explain the difference between determinate and indeterminate growth.
• Draw a simple inflorescence and label the peduncle, pedicel, and flower(s).
• Describe the differences between a bract and a leaf. | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/04%3A_How_Plants_Grow_Part_2/4.01%3A_Growth_Patterns_and_Inflorescences.txt |
Learning objectives
Learning Objectives
By the end of this lesson, you will be able to:
• Understand the role of the five major hormone groups in plant growth and development.
• Recognize that cells, tissues, and organs have unique competency to respond to specific hormones.
• Connect specific hormones to plant responses and how they are used in plant propagation.
How plants respond to hormones
The five major groups of plant hormones — auxins, cytokinins, gibberellins, ethylene, and abscisic — acid are distinguished by their chemical structures and the response they evoke within the plant (see Table 4.1). For any cell to respond to a hormone it must be competent to perceive the chemical. Some cells simply lack the ability to “see” the hormone and do not respond to its presence. Competency to perceive a hormone depends on a cell’s physiology when the hormone is present. If the hormone is perceived, its unique chemical structure causes a chain reaction or signal transduction that involves changes in gene expression and cell morphology. These cellular responses to hormones can lead to changes we see in the plant, such as movement towards light, a transition from vegetative growth to flowering, or the closing of leaf stomata due to drought stress.
The perception of the hormone occurs in cells and throughout a tissue or organ, depending on where the hormone is located, the concentration of the hormone, and the developmental state and physiological condition of the cell. Many cells within a tissue can respond in a coordinated manner, resulting in changes in the whole plant. Hormones are often made in one cell and translocated to other cells where they are perceived, and the response may occur far away from the site of hormone synthesis. Responses to hormones are studied through exogenous application of the chemical to a plant tissue — the hormone is applied to the outside (exo) of the plant and observations are made on how the plant responds. For hormones that are a gas, like ethylene, this means the hormone can be translocated from one plant to another plant. The plants are essentially talking to one another, using a wide variety of molecules.
Experiments in which hormones are exogenously applied to a plant reveal how plants respond to hormones; much of our knowledge about the role hormones play in plant growth is from this type of experiment. Whenever a hormone is exogenously applied, however, it is also interacting with all of the hormones present in the plant. These are endogenous hormones (endo means internal), and the cell responds according to the sum of all hormones in its presence. This can complicate the interpretation of responses to exogenous hormone applications.
The hormones used in plant propagation can be naturally occurring and found in many plants, or can be synthetic or synthesized to mimic the structure and response of a naturally occurring hormone. Synthetic hormones are often used instead of naturally occurring versions because they are less expensive to obtain, may cause greater or longer lasting responses, and can be less susceptible to degradation in the plant and during storage. Because exogenous application of hormones play a role in manipulating or disrupting plant growth, they are used extensively as herbicides (weed killers) and can be targeted to certain types of plants based on how certain species respond to the different structure.
Plant responses to hormones and their application in plant propagation
Auxin
Auxins are a group of related molecules that are involved in almost every aspect of the plant’s life cycle. Auxins stimulate growth through cell elongation, which is integral to the plant’s responses to environmental changes. Auxins are responsible for two types of growth responses: phototropism, the bending or growth of a shoot toward light, and gravitropism, a change in growth occurring after a change in gravitational force. The diagram below shows indoleacetic acid (IAA, illustrated with pink dots), a naturally occurring auxin, moving from the sunny to the shady side of a shoot tip. The differential accumulation of auxin on the shady side of the shoot causes those cells to increase growth and bends the shoot tip toward the light. Auxin’s stimulation of cell growth is also important in healing wounds and forming calluses after pruning.
The ability of auxin to regulate growth can be turned against weeds (plants out of place). The synthetic auxin 2,4-dichlorophenoxyacetic acid, or 2,4-D, is a common herbicide that interrupts normal growth regulation when applied to the plant, causing leaf drop and death. Because dicotyledonous (dicot) plants have a higher competency to respond to 2,4-D, 2,4-D can be used as a selective herbicide to kill dicot weeds in lawns and corn fields, which are resistant, monocotyledonous (monocot) grasses. The grass is unharmed due to its lower competency to respond, while the dicot plants are killed.
In general, auxins are produced in the young leaves of a plant and translocated downward to older tissues. This downward translocation controls apical dominance, where growth of axillary buds is suppressed. Removal (pinching) of the shoot tip where auxin is being produced, as shown in the three photos of mint below, releases the axillary buds from apical dominance and they begin to grow. This is a common horticultural practice, increasing branching and flower production. Pinching is often used in seedling plants such as basil or zinnias to get globe forms in a pot instead of tall, single-stemmed plants.
One of the most important uses of auxin in plant propagation is to stimulate the growth of adventitious roots — roots that emerge from anywhere on the plant other than from the roots — on shoot cuttings. The photo below shows cuttings from two different Acer ginnala (Amur maple) plants that have different competencies to form adventitious roots. Both cuttings were treated with auxin, but only the competent plant forms adventitious roots (on the left). The cutting from a plant that lacks competency to respond to auxin did not form roots (right) and will eventually die.
This form of asexual (clonal) propagation is used by both horticultural professionals and hobbyists. The competency for rooting cuttings can be species specific or seasonal. Collecting stems from a plant to use for cuttings can be more successful in the growing season, as with the Amur maples shown above. With plants such as grapes, however, cuttings are made and rooted during the winter when the vines are not actively growing. The video below demonstrates how shoot cuttings are taken from Amur maples, treated with auxin, and incubated in a high-humidity environment for several weeks to form adventitious roots. Exogenous application of auxin is not required for adventitious rooting of all plants. Some plants can form many adventitious roots without exogenous applications, because the endogenous auxin that occurs naturally in the shoot is sufficient for root formation.
Cytokinins
Like auxins, cytokinins are a group of related molecules that regulate growth and development. However, the plant’s response to cytokinin is very different from the responses to auxin. Cytokinin comes from the word cytokinesis, which means cell division. You will learn about cytokinesis, specifically mitosis, in Chapter 13.
Cytokinins promote cell division, where one cell splits and two new daughter cells are formed. Cytokinins are important regulators of plant growth and development.
Cytokinins have an interesting interaction with auxin in plants. In the 1950s, Skoog and Miller were researching the growth of N. tabacum stems in tissue culture. They discovered that they could use specific ratios of an auxin (IAA) and a cytokinin (kinetin) to direct the growth of the stem tissue in culture. A high ratio of cytokinin relative to auxin led to shoot formation, a higher level of auxin led to root formation, and equal levels of each produced callus growth, which is undifferentiated plant cell growth. Skoog and Miller’s transformational discovery formed the basis of the “MS” plant medium that remains popular for plant propagation using tissue culture.
Watch this video to learn more about the propagation of plants in synthetic media with exogenous hormones in tissue culture.
Gibberellins
Gibberellins, or gibberellic acid (GA), are a group of over 100 molecules that are primary regulators of stem elongation and seed germination. They were discovered during research on the cause of the “foolish seedling” disease of rice. The disease, characterized by tall plants with little grain, is caused by an infection with Gibberella fujikora, a parasitic fungus that produces GA in the rice shoots, causing increased stem elongation.
In Chapter 9.2, on seed physiology, you will learn that some seeds are dormant and do not germinate even when the proper environment is provided. Seed dormancy, which has several causes and evolutionary advantages, always has the common feature of preventing seed germination until the time, season, or seed physiology is correct. Planting a dormant seed or a dead seed gives the same result: no germination. For plant propagators, dormancy can be confusing, raising the question “are my seeds dead or are they dormant?” Either condition prevents germination and plant propagation. Treating seeds with GA is a common method to break dormancy and facilitate germination. GA treatment of Gentiana lutea (bitter root) seeds, for example, increases germination from 0% (no germination) to over 80% when treated with 100 parts per million (ppm) GA (see the graph of germination on the left). If a propagator of G. lutea had not known about seed dormancy, they may have assumed their bitter root seeds were dead. For most plants, GA is the endogenous hormone that triggers seed germination.
Abscisic acid
While GA facilitates seed germination, abscisic acid (ABA) inhibits it. Abscisic acid is a single molecule that regulates germination and the response of a plant to reduced water availability during drought stress. ABA levels increase as water becomes less available to the plant, evoking several responses, including the closing of stomates. Closing stomata slows transpiration (also called evapotranspiration), the movement of water in the plant from the root to stem to leaf and out through the stomata into the atmosphere. You’ll read more about stomata and the movement of water in Chapter 11, Plants and water.
Reducing water content is one of the final steps in seed maturation and is important for seed longevity by reducing metabolism to a minimum, which is the quiescent nature of mature seeds. Increasing endogenous ABA levels in seeds prepares them to survive lower water content, is important to seed maturation, and prevents precocious germination (vivipary). Seeds with low levels of ABA during seed development may prematurely germinate. Low ABA levels may result from a genetic mutation or environmental causes. Vivipary in some fruits is not uncommon and may occur during storage of fruit in the grocery store.
Ethylene
Ethylene is well known as the gaseous, ripening hormone. It also regulates seedling growth and the formation of root hairs, and can lead to epinasty — the bending of branches downwards.
Many plants are sensitive to the effect ethylene has on fruit ripening. The iconic examples are tomato and banana. These fruits are climacteric — they continue to ripen after harvest. The perception of ethylene by the cells that make up the fruit triggers the ripening process and the production of more ethylene. As the concentration of ethylene increases, so does the speed of the ripening. Picking immature or green fruit enables shipment over long distances, because the fruit is firmer and less likely to be damaged in transit. The green fruit can then be treated with ethylene from an ethylene generator (right) to accelerate ripening.
For other fruit crops, the introduction or production of ethylene is to be avoided to prevent over-ripening and spoilage. To prevent the generation of ethylene during fruit storage, ethylene is scrubbed from the air using an air filter system. Reducing the ethylene concentration means slower ripening and less spoilage.
The process of senescence is also triggered by ethylene production and is important in the cut flower industry. Keeping cut flowers away from gases with ethylene-like activity helps keep floral arrangements looking fresh. Reducing ethylene action prolongs the vase life of many cut flowers as well as the storage of fruits.
Review
The five major groups of plant hormones control many aspects of plant growth and development and have important applications in plant propagation. However, many other molecules are also key to the plant’s response to its environment. These highly diverse signal molecules modulate the plant’s physiology through complex interactions. A cell’s response to the many different hormones is a sum of its genetic makeup, its physiology, and the environment.
Table 4.1
Hormone Structure Synthesized versions General responses Application
Auxin (indoleacetic acid; IAA) Indole butyric acid (IBA); Naphthalene acetic acid (NAA), 2,4-Dichlorophenoxyacetic acid (2,4-D) Adventitious rooting, tropisms, apical dominance Adventitious rooting of shoot cuttings
Cytokinin (zeatin) Benzyladenine (BA, BAP or benzylaminopurine), Thidiazuron (TDZ), kinetin Cell division Shoot formation in plant cultures
Gibberellin (GA3 shown) Over 100 types, named by GAnumber (for example GA3) Promotes seed germination and stem elongation Germination of dormant seeds
Abscisic acid None, although it can be synthesized Seed dormancy, response to water stress, leaf drop Genetic manipulation for drought resistance
Ethylene Natural gas, propane and their byproducts from burning Fruit ripening, epinasty, root hair formation Promote or prevent fruit ripening
Review questions
• Describe the general response the plant has to each of the five major plant hormones and the factors that affect the response of a plant.
• Explain the difference between endogenous and exogenous plant hormones.
• Describe an application for each of the plant hormones in plant propagation specifically or horticulture in general. | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/04%3A_How_Plants_Grow_Part_2/4.02%3A_Plant_Hormones.txt |
Here are the terms from this week’s lessons that you will need to be familiar with for your assignments and for the quiz.
Chapter 4 flashcards
Abscisic acid A hormone that regulates seed maturation and responses to changes in water availability.
Adventitious root A root that emerges from anywhere on the plant other than from the roots.
Angiosperms A group of flowering plants whose seeds develop inside an ovary.
Annual plant A plant that is produced from seed in the spring and dies at the end of the growing season.
Apical dominance Where a shoot suppresses growth of floral or vegetative axillary buds below the growing point.
Auxins A group of related hormones that regulate many aspects of plant growth and development and are key to stimulating adventitious rooting.
Competency The ability to respond to a signal, such as a plant hormone.
Compound inflorescence An inflorescence with a group of flowers and includes a rachis.
Cytokinins A group of related molecules that regulate cell division and are key to stimulating adventitious shoot formation.
Determinate When the stem of a plant terminates in a flowering stalk and new stem growth continues from subterminal lateral buds.
Endogenous hormone A hormone that occurs within the plant.
Ethylene A gas that regulates fruit ripening and plant senescence.
Exogenous hormone The application of a hormone to a plant.
Floret A single flower in a compound inflorescence.
Flower A reproductive structure in a flowering plant.
Gibberellins A group of related molecules that regulate seed dormancy.
Gymnosperms A group of plants whose seeds are produced without the protection of an ovary.
Indeterminate When the apical meristem remains a vegetative meristem capable of forming new nodes and internodes throughout the season. Once the hormonal signals are right, reproductive axillary meristems at the nodes below the apical meristem produce inflorescences.
Inflorescence The complete flower structure of a plant; includes the flower, pedicle, rachis, and peduncle.
Natural hormone A hormone made by a plant.
Pedicel The short stalk that holds up the flower.
Peduncle The large, central stalk that attaches the rachi to the stem of the plant.
Perception The ability of a plant cell or tissue to detect a hormone that depends on a cell’s physiology at the time the hormone is present.
Perennial A plant that lives for more than two growing seasons (more than two years); perennials may be woody or herbaceous (the latter with underground perenniating structures).
Plant hormone A signal molecule that regulates growth, development, and responses to environmental and other signals, also known as a plant growth regulator or phytohormone.
Rachis The stalk of a flower that is situated between the peduncle and the pedicel on a compound leaf. Also the name for the central axis on a compound leaf where the leaflets are attached.
Reproductive meristem The apical meristem that transforms into the reproductive tissues (the inflorescence) of the plant.
Response The action taken by the plant after perception of a signal.
Senescence A regulated process that results in cell death and is associated with leaf fall and death of the plant.
Signal transduction The process in which the perception of a signal, such as a hormone, is moved within a cell, cell to cell, or throughout a tissue.
Simple inflorescence A type of inflorescence with a peduncle, rachis, pedicel, and single flower structure.
Synthetic hormone A hormone made by people; can mimic the response of a naturally occurring hormone.
Tropism A growth or turning response to an environmental or other signal such as phototropism (response to light) or gravitropism (response to gravity); can be controlled by auxin and other hormones.
Umbel An inflorescence with multiple flowers originating from a common point.
Woody perennial A plant that lives for more than a year, has hard rather than fleshy stems, and bears buds that survive above ground in winter. Trees, shrubs, many vines, and bamboo are examples of woody perennials. | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/04%3A_How_Plants_Grow_Part_2/4.03%3A_Terms.txt |
Learning objectives
By the end of this chapter, you will be able to:
• Recognize the internal cellular structure of leaves, shoots, and roots, and describe their specializations.
• Connect structure to processes involving gas, water, and photosynthate movement.
• Understand how and where photosynthesis occurs.
The panda eats shoots and leaves. Maybe a comma is out of place here or there, but in the plant each part has an orderly place and function. The fundamental vegetative (non-reproductive) organs of the plant are stems, roots, and leaves. These organs have unique tissues with unique arrangements that can be used in propagation.
05: Inside Plants
Learning objectives
By the end of this lesson you will be able to:
• Recognize the internal cellular structure of leaves.
• Describe how the structure facilitates photosynthesis.
• Describe how the structure facilitates gas exchange.
• Explain why leaves in autumn turn from green to yellow, orange, and red.
Leaf anatomy
Learning leaf anatomy is a bit like taking a sandwich apart and seeing what’s inside. We’ll start with the upper surface and progress down through the leaf. Here are the layers you will find:
• Upper epidermis with cuticle. The cuticle is a protective waxy coating of cutin on epidermis cells, restricting water loss and preventing disease.
• Palisade mesophyll — densely packed, columnar-shaped, elongated cells full of chloroplasts. Chloroplasts are structures inside plant cells that contain chlorophyll and are the site of light capture during photosynthesis. These are analogous to cortex parenchyma cells in the stem, but in the leaf they are specialized for light energy capture.
• Spongy mesophyll — loosely packed cells with large air spaces between them. The air spaces allow movement and exchange of gases, specifically oxygen, carbon dioxide, and water vapor. Spongy mesophyll cells also contain chloroplasts.
• Vascular bundlexylem, phloem, and bundle sheath cells along with nearby parenchyma and either sclerenchyma or collenchyma fibers for support.
• Lower epidermis with guard cells that regulate the size of the stomata, the gaps in the epidermis that allow gas exchange between the atmosphere and internal parts of the leaf.
In the graphic above, you can see the spongy and palisade mesophyll in detail. During the growing season, these cells are packed with chloroplasts containing the pigment chlorophyll. Chlorophyll absorbs red and blue wavelengths of light to power photosynthesis, and reflects green light back to our eyes, making leaves appear green to use in spring and summer.
Watch this video about colors we see in leaves:
Review this article, Why Leaves Change Color.
Chromoplasts (not to be confused with chloroplasts) are cellular organelles that contain types and colors of pigments other than the chlorophyll found in chloroplasts. In late summer and fall, the mesophyll cell chloroplasts produce chlorophyll at a slower rate than earlier in the year. As the existing chlorophyll reaches the end of its functional lifespan and eventually degenerates, the amount of chlorophyll declines over time. Because chlorophyll replacement doesn’t make up for chlorophyll loss, the green color fades from the leaves. Meanwhile, the non-green pigments in the chromoplasts hold their own or increase in quantity, including the yellow and orange from the carotenoid pigments and the red from the anthocyanin pigments.
Carotenoid pigments are present in the leaf all growing season, but during the warm part of the season they’re hidden by the high concentration of green-colored chlorophyll. When the cool autumn weather comes, the days shorten and the chlorophyll concentration in the chloroplasts declines. The carotenoids in the chromoplasts don’t degenerate as quickly as the chlorophyll does, so we get a beautiful display of oranges and yellows in the leaves once the green is gone. These orange and yellow colors can be counted on every year because the carotenoids are produced and present all year long.
In contrast to the carotenoid pigments, the amount of red color in leaves from the anthocyanins differs from autumn to autumn. Anthocyanins are produced primarily in the autumn in response to bright light and excess plant sugars in leaf cells. Warm, sunny days encourage sugar production in leaf mesophyll, and cool nights hinder the transport of these sugars out of the cells, so the sugars stay in leaves. The high sugar then stimulates anthocyanin production. Warm, bright days + cool nights = red leaves. In years with overcast days and warmer nights, there is less sugar production in the leaves and the sugars translocate (move out) from the leaf mesophyll cells to other locations in the tree, so there is less anthocyanin pigment produced and less red color in the leaves. You might see this happening on individual trees: on the sunlit, southwest side of the tree you might find leaves with more red than on the shaded, northeast side. This effect of weather on anthocyanin is particularly noticeable in trees such as sugar maples.
Some other woody plants, like sumac, seem to be bright red in later September and early October regardless of the weather conditions. Other trees, like birch and oak, will be yellow or tan even with warm bright days and cool nights.
Here is a cross section of a pear leaf showing the same cells illustrated in the graphic shown earlier.
The palisade mesophyll is highly adapted for capturing light energy. As noted earlier, the cells are packed tightly together, filled with chloroplasts, and make up the cell layer just under the protective epidermis on the top surface of the leaf oriented toward the sun. The spongy mesophyll cells below the palisade layer are less densely packed together, so the region is laced with air channels. This makes the spongy mesophyll highly adapted for gas movement and air exchange around the cells.
Guard cells surround a gap in the epidermis. This gap is called a stoma or stomate (plural = stomata), and is the portal through which gas exchanges between the interior and exterior of the leaf. Gases in the intercellular spaces between spongy mesophyll cells are free to move out of the stomata into the atmosphere, and atmospheric gasses are free to move in. As we will see later when we address photosynthesis, healthy plants must have the ability to move oxygen (a waste product of photosynthesis) out of the leaf, and carbon dioxide (a raw material for building sugars) into the leaf. Water vapor must also be able to move out of the leaf as part of the transpiration process.
The vascular bundle (the xylem and phloem in the graphic above) is highly adapted for transport of fluids. Water and dissolved minerals move up the xylem from the roots and into the leaf. Sugars produced in the leaf during photosynthesis move out of the leaf through the phloem and are translocated to other parts of the plant. The thick-walled bundle sheath cells that surround the xylem and phloem provide mechanical support, and contribute to some types of photosynthesis. Wikipedia has a good illustration showing the tissues associated with the vascular bundles. Take a look.
Review questions
1. Which layer of cells in the leaf are most highly adapted to intercept light? Describe three ways in which these cells are specialized for this purpose. Hint: two have to do with position or orientation in the leaf, and one with the plastids they contain.
2. Which leaf cell layers are key to gas exchange?
3. What happens to the green pigments in leaves when the weather turns cold in the fall? Why do some leaves turn yellow, orange, and red, instead of turning brown? | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/05%3A_Inside_Plants/5.01%3A_Inside_Leaves.txt |
Learning objectives
By the end of this lesson you will be able to:
• Discuss how stems grow by elongation and by increasing their girth or diameter.
• Identify the tissues that are initially produced by apical meristems and the cells into which they eventually mature.
• Distinguish monocot and dicot stems based on the arrangement of the vascular bundles.
• Describe the functions of some of the specialized cells in the stem.
Introduction to stems
Herbaceous plants are plants whose above-ground plant parts die back to the soil surface at the end of the growing season. Herbaceous plant shoots grow in length and diameter in the same way that roots do: the apical meristem at the tip of the stem produces new cells and then those new cells enlarge in length and volume in the region of elongation just behind the meristem. Stems of herbaceous plants typically do not thicken very much and rely instead on branching to grow laterally (although there are exceptions like sunflower and tomato whose stems do thicken noticeably). Branching of the shoot is initiated at nodes where there are axillary buds containing axillary meristems that grow into branches.
Continued growth of the stem in diameter, like you find in a tree where the trunk and branches increase in diameter each year, requires an active lateral meristem called the cambium. Cambium is a meristem in the vascular tissue positioned between the xylem and phloem that continues to produce new xylem cells toward the interior of the stem and new phloem cells toward the exterior. Production of xylem and phloem from cambium cells is called secondary growth and is typical of woody perennial plants. We will explore plants with secondary growth in a different lesson.
Some herbaceous plants are annuals, like beans and pansies, where the whole plant dies over the winter. These plants complete their life cycle from seed to flower to seed in one year. Other herbaceous plants, like Kentucky bluegrass and chrysanthemums, are herbaceous perennials where only the above-ground growth dies over winter (unless it is a really nasty winter). The root, or in some cases underground stem tissue, stores nutrients for the next season’s growth. In spring when soil and air temperatures are sufficiently warm, new shoots emerge from nodes on compact stem tissues often called crowns. The cells in the crown tissue survive the harsh winter temperatures because they accumulate sugars and other compounds that act as antifreeze compounds. They are located very close to the soil surface, or even protected a bit by the soil. This position on or in the soil, plus snow cover, results in much warmer temperatures around the crown than the air temperature above the snow. In fact, the air temperature can be -20°F above the snow and only a few degrees below freezing (32°F) around the crown.
Dicotyledonous stems
Watch this video for a detailed description of dicot stems (2:19).
This micrograph of a herbaceous dicot stem shows four basic parts (in order from outside to inside): epidermis, cortex, vascular bundle, and pith. Notice how the vascular bundles of dicots are arranged in a ring around the circumference of the plant stem with the cortex to the outside and pith to the inside.
Epidermis – This tough covering is a single layer of living cells. These cells are closely packed and function to protect the internal parts of the plant. The walls are thickened and covered with a thin waxy waterproof layer called the cuticle that reduces water loss from the plant. Stomata with guard cells are found in the epidermis, and these function to allow gasses into and out of the stem, similar to their function in leaves. In some stems either unicellular or multicellular hair-like outgrowths, called trichomes, appear from the epidermis. Below is an image of trichomes on a tomato stem, inflorescence, and leaf.
Cortex – Also known as the ground meristem, the cortex is found just inside the epidermis and extends toward the interior of the stem. It is made up of three types of cells: parenchyma, collenchyma, and sclerenchyma.
Vascular bundles – This region contains sclerenchyma fibers that strengthen the stem and provide protection for the vascular bundle. In dicots, the vascular bundles form a distinct ring. A mature vascular bundle consists of three main tissues – xylem, phloem, and cambium. The phloem is always located toward the outside of the bundle and the xylem always toward the center. The cambium separates the xylem and phloem, and, in those plants where secondary growth takes place, the cambium produces new xylem and phloem cells: xylem toward the center, phloem toward the outside.
The pith occupies the central part of the stem and is composed of thin-walled parenchyma cells often with larger intercellular spaces than you would find in the cortex.
In this cross section of a dicot stem note the collenchyma cells in the cortex just under the epidermis. Sunflower stems are quite tough, and this toughness is in part due to the layer of collenchyma cells positioned to give the stem mechanical stability. Toward the outside of each vascular bundle are fibers of sclerenchyma that also contribute to the sunflower stem’s toughness. Then, moving from the outside to the inside, you will find phloem, a layer of cambium, and then xylem. The pith is in the center.
Now you might recall that just above we said that herbaceous annuals like sunflower don’t have cambium to increase the girth of the stem, so what’s with the cambium in this picture of a sunflower stem? Well, you will see a layer of cambium between the xylem and phloem of dicot stems, and it is active for a while and produces a modest amount of xylem and phloem which contributes to the sunflower’s larger diameter stem. However, this cambium tissue is not continuously active as in woody stems, and the plant does not survive through the winter.
Monocotyledonous stems
The tissues making up monocot stems are essentially the same as what we saw in dicots with the main difference apparent in the placement of the vascular bundles. In monocots, vascular bundles are scattered throughout the stem instead of being oriented in a ring. Since there is no ring of vascular bundles, there is no “inside” pith and “outside” cortex. All the ground tissue is considered to be cortex.
In monocot vascular bundles the phloem is always oriented toward the outside of the plant and the xylem toward the inside. There is no cambium and no secondary growth. Around the outside of the vascular bundle is a layer of parenchyma cells called the bundle sheath. This layer of cells is very important in photosynthesis. For now we will consider it a protective covering and supportive sheath around the vascular bundle.
One final note
So why the palm tree? Because it is an exception.
A palm tree is a monocot, but unlike other monocots whose stems are quite thin (like grasses, for instance), their primary stems do increase in girth from year to year even though they do not have secondary cambium. Palms have a special layer of meristematic cells, called the primary thickening meristem, oriented toward the outside of the stem that each year can initiate new vascular bundles and new parenchyma cells. Each year the stem expands in girth as a result of the palm’s production of new parenchyma and vascular bundles. You don’t need to memorize this – it is just an example of an interesting exception to the rule.
Review questions
After completing this section, you should be able to answer these questions:
1. Herbaceous perennials die back to the ground in the spring. Where do they get the energy to grow the next spring, and from what tissue do new shoots emerge?
2. Dicots typically have a pith while monocots do not. Why?
3. Could you distinguish between a monocot and dicot stem based on the arrangement of the vascular bundles? | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/05%3A_Inside_Plants/5.02%3A_Inside_Stems.txt |
Learning objectives
By the end of this lesson you will be able to:
• Explain how roots elongate and increase in diameter via primary and secondary meristems.
• Identify the tissues in the root that originate from the root meristems and the cells into which they eventually mature.
• Distinguish between monocot and dicot roots.
• List the functions of the cells in plant roots.
Please read the OpenStax pages summarizing root biology. This resource reinforces several of the topics addressed below, so you may read it either before or after you complete this chapter. You don’t need to memorize the information there; use it to reinforce the content below.
Root review
The functions of roots include:
• Anchoring the plant in the soil (and stabilizing the soil).
• Supporting the upright growth of the plant.
• Providing a site for the symbiotic relationship of the plant with particular beneficial fungi and bacteria.
• Absorbing water and dissolved minerals from the soil.
• Storing nutrients like starch for subsequent use by the plant (tap roots and tuberous roots are examples of geophytes that store nutrients in roots).
Angiosperm (flowering) plants are often classified by whether they rely on a primary root system an adventitious root system. A plant doesn’t necessarily have only primary or just adventitious roots. One of these systems, however, will be dominant. Whether a root is considered primary or adventitious depends on whether the root traces back to the radicle (embryonic root) or arises from (normally underground) stem tissue.
Tap root (or primary root) system
Tap or primary roots arise as a continuation of the embryonic radicle tissue and persist into maturity. Secondary roots (also called lateral roots) arise from the primary root, and tertiary roots arise from the secondary. This primary –> secondary –> tertiary root formation is the usual rooting system for dicots. Next time you see a dandelion or other weed that doesn’t look like a grass, yank it up and look at the root system. The main root you see (assuming that it didn’t break off when you pulled it up) is probably a tap root. The photo on the right, above, demonstrates this point. It shows a young taproot system with many secondary roots branching off the primary root.
Adventitious or fibrous root system
In plants of this type, the primary root, which originates from the radicle, weakens prior to maturity and new, vigorous, adventitious roots arise from stem tissue. Adventitious roots may grow from nodes or might arise from the internodes. They originate from parenchyma cells in the cortex of the stem. Dig up a clump of turfgrass and look at the roots. Turfgrass has a fibrous root system, as does corn.
As noted above, although adventitious roots originate from the stem they don’t have to emerge from a node. While it’s not apparent in the photo, the adventitious corn roots you see above do trace back to a node. In contrast, in the photo of a tomato stem, below, we see emergence of adventitious roots from both node and internodal regions of the stem.
Internal root structure
Watch this video to take a closer look at root structure (6:21):
Root cap
Shaped like a thimble, this structure covers the tip of the root and provides protection as the root grows into the soil. These parenchyma cells are produced by the root’s meristem which is just behind the root cap. The outer cells of the root cap are continuously worn away through contact with the soil, and new cells are added to the inner portion.
In addition to protecting the interior of the root, the cap secretes a mucilage which stabilizes the water content of the surrounding soil, ensuring longer-lasting nutrition to the root system and making for easier root probing. Finally, the root cap contains statocytes, specialized cells that help the plant sense gravity and grow accordingly. These cells are full of starchy organelles which settle at the lowest part of the cell and encourage growth in that direction. If the root cap, with these statocytes, is removed, a plant may grow in random directions because it has lost the ability for gravitropism (growth in response to gravity).
Root meristem
The cells here divide rapidly via mitosis to form new cells. New cells are laid down toward the root cap to replace those worn away during root growth, and also laid down away from the root cap. These new cells laid away from the root cap elongate and then mature into more specialized root tissues.
Region or zone of elongation
In this region, the cells produced by the root meristem undergo rapid elongation — they expand in length and volume. Root growth is the result of two processes: new cell production by the root meristem, and subsequent elongation of those new cells. This growth pushes the root further into the soil and also expands the diameter of the root. Within the region of elongation just behind the meristem you will find the following undifferentiated tissues:
• Protoderm — new cells laid down toward the exterior of the root which will mature to become the root dermal tissue (primarily epidermis cells).
• Procambium — new cells in the central part of the root which will mature to become the vascular tissue (xylem, phloem, and vascular cambium), labeled in the illustration above this section as the vascular cylinder.
• Ground meristem — the new cells lying between the protoderm and procambium that will mature to become the cortex tissue (primarily parenchyma cells).
Region of differentiation (also called the region of maturation)
Here the root becomes thicker, and secondary or lateral roots are initiated. In this region the protoderm, procambium, and ground meristem cells undergo differentiation into the specialized cells associated with the dermal, vascular, and cortex tissues, as noted above.
Root-hairs begin to form in the region of differentiation; these are fine outgrowths of epidermis cell walls and membranes, and increase the area of absorption of the root.
Review questions
1. What two processes result in root growth?
2. Protoderm will differentiate or mature into what type of tissue? How about procambium? And ground meristem?
3. Do adventitious roots arise from stem tissue or from the primary root? Are they always found emerging from nodes or from internodes, or does it depend on the type of plant? | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/05%3A_Inside_Plants/5.03%3A_Inside_Roots.txt |
Chapter 5 flashcards
Adventitious roots Roots that emerge from the stem rather than roots.
Anthocyanin pigments Red pigments that are produced primarily in the autumn in response to bright light and excess plant sugars in leaf cells.
Apical meristem Group of more or less continually dividing cells located at the tip of a shoot or root.
Axillary bud Bud borne in the axil of a stem.
Axillary meristem Group of more or less continually dividing cells located at the axils of a stem.
Cambium Lateral meristem in vascular plants, including the vascular cambium and cork cambium, that forms parallel rows of cells resulting in secondary tissues.
Carotenoid pigments Yellow and orange pigments that are present in the leaf all growing season, but during the warm part of the season these colors are hidden by the high concentration of green-colored chlorophyll. They take longer to break down than chlorophyll.
Cortex Also known as the ground meristem, is found just inside the epidermis and extends toward the interior of the stem and root, and is made up of three types of cells: parenchyma, collenchyma, and sclerenchyma.
Crown Compact stem tissue at or near the soil surface.
Cuticle Protective waxy coating of cutin on epidermis cells that restricts water loss.
Cutin Water-resistant substance that coats the wall of the cell exposed to the environment and helps limit the loss of water that is inside of the plant to the atmosphere.
Dicotyledon (dicot) Seed plant that produces an embryo with paired cotyledons, floral organs arranged in cycles of four or five, and leaves with net-like veins.
Fibrous root Root system where the radicle grows and then rapidly slows or completely halts in growth. Once this happens roots will emerge above the radicle and from the stem tissue located below the soil.
Gravitropism Growth in response to gravity.
Guard cells Located on the epidermis and regulate the size of the stomata.
Herbaceous Plants whose above-ground parts die back to the soil surface at the end of the growing season.
Herbaceous annual Plants that completely die over winter. These plants complete their life cycle from seed to flower to seed in one year.
Herbaceous perennial Plants where only the above-ground growth dies over winter. The underground portion lives for more than two growing seasons (two years).
Mitosis Cell division where a cell divides into two identical daughter cells.
Monocotyledon (monocot) Seed plant that produces an embryo with a single cotyledon and parallel-veined leaves; includes grasses, lilies, palms, and orchids.
Phloem Tissue consisting of sieve tube and companion cells in the vascular system of plants that moves dissolved sugars and other products of photosynthesis from the leaves to other regions of the plant.
Pith Occupies the central part of the stem and is composed of thin-walled parenchyma cells often with larger intercellular spaces than you would find in the cortex.
Primary root Root that forms from the embryonic radicle.
Procambium New cells in the central part of the root that will mature to become the vascular tissue (xylem, phloem, and vascular cambium).
Protoderm New, primarily epidermis, cells laid down toward the exterior of the root which will mature to become the root dermal tissue.
Root cap Thimble-shaped mass of cells that covers and protects the root apical meristem from rocks, dirt, and pathogens.
Secondary growth Production of xylem and phloem from cambium cells.
Secondary root Root that forms off of the primary root.
Statocytes Specialized cells that help the plant to sense gravity and grow accordingly.
Stomate/Stoma/Stomata Gap in the epidermis that allows gas exchange between the atmosphere and internal parts of the leaf.
Tap root Main root of a plant, usually stouter than the lateral roots and growing straight downward from the stem.
Translocation Movement of a substance from one place to another.
Trichome Either unicellular or multicellular hair-like outgrowths arising from the epidermis; found on stems.
Vascular bundle System containing vessels that carry or circulate fluids and dissolved minerals in the plant; composed of xylem, phloem, and bundle sheath cells.
Xylem Supporting and water-conducting tissue of vascular plants.
Zone of Differentiation Area in roots where tissues are formed (expand in width).
Zone of Elongation Area in roots where recently produced cells grow and elongate prior to differentiation. | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/05%3A_Inside_Plants/5.04%3A_Terms.txt |
Learning objectives
• Compare the functions of the diverse cell types and their organelles.
• Understand how cells build the plant and their origins in meristematic tissue.
Cells are the building blocks of the plant. Even the mightiest oak begins as a single, microscopic cell produced by fertilization. That single cell replicates, differentiates, and develops into the complex tissues, organs, and systems of the plant. In this chapter we’ll will learn about the internal workings of plant cells and how those cells, some living and some dead, orchestrate the plant’s life cycle.
Thumbnail: Trichomes extending from the surface of a leaf. Marc PerkinsCC BY-NC 2.0
06: Cells Tissues and Woody Growth
Learning objectives
By the end of this lesson you will be able to:
• Label the parts of a plant cell.
• List the types of tissues in a plant and describe where they are located and the specialized cells that make up each of these tissues.
• Summarize the key functions of those tissues.
Plant cell
The graphic below illustrates the key parts of the plant cell.
Cell wall
The outer covering of the cell, the cell wall is a rigid membrane that contains cellulose (a carbohydrate that is indigestible for humans). The cell wall protects the parts inside, and the cellulose molecules in the wall provide the support and rigidity needed to maintain the cell’s three-dimensional structure.
Cell membrane
The cell membrane is made up of layers of protein and lipid (fats and oils are examples of lipids). The cell membrane is semi-permeable — it allows select compounds in and out, but blocks other types of compounds. If the cell were like a bicycle tire, the cell wall would be the thick, protective outer tire tread and the cell membrane would be the inner tube.
Chloroplast
An organelle (“organelle” is the generic name for a plant organ) that contains chlorophyll. In the chloroplast, light energy is captured and the first steps are taken in the chemical pathway that converts the energy in light into forms of energy that the plant can transport and store, like sugar and starch. Chloroplasts are not evenly distributed throughout the plant but, as you might expect, are concentrated in parts of the plant that are exposed to and oriented toward the sun. A plant cell in the leaf blade will have many chloroplasts, while cells in the middle of the stem will have few or none.
Mitochondria
(Singular = mitochondrion)
The mitochondria is where stored sugars from photosynthesis are metabolized to produce forms of energy that the plant can use for growth. This metabolism is known as respiration and uses oxygen to convert sugars (and other carbohydrates) to energy and carbon dioxide. This is the cell’s power plant. All cells have numerous mitochondria.
Nucleus
An organelle that contains the chromosomes. Chromosomes contain the genetic material (deoxyribonucleic acid; DNA) that is carried within each cell and that directs which chemical reactions are turned on and off in the cell. Chromosomes are the hereditary material passed on to new cells and to subsequent generations. Each cell has one nucleus.
Vacuole
An organelle containing various fluids, ions, chemical energy, and waste products from the cell. The vacuole takes up much of the cell volume and gives shape to the cell.
Cytoplasm
The fluid inside the cell membrane in which the organelles and other plant cell parts are suspended.
Middle lamella
A material containing pectin that forms between cells and cements the cell wall of one cell to the cell wall of an adjacent cell. If bricks in a wall are like cells in a plant, the middle lamella in the plant is like the mortar between bricks in the wall.
Plant cells have other parts as well, but these are the key ones to know and understand now.
Review questions
1. What is the difference in function between the cell wall and the cell membrane?
2. What is the mortar that holds cells together? If lettuce is grown in a soil with low calcium content, the outer edges of leaves can degenerate and die, causing tip burn. Could this involve the mortar that holds cells together?
3. Where is light energy captured?
4. What happens in the mitochondria, and what is the connection between that function in mitochondria and the function of chloroplasts?
Tissues
A tissue is a group of cells that share a function. The cells within a tissue may differ from one another, but they all contribute to a particular function. We’re going to look at three types of tissues: dermal, cortex, and vascular.
Dermal tissue
Dermal tissues (derma is Greek for “skin”) are on the outside of the plant and provide protection for the plant cells they surround. The cells making up dermal tissues are tough so that they can protect against mechanical challenges to the plant, like abrasion. They have thick cell walls. In the shoot, the epidermis cells, which are the main cell type in dermal tissue, secrete a water-resistant substance called cutin (a waxy polymer), which coats the wall of the cell exposed to the environment. This coating helps limit the loss to the atmosphere of water that is inside the plant. Cutin is absent or greatly reduced in root tissue because roots need to reach out into the soil to absorb water and nutrients.
The epidermis is the outermost layer of cells in the plant. It is normally only one cell thick, but in some cases the epidermis can be a few cells thick. Epidermis cells typically have few if any chloroplasts. They are often called pavement cells because they are flat like tiles or puzzle pieces. Depending on the plant, the epidermis may have hairs, or trichomes, that extend out from the plant. Some of these trichomes are associated with glands that contain oils or other substances secreted by the plant.
The epidermis contains pairs of guard cells that will open to form stomata (Greek stoma = mouth; an opening in the leaf surface) through which gasses can move into and out of the deeper cell layers in the leaf. These guard cells are found most abundantly on the underside of leaves, but may also be on the upper leaf surface and on the stems.
The root has dermal tissue as well. The predominant cell type, like in the shoot, is also epidermis, but as noted above there is no cutin covering the root epidermis because the root is underground and less prone to dehydration. There are no guard cells or trichomes, but there are root hairs . The root hair is a very small-diameter extension of the epidermis cell wall and cell membrane that extends out into the growth medium. Water and nutrients enter the plant through absorption into the root hairs.
Review questions
1. What unique feature of the epidermis is found in roots and not shoots?
2. What is the function of the waxy cutin layer? Why don’t you find it on the root epidermis?
3. Are stomata found in roots, shoots, or both? Why does this make sense?
4. What’s the difference between a cell and a tissue?
Cortex or ground meristem tissue
The cortex (sometimes called “ground meristem“) tissue is found just inside the epidermis and extends toward the interior of the stem and root. Some types of plants also contain cortex tissue at the very center of the stem called the pith, but you won’t find pith in roots or in all plant stems. Cortex cells provide structural support for the stems. In leaves, this tissue just inside the epidermis is called the mesophyll (“middle of the leaf”). Mesophyll tissue is the site of most photosynthesis reactions in the leaf.
Three types of cells make up the cortex:
Parenchyma
• The most common type of cortex cell.
• Has thin cell walls (called a primary wall in the graphic below).
• The mature cell is alive.
• Has the ability to begin dividing to help heal wounds (by covering the wound with plant tissue called callus).
• Will also divide to initiate adventitious roots on stem cuttings.
• Site of many other functions, such as photosynthesis and storage of starch and other chemical compounds.
• Leaf mesophyll tissue is a type of parenchyma that is packed with chloroplasts.
Collenchyma
• A living cell at maturity.
• Cell walls are thicker than the thin parenchyma cell walls, which give collenchyma strength. However, these cells remain somewhat flexible compared to sclerenchyma, which you will read about next.
• The cells can connect together to form resilient strands, like the strands of a celery stalk. These strands provide support for young tissues.
• Because the cells are alive, they can respond to external stimuli. If the plant is regularly shaken by wind, for example, the collenchyma cells will respond by producing thicker cell walls for greater support of the plant stem so that it can remain upright.
Sclerenchyma
• This type of cell has a primary and secondary cell wall. The primary cell wall, on the outside of the cell, is rich in cellulose, just like other plant cell walls. Once the cell has reached its final size, a secondary cell wall is deposited just inside the primary wall. The secondary wall has a high concentration of lignin that gives the cell rigidity. This rigid, lignified secondary cell wall is responsible for sclerenchyma’s hardness and strengthening properties. Sclerenchyma comes in two types:
• Fibers (see below) formed from long strands of sclerenchyma. These tough fibers give the plant rigidity. We extract these fibers from plants and use them in fabrics, carpets, and rope. Examples of plant fibers made up of sclerenchyma cells include jute, hemp, and flax (the fabric made of flax fibers is called linen). Cotton is not in this list; it is an epidermal fiber produced by the plant’s seed coats.
• Sclereids are cells with hard, tough cell walls. Sclereid cells can coalesce and cover other plant parts. For instance, they form the hard covering around the seeds (the endocarp) of stone fruits like cherries, the hard shell around walnuts, and the hard covering of coconut. Sclereids also make up the grit that crunches between your teeth when you eat a pear.
• Sclerenchyma cells are dead at maturity. They don’t thicken in response to external stimuli the way collenchyma can.
Review questions
1. Which cortex cells are alive and which are dead when mature?
2. Which cells make up the tough fibers from which rope and fabrics can be made?
3. Which cells divide to initiate adventitious roots?
4. What tissue in the leaf corresponds to the cortex in the stem?
Vascular tissue
Vascular tissues form the plumbing system in the plant through which water, nutrients, sugars, and other compounds flow. These plumbing pipes and associated cells are bundled together in the plant in a structure called the vascular bundle. There are three main types of vascular tissue: xylem, phloem, and vascular cambium. Xylem and phloem are composed of different types of cells, listed below.
Xylem
• Moves water in the plant.
• The water flow is unidirectional. Water in xylem heads from root to stem to leaf and then out of the plant stomates through a process called transpiration.
• The part of the tree that we call “wood” is made up of xylem.
• These cells are dead at maturity, and they are hollow.
Xylem tissue is composed of four different types of cells:
Vessels
Elongated cells that connect end to end to form tubes. The cells are dead at maturity. The end walls of the vessels are perforated, so water can move freely through the holes and flow from cell to cell. Vessels have a relatively large diameter compared to other xylem cells and allow greater movement of water.
Tracheids
These cells are elongated and narrower than vessels, and connect by overlapping at their ends. These cells are also dead at maturity and contain pits through which water can move. Tracheids appear earlier in the paleontological record of plant evolutionary development than vessels and are thus considered “primitive” (not inferior, but appearing earlier in evolutionary time). Vessels are a subsequent evolutionary adaptation that allow for greater water flow because of their larger diameter.
Xylem fibers
Sclerenchyma cells lying near the vessels and tracheids, and thus part of the vascular bundle. They are strung together end to end like the vessels and tracheids, but unlike those water carriers they have no pits or perforations and instead have thick primary and secondary cell walls. They provide flexible support for the plant from within the vascular bundles.
Xylem parenchyma
In woody plants there are parenchyma cells around the vascular bundles that extend horizontally through the xylem (the woody part of the plant) and develop into rays moving laterally from the center to the exterior of the plant. Most of the vascular cell types are arranged in a linear fashion parallel to the long axis of the stem, but parenchyma rays are arranged laterally from the middle of the stem out toward the epidermis. They function to conduct water through the wood (xylem). Oak furniture for example, it will have a “grain” which is caused by the annual rings of xylem, and will have rays that, on edge, look like small pits in the wood. We will see this in later lectures when we deal more extensively with wood and secondary growth. As you can see in the photo to the right, some of the natural markings you see in an instrument’s wood are from parenchyma rays.
Phloem
• Moves some nutrients taken up by the roots to other parts of the plant.
• Moves sugars manufactured in leaves by photosynthesis, and other plant compounds such as plant hormones like auxin, to other parts of the plant.
• The flow in the phloem is multi-directional among leaf, stem, and root.
Phloem tissue also has four types of cells:
Sieve tube members
Elongated cells that join end to end to form tubes for passage of liquids. The end walls have pores. Unlike xylem cells, these cells are still alive. They have a thin cell membrane containing a layer of living protoplasm that hugs the wall of the cell.
Companion cells
Associated with sieve tube members. Contain a nucleus, may direct the metabolism of the sieve tube member, and are alive.
Phloem fibers (sclerenchyma cells)
Provide support, same as for xylem.
Phloem parenchyma cells
Adjoin the sieve tube cells, same as for xylem.
Vascular cambium
This third type of vascular tissue is a meristematic region (meaning that the cells can actively divide to form new growth) where new vascular tissues originate in plants with secondary growth, like trees. We will study secondary growth in Chapter 6.2.
Review questions
1. What substance flows in the xylem? Does it flow both directions or only up from the roots to the leaves?
2. What are examples of substances that flow in the phloem? Do these flow both directions or only from roots to leaves?
3. Which vascular cells are dead and which are alive at maturity?
4. Look at a piece of wooden furniture near where you are sitting. What type of plant tissue and cell do you see? Look at the natural markings in the wood. What are those tissues and cells? | textbooks/bio/Botany/The_Science_of_Plants_-_Understanding_Plants_and_How_They_Grow_(Michaels_et_al.)/06%3A_Cells_Tissues_and_Woody_Growth/6.01%3A_Plant_Cells_and_Tissues.txt |
Subsets and Splits