patrickbdevaney/mia9 · Datasets at Hugging Face

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in understory composition (F1,68 = 1.24, p = 0.251). While not conclusive, this result suggests that the
light environment’s effects on the soil microbiome is unlikely to be driven by changes in the plant
understory composition.
4.2. Biotic Factors: The Role of Understory Plant Communities and Tree Density in Fungal Community
Diversity and Composition
Our study showed that biotic factors may also have consequences for the Everglades tree
islands soil fungi. We found that the characteristics of the understory plant community explained
variation in fungal community diversity, richness, and composition. For instance, as understory plant
community evenness increased, so did both fungal diversity and richness. This relationship may stem
from differences among plant species in their priming of soil microbial communities [75] and/or their
contributions to the leaf litter [76]. Plants can actively manipulate the soil microbial community through
the release of root exudates [77] and allelochemicals [78], and this priming can be species-specific.
Similarly, plants can have species-specific differences in their leaf litter, and the composition of leaf litter
can influence fungal communities [79]. Soil priming and litter deposition by a more even understory
plant community may promote a more even distribution of soil microhabitats for fungal taxa to use,
thereby fostering the greater fungal diversity we found. We also demonstrated that differences in
plant community composition among sites are significantly related to differences in fungal community
composition. Unlike the effects of manipulated variables such as core type and tree density, we cannot
determine the direction of interaction (i.e., plant understory community composition is driving fungal
community composition, the reverse, or both are responding to an external pressure). However, it is
well known that fungal and plant communities are interlinked [80]. Understory plant communities
may change fungal communities through their root exudates [77], leaf litter [81,82], or by acting
as hosts for pathogenic or mutualistic fungi [83]. Furthermore, a thriving understory community
may provide shade, thus changing the microhabitat conditions of soil moisture. On the other hand,
fungal composition may alter plant composition through nutrient availability [84], decomposition [85],
water availability [9], pathogen load [86], or mutualistic interactions [87]. Most likely, both the
Diversity 2020, 12, 0324 11 of 17
fungal and plant communities are affecting one another via plant-soil feedbacks [88] and are also
mutually responding to major abiotic factors such as hydrology. Future work that manipulates
these components (i.e., abiotic factors, microbial and plant community characteristics) using factorial
mesocosm experiments is needed to fully determine the strength and direction in which these
communities are affecting one another, and how much outside habitat characteristics contribute to
this relationship. In addition, the initial tree planting density was identified by model selection as
part of the best model for fungal community richness. While its effect was not significant within the
best model (nor was tree density as commonly implicated as the understory plant community in our
analyses), tree density’s inclusion in the best model hints at a role for this experimentally manipulated
factor in influencing fungal communities. Future studies investigating the effects of tree composition
on fungal communities could provide additional insights into consequences for fungi that investigating
tree density alone may miss.
4.3. Fungal Functional Guilds on Tree Islands
In addition to characterizing fungal diversity and composition, our study provided initial insight
into fungal contributions to ecosystem services by characterizing the distribution of fungal functional
guilds on tree islands. While not all fungal taxa could be characterized into functional groups by
FUNGuild and functions sometimes differ between ecosystems [89], this approach represents a first step
in understanding how different restoration decisions and environmental variation may impact fungal
roles within Everglades tree islands. For example, we found that the number of guilds was significantly
greater in sites with a more even plant understory community, which is in line with the greater fungal
taxa diversity at these sites. The arbuscular mycorrhizal fungal guild (fungal mutualists that associate
with plant roots and trade water/nutrients acquired through hyphal networks for photosynthetic
carbon) was present at all five of the sites with the highest plant understory evenness, while the five sites
with the lowest plant evenness shared the ‘tri-guild’ of dung saprotroph-wood saprotroph-undefined
saprotroph in common. More broadly, we found that some guilds were often missing from the
sites with the low functional richness. In particular, we noted that 5 of the 9 saprotroph guilds
(i.e., dung, leaf, soil, wood, undefined, and undefined-wood saprotroph guilds) were present in none
of the 15 most guild-poor sites. While two of these guilds—leaf and undefined-wood saprotroph—were
also commonly absent in guild-rich sites, this general loss of saprotroph guilds in guild-poor sites
suggests that functional losses may first affect decomposition services.
When we examined the top three most common individual guilds of fungi, only pathogen–wood
saprotrophs were affected by any abiotic or biotic factors. Specifically, as the relative water level
increased, pathogen-wood saprotrophs’ relative abundance decreased, which indicates that changes in
water management may have cascading effects on pathogen-wood saprotroph abundance. In addition
to the possible direct effects of water on pathogens, increases in tree stress caused by low water levels
may make trees more susceptible to pathogens, increasing the abundance of this guild. While some tree
island plants prefer lower water levels, flood-tolerant trees are often more stressed when water levels
drop (stress indicated by leaf loss; Sah, unpublished observation), which could increase the pathogen load
in drier sites. The relationship between water level and pathogen abundance detected in this study is
important to consider when managing tree islands, as lower water levels could possibly result in more
fungal pathogens and lower overall fungal diversity. Due to the possible dual function of the species
in this guild, future studies are needed to determine if plant pathogen-wood saprotrophs taxa are
acting more as pathogens or decomposers across tree islands. This additional information on fungal
function could help inform management decisions, since plant pathogens could be detrimental to tree
island stability, while wood saprotrophs may be important for soil formation [36,90]. Alternatively,
members of this dual-function guild may be plant pathogens that decompose the woody vegetation of
their host once it declines and/or dies. A more nuanced understanding of the function and life histories
of taxa within this guild may be especially important, as manipulations of Everglades hydrology as
well as increases in hydroperiod have led to the loss of soil on tree islands [41,91].
Diversity 2020, 12, 0324 12 of 17
While these results provide a crucial first look at the consequences of management decisions and
environmental variation for the fungal community function, substantial gaps still remain to be filled.
For example, we found that many taxa were not identifiable at the species level, making it difficult to use
the FUNGuild database to characterize the functions of these diverse taxa (likely including taxa unique
to the imperiled Everglades). Further, using amplicon sequencing alone makes it difficult to gain a full
perspective into community function [92]. We suggest that future work investigate function through
complementary approaches, such as functional assays, metatranscriptomics, and the direct assessment
of fungal structures. For example, growth under different resource conditions and functional gene
assays could inform our understanding of the primary mode of nutrition and assess some functional
effects (e.g., [93,94]). Metatranscriptomic studies could further help elucidate functional responses by
determining which functional genes have expression that is actively being up- and down-regulated
within communities experiencing different management decisions [95]. In addition, studies of fungal
structures would provide more insight into fungal diversity and how environmental variables influence
the distribution of life history stages (i.e., hyphae, spores, fruiting bodies) of taxa.
5. Conclusions and Future Work
This study demonstrates that soil fungal communities on Everglades tree islands can be driven
by abiotic and biotic factors, some of which are determined by management decisions. Our results
indicate that early restoration decisions can have long-term consequences for fungal communities and
suggest that a drier future in the Everglades could reduce fungal diversity on imperiled tree islands.
In addition to hydrology and tree establishment, future restoration projects may want to consider the
understory plant community, as our study shows a relationship between the understory community
and fungal diversity and function. In our opinion, there are at least two general types of studies that
are likely to be profitable going forward. First, additional manipulative experiments at macrocosm and

in understory composition (F1,68 = 1.24, p = 0.251). While not conclusive, this result suggests that the

light environment’s effects on the soil microbiome is unlikely to be driven by changes in the plant

understory composition.

4.2. Biotic Factors: The Role of Understory Plant Communities and Tree Density in Fungal Community

Diversity and Composition

Our study showed that biotic factors may also have consequences for the Everglades tree

islands soil fungi. We found that the characteristics of the understory plant community explained

variation in fungal community diversity, richness, and composition. For instance, as understory plant

community evenness increased, so did both fungal diversity and richness. This relationship may stem

from differences among plant species in their priming of soil microbial communities [75] and/or their

contributions to the leaf litter [76]. Plants can actively manipulate the soil microbial community through

the release of root exudates [77] and allelochemicals [78], and this priming can be species-specific.

Similarly, plants can have species-specific differences in their leaf litter, and the composition of leaf litter

can influence fungal communities [79]. Soil priming and litter deposition by a more even understory

plant community may promote a more even distribution of soil microhabitats for fungal taxa to use,

thereby fostering the greater fungal diversity we found. We also demonstrated that differences in

plant community composition among sites are significantly related to differences in fungal community

composition. Unlike the effects of manipulated variables such as core type and tree density, we cannot

determine the direction of interaction (i.e., plant understory community composition is driving fungal

community composition, the reverse, or both are responding to an external pressure). However, it is

well known that fungal and plant communities are interlinked [80]. Understory plant communities

may change fungal communities through their root exudates [77], leaf litter [81,82], or by acting

as hosts for pathogenic or mutualistic fungi [83]. Furthermore, a thriving understory community

may provide shade, thus changing the microhabitat conditions of soil moisture. On the other hand,

fungal composition may alter plant composition through nutrient availability [84], decomposition [85],

water availability [9], pathogen load [86], or mutualistic interactions [87]. Most likely, both the

Diversity 2020, 12, 0324 11 of 17

fungal and plant communities are affecting one another via plant-soil feedbacks [88] and are also

mutually responding to major abiotic factors such as hydrology. Future work that manipulates

these components (i.e., abiotic factors, microbial and plant community characteristics) using factorial

mesocosm experiments is needed to fully determine the strength and direction in which these

communities are affecting one another, and how much outside habitat characteristics contribute to

this relationship. In addition, the initial tree planting density was identified by model selection as

part of the best model for fungal community richness. While its effect was not significant within the

best model (nor was tree density as commonly implicated as the understory plant community in our

analyses), tree density’s inclusion in the best model hints at a role for this experimentally manipulated

factor in influencing fungal communities. Future studies investigating the effects of tree composition

on fungal communities could provide additional insights into consequences for fungi that investigating

tree density alone may miss.

4.3. Fungal Functional Guilds on Tree Islands

In addition to characterizing fungal diversity and composition, our study provided initial insight

into fungal contributions to ecosystem services by characterizing the distribution of fungal functional

guilds on tree islands. While not all fungal taxa could be characterized into functional groups by

FUNGuild and functions sometimes differ between ecosystems [89], this approach represents a first step

in understanding how different restoration decisions and environmental variation may impact fungal

roles within Everglades tree islands. For example, we found that the number of guilds was significantly

greater in sites with a more even plant understory community, which is in line with the greater fungal

taxa diversity at these sites. The arbuscular mycorrhizal fungal guild (fungal mutualists that associate

with plant roots and trade water/nutrients acquired through hyphal networks for photosynthetic

carbon) was present at all five of the sites with the highest plant understory evenness, while the five sites

with the lowest plant evenness shared the ‘tri-guild’ of dung saprotroph-wood saprotroph-undefined

saprotroph in common. More broadly, we found that some guilds were often missing from the

sites with the low functional richness. In particular, we noted that 5 of the 9 saprotroph guilds

(i.e., dung, leaf, soil, wood, undefined, and undefined-wood saprotroph guilds) were present in none

of the 15 most guild-poor sites. While two of these guilds—leaf and undefined-wood saprotroph—were

also commonly absent in guild-rich sites, this general loss of saprotroph guilds in guild-poor sites

suggests that functional losses may first affect decomposition services.

When we examined the top three most common individual guilds of fungi, only pathogen–wood

saprotrophs were affected by any abiotic or biotic factors. Specifically, as the relative water level

increased, pathogen-wood saprotrophs’ relative abundance decreased, which indicates that changes in

water management may have cascading effects on pathogen-wood saprotroph abundance. In addition

to the possible direct effects of water on pathogens, increases in tree stress caused by low water levels

may make trees more susceptible to pathogens, increasing the abundance of this guild. While some tree

island plants prefer lower water levels, flood-tolerant trees are often more stressed when water levels

drop (stress indicated by leaf loss; Sah, unpublished observation), which could increase the pathogen load

in drier sites. The relationship between water level and pathogen abundance detected in this study is

important to consider when managing tree islands, as lower water levels could possibly result in more

fungal pathogens and lower overall fungal diversity. Due to the possible dual function of the species

in this guild, future studies are needed to determine if plant pathogen-wood saprotrophs taxa are

acting more as pathogens or decomposers across tree islands. This additional information on fungal

function could help inform management decisions, since plant pathogens could be detrimental to tree

island stability, while wood saprotrophs may be important for soil formation [36,90]. Alternatively,

members of this dual-function guild may be plant pathogens that decompose the woody vegetation of

their host once it declines and/or dies. A more nuanced understanding of the function and life histories

of taxa within this guild may be especially important, as manipulations of Everglades hydrology as

well as increases in hydroperiod have led to the loss of soil on tree islands [41,91].

Diversity 2020, 12, 0324 12 of 17

While these results provide a crucial first look at the consequences of management decisions and

environmental variation for the fungal community function, substantial gaps still remain to be filled.

For example, we found that many taxa were not identifiable at the species level, making it difficult to use

the FUNGuild database to characterize the functions of these diverse taxa (likely including taxa unique

to the imperiled Everglades). Further, using amplicon sequencing alone makes it difficult to gain a full

perspective into community function [92]. We suggest that future work investigate function through

complementary approaches, such as functional assays, metatranscriptomics, and the direct assessment

of fungal structures. For example, growth under different resource conditions and functional gene

assays could inform our understanding of the primary mode of nutrition and assess some functional

effects (e.g., [93,94]). Metatranscriptomic studies could further help elucidate functional responses by

determining which functional genes have expression that is actively being up- and down-regulated

within communities experiencing different management decisions [95]. In addition, studies of fungal

structures would provide more insight into fungal diversity and how environmental variables influence

the distribution of life history stages (i.e., hyphae, spores, fruiting bodies) of taxa.

5. Conclusions and Future Work

This study demonstrates that soil fungal communities on Everglades tree islands can be driven

by abiotic and biotic factors, some of which are determined by management decisions. Our results

indicate that early restoration decisions can have long-term consequences for fungal communities and

suggest that a drier future in the Everglades could reduce fungal diversity on imperiled tree islands.

In addition to hydrology and tree establishment, future restoration projects may want to consider the

understory plant community, as our study shows a relationship between the understory community

and fungal diversity and function. In our opinion, there are at least two general types of studies that

are likely to be profitable going forward. First, additional manipulative experiments at macrocosm and