patrickbdevaney/mia9 · Datasets at Hugging Face

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tool for improving terrestrial restoration but are often overlooked in both restoration planning and
the assessment of success [13]. Research has shown that fungal amendment can improve the fertility
Diversity 2020, 12, 0324; doi:10.3390/d12090324 www.mdpi.com/journal/diversity
Diversity 2020, 12, 0324 2 of 17
and water availability of soil [14] and the establishment, growth, and survival of seedlings in restored
habitats [15]. However, the value of fungal communities for improving restoration success likely
depends on their composition and diversity, as these properties can influence both their direct and
indirect effects on ecosystems. For example, a greater diversity of mycorrhizal fungi often results
in a more efficient exploitation of phosphorus and therefore greater plant growth [16,17]. Similarly,
a recent study showed that as microbial diversity increased, so did the simultaneous maintenance
of diverse ecosystem functions and services [18]. Previous restoration studies have demonstrated
how important the origin of fungal inocula can be for the overall productivity and plant community
composition of degraded lands [19,20]. Further, inoculating with more complex and field-acquired
soil microbial communities often results in greater plant growth than commercially available fungi
(usually single-strain mycorrhizal inocula) [21,22], suggesting that the diversity and composition of
the fungal community added is important for restoration success. While it is possible to use fungi
in restoration without detailed knowledge of their communities, understanding the environmental
factors that affect these assemblages can help steer management decisions to increase the benefit of
fungal amendments and improve the conservation of fungal diversity in threatened ecosystems.
One imperiled habitat for which understanding soil fungal communities could help achieve
meaningful restoration goals are the tree islands of the Florida Everglades. The Greater Everglades
Ecosystem, which originally spanned over 10,000 km2 of South Florida, is the largest designated
wilderness in the Eastern United States, a NaturalWorld Heritage Site, a RamsarWetland of International
Importance, and home to 103 threatened or endangered plants and animals [23]. Unfortunately, this
unique ecosystem is highly threatened by habitat destruction and the hydrologic changes required
for urbanization and agriculture as well as by invasive species, climate change, and pollution [24–26].
These changes have negatively impacted both the aquatic and terrestrial biodiversity of this system
(e.g., estimated declines of up to 90% in some wading bird populations and 90–98% declines in
small mammal populations within Everglades National Park; [25,27]). While much of the Everglades
landscape is a freshwater wetland characterized by sawgrass marsh and persistently flooded sloughs,
tree islands—aggregations of woody vegetation on elevated peat or limestone—are important features
of this ecosystem [28]. In addition to being critical habitats for resting and foraging wading birds,
American alligators, white-tailed deer, and other animals [29], tree islands are biogeochemical hotspots
within an otherwise nutrient-poor ecosystem. Despite making up a relatively small portion of the
landscape (e.g., approximately 4% historically in the central Everglades), tree islands are estimated to
sequester approximately 67% of the phosphorus in the Everglades (up to 100 times more phosphorus
than the surrounding wetlands) and promote the retention of nitrogen by the landscape [28,30,31].
Urbanization since the 1950s in South Florida has led to anthropogenically driven changes to Everglades
hydrology, which is believed to be the main driver of tree island loss (up to 87% in some areas) [32].
As tree mortality increases, the transition from a “healthy” tree island into a treeless “ghost” island
is accompanied by a release of sequestered nutrients into the surrounding wetland habitats [30].
This nutrient release is thought to have cascading effects on ecosystem and species dynamics in
these impacted landscapes (e.g., invasive cattails outcompete native sawgrass in high-phosphorus
areas; [33]).
As a result of the importance of tree islands in the Everglades and their substantial decline,
the restoration of ghost islands and creation of constructed tree islands is an important piece of
the Comprehensive Everglades Restoration Plan [34]. There are several reasons that soil fungi may
be especially integral to the success of tree island restoration. First, as the primary decomposers,
soil fungi are likely to play a central role in regulating soil formation [35,36], which is a goal for the
restoration of both degraded tree islands and self-perpetuating, fully-functioning constructed tree
islands. Second, soil fungi can be important in nutrient immobilization (e.g., fungi are responsible
for the immobilization of approximately 20–30% of global phosphorus pools; [1,5]), which could
help sequester phosphorus and nitrogen within islands and reduce leaching into the surrounding
wetlands. Third, fungal mutualists (e.g., mycorrhizal fungi) may increase tree island stability by
Diversity 2020, 12, 0324 3 of 17
increasing tree resilience to natural and anthropogenic stress [9], and fungal pathogens may be crucial
for restoring a natural tree community composition by regulating the abundance of dominant plant
species [37]. While fungal communities in the peat and periphyton of the Everglades wetlands have
been investigated in a few cases [38–40], the terrestrial fungal communities of Everglades tree islands
are unexplored. In fact, we are aware of no studies of the diversity or composition of soil fungal
communities on Everglades tree islands. To improve the protection, and even utilization, of fungal
diversity in the restoration of tree islands, studies of the factors that structure these fungal communities
are needed. Here, we use a set of eight experimental Everglades tree islands, in which abiotic and
biotic factors have been manipulated to understand tree island formation, to better identify how
microhabitat environmental variation and experimental restoration decisions may influence fungal
diversity, composition, and functional guilds.
2. Materials and Methods
2.1. Study Site and Environmental Data Collection
We studied tree island soil fungal communities at the approximately 32-ha Loxahatchee
Impoundment Landscape Assessment (LILA) facility in Loxahatchee National Wildlife Refuge in
Palm Beach County, Florida, USA (26.489◦ N, 80.219◦ W). LILA contains eight approximately 2500 m2
experimental tree islands that were constructed in 2003 through a collaboration between the South
Florida Water Management District and the Army Corps of Engineers. LILA is especially suitable
for investigating how the soil microbiome responds to different restoration decisions, because the
construction of tree islands allowed landscape-level experimental manipulations of tree island
characteristics. For instance, the islands’ cores (i.e., bases of the islands) were manipulated to
represent two common island types in the Everglades: peat core and limestone core islands [41].
Using locally sourced peat and limestone derived from the habitat adjacent to the current LILA facility,
half of the experimental islands were constructed with peat cores and half were constructed with
limestone cores (Figure S1); then, all the islands were covered with a top layer of peat substrate [42].
Similarly, each of the eight experimental islands was split into quadrants in which a mixture of 10 tree
species were planted at four different densities (1 m, 1.67 m, 2.33 m, and 3 m spacing) in 2006 and
2007 (Figures S1 and S2). Given the importance of plant-fungal interactions, tree planting density may
be a biotic factor that strongly affects fungal community composition. In addition, LILA has other
readily available data on microhabitat variation within and among islands that can help inform our
understanding of the soil microbiome. For example, because the water level is continuously monitored
within the macrocosms and the topography of each island is well mapped, it is possible to track the
hydrology of microhabitats using the DBHydro project from the South Florida Water Management
District [42]. Using surface water-level data and the elevation of each site, we calculated the average
site-specific ‘relative water level’ for all plots in 2018 (the year fungi were sampled) following the
methods in [43]. Further, understory plant communities that recruited to these experimental tree islands
have been monitored since 2009 [42], allowing for consideration of the understory plant community
in structuring soil microbiomes. For these understory plant communities, we calculated Shannon
diversity, Pielou’s evenness, and plant richness for use in our analyses. During the monitoring of
each site, understory plant biomass was estimated (by applying allometric equations developed from
separate biomass collection plots to estimates of plant cover). To gain insight into the light environment
(another abiotic feature of interest), hemispherical canopy photographs were also taken using a digital
camera (Nikon Coolpix 995; Nikon, Tokyo, Japan) equipped with a hemispherical lens (Nikon Fisheye
Converter FC-E8 0.21×, Tokyo, Japan) at each site, and canopy openness was determined using the
software Gap Light Analyzer (GLA), version 2.0, Burnaby, BC, Canada [44].

tool for improving terrestrial restoration but are often overlooked in both restoration planning and

the assessment of success [13]. Research has shown that fungal amendment can improve the fertility

Diversity 2020, 12, 0324; doi:10.3390/d12090324 www.mdpi.com/journal/diversity

Diversity 2020, 12, 0324 2 of 17

and water availability of soil [14] and the establishment, growth, and survival of seedlings in restored

habitats [15]. However, the value of fungal communities for improving restoration success likely

depends on their composition and diversity, as these properties can influence both their direct and

indirect effects on ecosystems. For example, a greater diversity of mycorrhizal fungi often results

in a more efficient exploitation of phosphorus and therefore greater plant growth [16,17]. Similarly,

a recent study showed that as microbial diversity increased, so did the simultaneous maintenance

of diverse ecosystem functions and services [18]. Previous restoration studies have demonstrated

how important the origin of fungal inocula can be for the overall productivity and plant community

composition of degraded lands [19,20]. Further, inoculating with more complex and field-acquired

soil microbial communities often results in greater plant growth than commercially available fungi

(usually single-strain mycorrhizal inocula) [21,22], suggesting that the diversity and composition of

the fungal community added is important for restoration success. While it is possible to use fungi

in restoration without detailed knowledge of their communities, understanding the environmental

factors that affect these assemblages can help steer management decisions to increase the benefit of

fungal amendments and improve the conservation of fungal diversity in threatened ecosystems.

One imperiled habitat for which understanding soil fungal communities could help achieve

meaningful restoration goals are the tree islands of the Florida Everglades. The Greater Everglades

Ecosystem, which originally spanned over 10,000 km2 of South Florida, is the largest designated

wilderness in the Eastern United States, a NaturalWorld Heritage Site, a RamsarWetland of International

Importance, and home to 103 threatened or endangered plants and animals [23]. Unfortunately, this

unique ecosystem is highly threatened by habitat destruction and the hydrologic changes required

for urbanization and agriculture as well as by invasive species, climate change, and pollution [24–26].

These changes have negatively impacted both the aquatic and terrestrial biodiversity of this system

(e.g., estimated declines of up to 90% in some wading bird populations and 90–98% declines in

small mammal populations within Everglades National Park; [25,27]). While much of the Everglades

landscape is a freshwater wetland characterized by sawgrass marsh and persistently flooded sloughs,

tree islands—aggregations of woody vegetation on elevated peat or limestone—are important features

of this ecosystem [28]. In addition to being critical habitats for resting and foraging wading birds,

American alligators, white-tailed deer, and other animals [29], tree islands are biogeochemical hotspots

within an otherwise nutrient-poor ecosystem. Despite making up a relatively small portion of the

landscape (e.g., approximately 4% historically in the central Everglades), tree islands are estimated to

sequester approximately 67% of the phosphorus in the Everglades (up to 100 times more phosphorus

than the surrounding wetlands) and promote the retention of nitrogen by the landscape [28,30,31].

Urbanization since the 1950s in South Florida has led to anthropogenically driven changes to Everglades

hydrology, which is believed to be the main driver of tree island loss (up to 87% in some areas) [32].

As tree mortality increases, the transition from a “healthy” tree island into a treeless “ghost” island

is accompanied by a release of sequestered nutrients into the surrounding wetland habitats [30].

This nutrient release is thought to have cascading effects on ecosystem and species dynamics in

these impacted landscapes (e.g., invasive cattails outcompete native sawgrass in high-phosphorus

areas; [33]).

As a result of the importance of tree islands in the Everglades and their substantial decline,

the restoration of ghost islands and creation of constructed tree islands is an important piece of

the Comprehensive Everglades Restoration Plan [34]. There are several reasons that soil fungi may

be especially integral to the success of tree island restoration. First, as the primary decomposers,

soil fungi are likely to play a central role in regulating soil formation [35,36], which is a goal for the

restoration of both degraded tree islands and self-perpetuating, fully-functioning constructed tree

islands. Second, soil fungi can be important in nutrient immobilization (e.g., fungi are responsible

for the immobilization of approximately 20–30% of global phosphorus pools; [1,5]), which could

help sequester phosphorus and nitrogen within islands and reduce leaching into the surrounding

wetlands. Third, fungal mutualists (e.g., mycorrhizal fungi) may increase tree island stability by

Diversity 2020, 12, 0324 3 of 17

increasing tree resilience to natural and anthropogenic stress [9], and fungal pathogens may be crucial

for restoring a natural tree community composition by regulating the abundance of dominant plant

species [37]. While fungal communities in the peat and periphyton of the Everglades wetlands have

been investigated in a few cases [38–40], the terrestrial fungal communities of Everglades tree islands

are unexplored. In fact, we are aware of no studies of the diversity or composition of soil fungal

communities on Everglades tree islands. To improve the protection, and even utilization, of fungal

diversity in the restoration of tree islands, studies of the factors that structure these fungal communities

are needed. Here, we use a set of eight experimental Everglades tree islands, in which abiotic and

biotic factors have been manipulated to understand tree island formation, to better identify how

microhabitat environmental variation and experimental restoration decisions may influence fungal

diversity, composition, and functional guilds.

2. Materials and Methods

2.1. Study Site and Environmental Data Collection

We studied tree island soil fungal communities at the approximately 32-ha Loxahatchee

Impoundment Landscape Assessment (LILA) facility in Loxahatchee National Wildlife Refuge in

Palm Beach County, Florida, USA (26.489◦ N, 80.219◦ W). LILA contains eight approximately 2500 m2

experimental tree islands that were constructed in 2003 through a collaboration between the South

Florida Water Management District and the Army Corps of Engineers. LILA is especially suitable

for investigating how the soil microbiome responds to different restoration decisions, because the

construction of tree islands allowed landscape-level experimental manipulations of tree island

characteristics. For instance, the islands’ cores (i.e., bases of the islands) were manipulated to

represent two common island types in the Everglades: peat core and limestone core islands [41].

Using locally sourced peat and limestone derived from the habitat adjacent to the current LILA facility,

half of the experimental islands were constructed with peat cores and half were constructed with

limestone cores (Figure S1); then, all the islands were covered with a top layer of peat substrate [42].

Similarly, each of the eight experimental islands was split into quadrants in which a mixture of 10 tree

species were planted at four different densities (1 m, 1.67 m, 2.33 m, and 3 m spacing) in 2006 and

2007 (Figures S1 and S2). Given the importance of plant-fungal interactions, tree planting density may

be a biotic factor that strongly affects fungal community composition. In addition, LILA has other

readily available data on microhabitat variation within and among islands that can help inform our

understanding of the soil microbiome. For example, because the water level is continuously monitored

within the macrocosms and the topography of each island is well mapped, it is possible to track the

hydrology of microhabitats using the DBHydro project from the South Florida Water Management

District [42]. Using surface water-level data and the elevation of each site, we calculated the average

site-specific ‘relative water level’ for all plots in 2018 (the year fungi were sampled) following the

methods in [43]. Further, understory plant communities that recruited to these experimental tree islands

have been monitored since 2009 [42], allowing for consideration of the understory plant community

in structuring soil microbiomes. For these understory plant communities, we calculated Shannon

diversity, Pielou’s evenness, and plant richness for use in our analyses. During the monitoring of

each site, understory plant biomass was estimated (by applying allometric equations developed from

separate biomass collection plots to estimates of plant cover). To gain insight into the light environment

(another abiotic feature of interest), hemispherical canopy photographs were also taken using a digital

camera (Nikon Coolpix 995; Nikon, Tokyo, Japan) equipped with a hemispherical lens (Nikon Fisheye

Converter FC-E8 0.21×, Tokyo, Japan) at each site, and canopy openness was determined using the

software Gap Light Analyzer (GLA), version 2.0, Burnaby, BC, Canada [44].