diversity

Review
Soil Fungal Community and Potential Function in Different
Forest Ecosystems
Xiaoli Li † , Zhaolei Qu † , Yuemei Zhang, Yan Ge and Hui Sun *

Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry
University, Nanjing 210037, China; lixiaoli90717@163.com (X.L.); qzl941211@njfu.edu.cn (Z.Q.);
zymei23394@njfu.edu.cn (Y.Z.); geyan@njfu.edu.cn (Y.G.)
* Correspondence: hui.sun@njfu.edu.cn
† These authors contributed equally to this work.

Abstract: Forests acting as carbon storage and sequestration play an essential role in the global
nutrient cycle, in which fungi are active participants. The forests cover almost all regions from
the boreal, temperate to the subtropical and tropical forests. The relative proportion of carbon
sequestrated in forest soil varies from approximately 85% of the terrestrial carbon pool in boreal
forests to 60% in temperate forests and to 50% in tropical rainforests. Fungi as decomposers of organic
matter and root-associated mediators of belowground carbon transport and respiration are the key
drivers of the carbon cycle in forests. For example, saprophytic fungi can degrade soil organic matter
to release carbon into the soil, whereas symbiotic fungi could form symbiosis with plants, through
which plant and fungi can benefit each other with nutrient flow. Given the importance of fungi in
the ecological environment, this paper summarizes the importance of soil fungi in terms of fungal
diversity and function in forest ecosystems.

Keywords: boreal forests; temperate forests; subtropical and tropical forests; fungal community
diversity; fungal function
Citation: Li, X.; Qu, Z.; Zhang, Y.; Ge,
Y.; Sun, H. Soil Fungal Community
and Potential Function in Different
Forest Ecosystems. Diversity 2022, 14,
1. Introduction
520. https://doi.org/10.3390/
d14070520 The forests cover almost all regions from the boreal to the tropical forests and provide
critical environmental services by acting as carbon sinks, conserving biodiversity, protecting
Academic Editors: Michael Wink and
soils, and providing timber resources [1]. One third of the total global fossil fuel emissions
Natālija Burn, eviča
estimated was absorbed by forests [2]. In fact, the forest ecosystems contain 80% of the
Received: 26 May 2022 terrestrial carbon and 70% of the soil organic carbon [3,4]. The relative proportion of carbon
Accepted: 27 June 2022 sequestrated in forest soil varies from approximately 85% of the terrestrial carbon pool
Published: 28 June 2022 in boreal forests to 60% in temperate forests and to 50% in tropical rainforests [5]. This
carbon is derived mainly from plant leaf litter and root systems, in which the soil fungi
Publisher’s Note: MDPI stays neutral
act as the main decomposers [6,7] and regulators [8,9]. For example, saprophytic fungi
with regard to jurisdictional claims in
published maps and institutional affil-
decompose organic matter to participate in the carbon cycle [10], while mycorrhizal fungi
iations.
help plants obtain mineral nutrition from the soil and participate in the carbon balance
of forest ecosystems [11]. Therefore, the soil fungi play crucial roles in nutrient cycles in
forest ecosystems. In addition, the forest soil fungi are influenced by a variety of biotic
and abiotic factors, including the climate, soil physicochemical properties, and microbial
Copyright: © 2022 by the authors. interactions [12,13]. In this review, we summarize the soil fungal community structure
Licensee MDPI, Basel, Switzerland. and function in different forest ecosystems (boreal, temperate, tropical, and subtropical
This article is an open access article forest) to highlight the importance of forest soil microbes in changing climate. The recent
distributed under the terms and developed technologies to study the forest soil microbiome also are summarized.
conditions of the Creative Commons
Attribution (CC BY) license (https://
creativecommons.org/licenses/by/
4.0/).

Diversity 2022, 14, 520. https://doi.org/10.3390/d14070520 https://www.mdpi.com/journal/diversity

Diversity 2022, 14, 520 2 of 12

2. Soil Fungal Community Structure and Function in Boreal Forests

2.1. Soil Fungal Community Diversity and Structure
The boreal forest is among the largest forest ecosystem in the world [14] and stores
33% of the earth’s total carbon, most of which is stored in the soil [2]. Fungi are the key
drivers of the carbon cycle in boreal forests as decomposers of organic matter and root-
associated mediators of belowground carbon transport and respiration [15,16]. The changes
in fungal diversity and community composition within an ecosystem often follow the shift
of aboveground forests, while the dynamic of root-associated and soil fungi is an important
additional factor explaining carbon accumulation and guaranteeing the establishment and
stability of aboveground forest [17]. The boreal forest harbored higher soil fungal diversity
and species richness than other forest ecosystems [18]. The fungal diversity in different soil
layers showed clear vertical difference [19], which, in general, is more likely to be indirectly
influenced by variations in environmental or nutrient partitioning due to the soil depth [20].
More specifically, the fungal diversity and species richness decreased along increased soil
depth. The raw litter layer harbored the highest fungal diversity and species richness due
to the high content of soil organic matter [19,21].
The fungal composition at the taxonomic level also showed distinct differences in
vertical gradients across different soil layers in boreal forests. Basidiomycota dominated the
fungal communities in each of the soil horizons with a similar relative abundance of over
60% [19]. Many members of Basidiomycota were generalist, with some ectomycorrhizal
fungi being able to serve as saprophytes at the same time [19]. Lactarius rufus (belonging to
Basidiomycota), which could form ectomycorrhiza with Scots pine, was the most abundant
species in all soil horizons across different seasons, respectively [19]. The community
differences at higher taxonomic level (e.g., phylum) between the horizons were largely a
consequence of shifts in the abundances of Ascomycota and Zygomycota. Ascomycota had
higher relative abundance in the raw litter layer, which then decreased with the increasing
soil depth. In contrast, Zygomycota increased in abundance [19,21]. Most members of
Ascomycota are saprophytic fungi, while that of Zygomycota are mycorrhizal fungi [22],
which tend to become more abundant with root extension. Russula and Lactarius were more
abundant in the litter layer, whereas Cortinarius and Tricholoma were more abundant in
the deeper humus layer [21]. The difference in nutrient acquisition strategies might be the
reason as Cortinarius and Tricholoma could preferentially utilize nitrogen from the deeper
humus layer, while Russula and Lactarius acquired nitrogen from the forest litter layer [21].

2.2. The Effects of Wildfire on Soil Fungal Community

The wildfire is one of the common natural disturbances in boreal forests and signifi-
cantly affects the soil fungal community. The fire can affect the soil fungi either directly via
the heat produced by the fire causing fungal mycelia to die [23] or indirectly via changing
the soil properties, such as soil pH and nutrient contents [24]. The lowest fungal diver-
sity and species richness were found in the forests, where the fires have just occurred
(0–3 years) [24]. With the increasing time of post-fire, the fungal diversity and species
richness increased and stabilized after several decades [23–26]. Wildfires also occur in other
environments apart from boreal forests. They are especially more prevalent in Mediter-
ranean forests, in which the soil fungal diversity exhibited the similar trend after wildfire
in the boreal forests [27]. Meanwhile, the intensity of the fire can alter the soil pH, which
affects the fungal diversity. In general, the fungal diversity and species richness decrease
with the increasing of fire intensity in both Mediterranean and boreal forest [23,27,28].
Fire also affects the fungal community composition in the soil. Generally, the abun-
dance of Ascomycota increases and that of Basidiomycota decreases shortly after the fire
occurred [24,29]. The increased abundance of Ascomycetes is attributed to their tolerance
of high soil pH and other physicochemical consequences caused by wildfire [30]. Many
members of Basidiomycota are mycorrhizal fungi, and the occurrence of fire leads to a
decrease in the host plants, resulting in decreased abundance of mycorrhizal fungi. Some of
the mycorrhizal fungi increased in abundance after fire. For example, a higher abundance
Diversity 2022, 14, 520 3 of 12

of Russula decolorans is commonly found in the forest with short post-fire history (3 years).
It is likely that the plants’ roots that survived the fires may provide shelter for some my-
corrhizas and fungal endophytes, e.g., R. decolorans [31]. Cortinarius spp. are thought to
be vulnerable to fire and typically become more abundant 40–60 years post-fire in boreal
forests. Moreover, Suillus spp. seem not affected by the fire in forest soil; although, they
may be involved in carbon and nitrogen cycling processes [23,24]. Additionally, the high
abundance of Rhizopogon was observed only in the Mediterranean forests after fires but not
in the boreal forests [27,32]. The adaptation of this genus to fire is due to their rhizomorphs
and mycelia, which can extend considerable distances from the tree root, and hence they
have a greater chance of survival after a fire [33].

2.3. Soil Fungal Community Function

In boreal forests, the soil fungal community function showed temporal and spatial
changes [19]. The saprotrophic fungi dominated the community in March and the commu-
nity shifted gradually to symbiotic fungi dominance during the growing season (April to
June) [34–36], as the saprotrophs are metabolically more active during periods of minimal
or no photosynthesis in plants [36]. Spatially, the saprophytic fungi usually dominated
the litter horizons with little seasonal variation, whereas the symbiotic fungi, especially
ectomycorrhizas, were more abundant in the organic and mineral soil horizons [19,37,38].
The occurrence of wildfire in boreal forests can cause significant shift in fungal commu-
nity function. The forests where fires had occurred a long time ago (e.g., 152 years post-fire)
had higher abundance of the genes encoding chitinases, whereas the genes encoding the
hemicellulose-degrading enzymes were more abundant in forests two years post-fire [24].
The increased fire frequency, or decreased fire return interval, could lead to losses in fungi
that are important for carbon sequestration and could destabilize boreal regions as a car-
bon sink, particularly with additive carbon losses [39]. The proportions of mycorrhizal
and saprotrophic fungi observed in the forests were strongly affected by the fire in the
boreal and Mediterranean pine forest, with no mycorrhizal taxa observed one year after
the fire and only a few observed in plots five years after the fire [27]. Unlike boreal forests,
Mediterranean forests were able to observe mycorrhizal fungi one year after the fire. It
is possible that the humid climatic environment of Mediterranean forests improves the
adaptation of mycorrhizal fungi to fires [27]. Moreover, in addition to the course post-fire,
the intensity of fire also affects the soil fungal community functions. It was proven that the
increased fire severity can decline the species richness of mycorrhizas and saprotrophs in
boreal forest [23] (Table 1).

3. Soil Fungal Community Structure and Function in Tropical and Subtropical Forests
3.1. Soil Fungal Community Diversity and Structure
Contrary to the boreal forests as carbon sequestration, the tropical forests play a critical
role in the changing atmospheric carbon concentrations. They serve as an important source
of carbon emissions and carbon sink as a result of the logging and burning [40]. Due to the
significance of fungi in soil carbon dynamics, they are becoming non-negligible in tropical
and subtropical forest ecosystems [41]. However, the study on the soil fungal community
in tropical and subtropical forests is not as common as in the boreal forests. Among forest
systems (boreal, temperate, tropical, and subtropical forest), the temperate forests have
the highest soil fungal diversity, followed by the boreal forests, and then tropical and
subtropical forests. The low diversity in tropical and subtropical forests may be due to
the high plant diversity in the regions [42,43]. Gilbert (2005) suggested that the high plant
diversity in tropical or subtropical systems resulted in a decrease in fungal specificity due
to a lack of selective pressure for specialization, often resulting in low fungal diversity.
Peatland forest is one of the most common forest types in tropical and subtropical re-
gions [44,45]. The fungal diversity in peatland forest is associated with some anthropogenic
disturbances, such as deforestation and drainage, which can have significant impacts on
soil fungal community [46]. For example, the soil fungal richness tends to be higher in
Diversity 2022, 14, 520 4 of 12

pristine peatland than in disturbed peatland [46,47]. In subtropical forests, the soil fungi
diversity and richness were significantly higher in the organic horizons than in the mineral
horizons [48]. This pattern of variation is similar to that in the boreal forests, and the nutri-
ent changes across soil profiles significantly and contributes to such observations [48,49].
Peatlands also are common in boreal forests. The fungal richness was higher in the drier
boreal mire forests compared to the wet peatlands, suggesting that the decrease in water
level in boreal peat forests favors the growth of fungi [50].
Similarly, as in the boreal forests, Ascomycota and Basidiomycota are the two dom-
inant phyla in tropical forests, which accounted for half of the fungal community in
abundance [46]. The abundance of Ascomycota was the highest in tropical forest soils than
in other forest ecosystems [12]. Ascomycota is the most species-rich fungal phylum with
the ability to degrade organic substrates (wood, leaf litter, etc.); it is also one of the most
represented fungal guilds involved in saprotrophic behavior [12,51]. Since more litters are
produced in tropical forests than other forests and the degradation rate of organic matter
is faster, which can cause the increased abundance of Ascomycota. The phosphorus (P)
content is normally low in the tropical forests, especially in peatland forest, which is an
important factor affecting the soil fungal community [52]. With the decrease in phosphorus
content in the soil, the fungal community shifts gradually from the saprotrophic (e.g.,
Mortierellaceae and Mycenaceae) dominance to saprotrophic and parasitic coexistence
(e.g., Cordycipitaceae, Annulatascaceae, Teratosphaeriaceae, and Sympoventuriaceae) and
then to the endophytic and epiphytic dominance (e.g., Clavicipitaceae) [53]. The natural
peatland soils normally harbor more Gliocephalotrichum and Gymnopilus with saprotrophic
ability than disturbed peatland (e.g., drainage and selective logging) [46,54].
In the subtropical forests, the abundance of Basidiomycota increased along the soil
depth from the organic horizon (loose and partly decayed organic matter) to the mineral
horizon [48,55,56]. This might be due to their symbiotic relationships with plant roots [57].
Mycena, Sistotrema, and Cryptoccocus (saprophytic fungi) were the most abundant genera
in the litter horizon, while Russula and Lactarius (symbiotic fungi) were more abundant in
the deeper soil horizon [48]. The plant renewal rates are faster in humid subtropical areas,
and the litter in organic horizon is more abundant [58,59]; fungi that feed on cellulose and
lignin tend to be more abundant [60], while the mycorrhizal fungi are more associated with
plant root in the deeper soil horizon [57].

3.2. Soil Fungal Community Function

The tropical forests with the highest biodiversity on earth hide a large number of fungal
species. Symbiotic fungi, especially endomycorrhizal, dominated the soil fungal commu-
nity in tropical and subtropical forests [43]. The relative abundance of Ectomycorrhizal
fungi (EcMF) was significantly lower than that in the boreal and temperate forests [43].
The surface litter layer was dominated by the saprophytic fungi, while the mycorrhizal
fungi dominated in the deeper mineral soils, similar to that in the boreal and temperate
forests [37].
The availability of P is thought to be one of the important factors affecting many
biological processes in lowland tropical forests [61], which is a limiting nutrient in these
forests [62,63]. The role of arbuscular mycorrhizal fungi (AMF) in P acquisition is well
known [64], and there is evidence that different AMF differs in their ability to acquire and
transport P to the plant host [65]. The shift in phosphorus acquisition strategies of AMF
may cause the segregation of ecological niches [66]. In tropical and subtropical forests,
the thicknesses of litter layers can determine AMF colonization due to the differences
in phosphorus sources; for example, the thicker litter layers tend to harbor more AMF
fungi [67]. With the increasing amount of litter, the AMF fungal hyphae proliferate in
organic substrates [68] and grow into decomposing leaf litter [69,70], suggesting that AMF
fungi may represent important pathways for plant uptake of nutrients in tropical and
subtropical forests. Apart from this, the tropical and subtropical rainforests are character-
ized by a high presence of organic matter, and they can produce more litter than other
Diversity 2022, 14, 520 5 of 12

ecosystems [71]. Such conditions result in an enrichment of pathogenic and saprotrophic

fungi, while symbiotic fungi are present in lower number [71] (Table 1).

4. Soil Fungal Community Structure and Function in Temperate Forests

In temperate forests, the trend of soil fungal diversity along the vertical gradient is
different from that in boreal, tropical, and subtropical forests. The fungal diversity and
richness in the organic layer are higher than that in the mineral layer. Thoroughly, the
fungi diversity and richness decreased in the organic soil from the raw litter layer to the
humus layer and increased the mineral soil from the surface mineral layer to the mineral
subsoil layer [72]. In addition, the forest stand age and moss cover are the most important
predictors of fungal richness in temperate forests [73]. The fungal species richness showed
decreasing trend in general with stand age (2-, 65-, and 110-year); that is, the fungal species
richness was higher in 2-year than that in 110-year [74–76]. A decrease in fungal species
richness was observed when the moss cover was higher [73]. Mosses are known to be
recalcitrant substrates and can affect fungal growth by maintaining high water level and
slowing down the nutrient cycle [77]. They also produce secondary metabolites, which
are difficult to degrade by most saprophytic fungi [78]. Only a few specialized fungi can
decompose moss tissues [44,79].
The overall soil fungal community is dominated by Basidiomycota and Ascomy-
cota in the temperate forest. With the increase in the soil depth (from litter, humus, and
mineral layer), the abundances of Ascomycota decreased and those of the Basidiomy-
cota increased [80]. Agaricales, Helotiales, and Russulales are the fungal taxa commonly
found in temperate forests [81–85]; similarly, these three taxa are frequently observed
in boreal forests [23,86,87]. Fungi in the litter layer of temperate forests were more sus-
ceptible to seasonal influences [80]. In winter, some of the saprotrophs associated with
litter decomposition significantly increased in abundance, e.g., Naevala, Rhodotorula and
Cryptococcus [88]. The summer was characterized by a dramatic increase in of EcMF. For
example, the abundance of Amanita, Lactarius, and Russula significantly increased [80]. The
increased abundance of EcMF in late summer or autumn also has been reported previ-
ously in the boreal forests [89,90]. The species Mortierella alpina and Mucor hiemalis were
more abundant mainly in the organic horizon than in the mineral layer [72], as they are
common decomposers of litters from broadleaved trees [91,92]. With the increase in soil
depth, the abundance of Phlebopus roseus and Sarocladium terricola increased, becoming
the dominant fungal species in the mineral layer [72]. P. roseus and S. terricola can use
organic derivatives as sole nutrient sources via excreting extracellular enzymes to directly
cleave C–N–P bonds [93,94], which allow them to survive in the deeper mineral soil, a
nutrient-poor environment.
Temperate forests cover the second largest area with a high plant diversity, in addition
to the boreal forests [95]. The saprophytic fungi account for over half of the fungal commu-
nity in the soil and litters, respectively, whereas other functional groups (e.g., symbiotrophs
and pathogens) are also essential [96]. The temperate forests possess more seasonal climatic
characteristics, in which the soil fungal potential functions are linked to the changes in
aboveground hosts and seasons. In temperate broadleaf and coniferous forests, changes in
litter type from the aboveground hosts resulted in significant variations in the distribution
of saprotrophic fungi [97]. In general, the litter from evergreen host, containing more
recalcitrant compounds, is decomposed slower than that from the deciduous host [98]. This
difference in decomposition rate would affect the energy acquisition of the saprotrophic
fungi. Therefore, the EcMF are still active in the evergreen forest as the carbon supply
from symbiotic trees, while the saprotrophic fungi might be suppressed by the recalcitrant
substrate. Seasonally, a higher abundance of EcMF was observed in mid-summer as the
trees could allocate more of the newly synthesized carbon [90,99], whereas the abundance
of saprotrophic fungi was significantly lower due to the inhibition of EcMF [100] (Table 1).
Diversity 2022, 14, 520
Table 1. Soil fungal diversity, community composition, and function in different forest ecosystems.
Forest Type Fungal Diversity
(1) Higher fungal diversity and species richness than that in
tropical and subtropical forests [18].
(2) The fungal diversity and species richness decreased
along increased soil depth [19,21].
(3) The lowest fungal diversity and species richness were
Boreal forest found in the forests where the fires had just occurred
(0–3 years). With the increasing time of post-fire, the
fungal diversity and species richness increased and
stabilized after several decades [23–26].
(4) The fungal diversity and species richness decreased
with the increasing of fire intensity [23,27,28].
(1) Harbored the lowest soil fungal diversity and species
richness than other forest ecosystems [42,43].
(2) The soil fungal richness tended to be higher in pristine
Tropical and
peatland than that in disturbed peatland [46,47].
subtropical forests
(3) The soil fungi diversity and richness were significantly
higher in the organic horizons than that in the mineral
horizons in subtropical forests [48].
(1) The fungi diversity and richness decreased in the
organic soil from the raw litter layer to the humus layer
and increased the mineral soil from the surface mineral
Temperate forests layer to the mineral subsoil layer [72].
(2) The fungal species richness showed decreasing trend in
general with forest stand age [74–76].
(3) A decrease in fungal species richness was observed
when the moss cover was higher [73].
Community Composition
(1) Basidiomycota dominated the fungal
communities in each of the soil horizons with
a similar relative abundance of over 60% [19].
(2) Ascomycota tended to have higher relative
abundance in the raw litter layer and then
decreased with the increasing soil depth,
whereas Zygomycota increased in
abundance [19,21].
(3) The abundance of Ascomycota increased and
that of Basidiomycota decreased shortly after
the fire occurred [24,29].
(1) The abundance of Ascomycota was the
highest than that in other forest
ecosystems [12,46].
(2) The abundance of Basidiomycota increased
along the soil depth from the organic horizon
(loose and partly decayed organic matter) to
the mineral horizon [48,55,56].
(1) With the increase in the soil depth (from litter,
humus, and mineral layer), the abundances of
Ascomycota decreased and those of
Basidiomycota increased [80].
(2) Mortierella alpina and Mucor hiemalis were
more abundant mainly in the organic horizon
than in the mineral layer, with the increase in
soil depth, the abundance of Phlebopus roseus
and Sarocladium terricola increased, becoming
the dominant fungal species in the mineral
layer [72].
6 of 12
Community Function
(1) The saprotrophic fungi dominated the community in March and
the community shifted gradually to symbiotic fungi dominance
during the growing season (April to June) [34–36].
(2) The forests where fires had occurred a long time ago had higher
abundance of genes encoding chitinases, whereas the genes
encoding the hemicellulose-degrading enzymes were more
abundant in forests with a short history of fires [24].
(3) The proportions of mycorrhizal and saprotrophic fungi were
strongly affected by the fire. No mycorrhizal taxa observed one
year after the fire and only a few observed 5 years after the
fire [27].
(4) The increased fire severity can decline the abundance of
mycorrhizas and saprotrophs [23].
(1) Symbiotic fungi, especially endomycorrhizas dominated the
fungal community [43].
(2) The thicker litter layers tended to harbor more Arbuscular
mycorrhizal fungi AMF [67].
(3) Enrichment of pathogenic and saprotrophic fungi, while symbiotic
fungi were present in lower number due to high amount of
organic matter [71].
(4) The natural peatland soils normally harbored more saprotrophic
fungi than the disturbed peatland [46,54].
(1) The saprophytic fungi accounted for over half of the fungal
community in the soil and litters, respectively [96].
(2) Seasonally, a higher abundance of Ectomycorrhizal fungi (EcMF)
was observed in mid-summer, whereas the abundance of
saprotrophic fungi was significantly lower due to the inhibition of
EcMF [90,99,100].
Diversity 2022, 14, 520 7 of 12

5. DNA-Based High-Throughput Sequencing (HTS) Method to Study Fungal

Community and Function in Forest Soil
It is challenging to identify soil fungi in forests by traditional culturable methods
as most of the microbes in the soil cannot be cultured. With the rapid development
of molecular techniques and sequencing technologies, advanced methods are currently
available to assess the microbial community in natural environments, including forest
systems [101]. Furthermore, high-throughput sequencing (HTS) is one of the most com-
monly used methods to investigate the microbial community composition and functions
from environment, including the amplicon-based and whole genome shotgun (WGS) se-
quencing [102]. Metagenomics, with aid of HTS, is the study of the metagenome or the
collective genome of microorganisms from an environmental sample [103], which can
provide information on both microbial phylogenies and community metabolic functions,
the evolutionary linkages between them, as well as the potential novel metabolites or
enzymes in the environment [104]. The amplicon-based metagenomics is a highly targeted
specific genomic region of HTS, which can discover the microbial composition by detection
of the variations within the region of interest [105]. The targeted regions in microbial study
are usually 16S rRNA gene for bacteria, internal transcribed spacers (ITS) for fungi, and
18S rRNA gene for micro- and unicellular eukaryotes across multiple species [105,106].
Moreover, WGS has been increasingly recognized as the most comprehensive and ro-
bust approach for metagenomics research [107]. When compared with amplicon-based
metagenomics, it offers the advantage of identification of species-level taxonomy and the
estimation of metabolic pathway activities from human and environmental samples. In ad-
dition, several DNA-based high-throughput methods have been developed to study the soil
microbial community function, e.g., GeoChip and quantitative microbial element cycling
(QMEC) [108,109]. The GeoChip is a DNA microarray designed to identify the functional
genes involved in different biogeochemical processes, such as C, N, S, and P cycling [108].
The GeoChip array contains probes of gene markers covering microorganisms from ar-
chaea, bacteria, and fungi, which has been widely used as a high-throughput, metagenomic
tool for profiling environmental microbial community. It is particularly useful in terms
of community metabolic potential, functional structure and diversity, and correlation of
microbial community structure to ecosystem functioning [24,108]. Quantitative microbial
element cycling is a recently developed high-throughput quantitative PCR-based chip
that quantifies microbial elemental cycles for assessing the genetic potential of microbiota
involved in carbon, nitrogen, phosphorus, and sulfur cycles [109]. It can identify the struc-
tures, abundances, and diversities of the functional genes. QMEC contains 72 primer pairs
targeting 72 microbial functional genes for C, N, P, S, and methane metabolism [109], which
has been used to determine the absolute abundance of microbial functional genes in soil
and sediment. For example, Chen et al. (2020) analyzed the genes involved in nitrification
and denitrification in soil after fertilizer application [110].

6. Conclusions
Given the importance of fungi, variations in climatic conditions, and plant diversity
in different forest ecosystems, the soil fungal community diversity and function differ
to some extent along the temperature zones. Overall, the boreal forests harbored the
highest soil fungal diversity and richness, followed by the temperate forests, and then
the tropical and subtropical forests. The fungal diversity and richness declined along
vertical gradients and saprophytic fungi dominated the litter layer in all forest ecosystems
(boreal, temperate, tropical, and subtropical forest). Ectomycorrhizas are predominant
in the mineral layers in boreal and temperate forests, while endomycorrhizal fungi are
more abundant in the mineral layers in tropical and subtropical forests. The occurrence of
boreal forest fires increases the abundance of genes encoding chitinase and hemicellulose-
degrading enzymes and decreases the abundance of mycorrhizal and saprophytic fungi in
the soil. Seasonally, the abundances of ectomycorrhizas are higher in summer and lower
in winter in temperate forests, whereas the abundances of saprophytes have the opposite
Diversity 2022, 14, 520 8 of 12

trend, that is, higher abundance in winter and lower abundance in summer. Moreover,
recently developed high-throughput sequencing and metagenomics have greatly facilitated
the microbial study in forest ecosystems and enable us to better understand the forest
ecosystem functions.

Author Contributions: H.S. conceived the ideas, designed methodology, and received the funding.
X.L., Z.Q., Y.Z. and Y.G. contributed to the writing of the manuscript. All authors have read and
agreed to the published version of the manuscript.
Funding: The research was supported by the National Natural Science Foundation of China (31870474)
and the research funding for Priority Academic Program Development (PAPD) of Jiangsu Higher
Education Institutions.
Institutional Review Board Statement: Not applicable.
Informed Consent Statement: Not applicable.
Data Availability Statement: Not applicable.
Conflicts of Interest: The authors declare no conflict of interest.

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