Biogeography of ectomycorrhizal fungi associated with alders (Alnus spp.) in relation to biotic and abiotic variables at the global scale

Community composition of phytopathogenic fungi significantly influences ectomycorrhizal fungal communities during subtropical forest succession

Ectomycorrhizal fungi (EMF) can form symbiotic relationships with plants, aiding in plant growth by providing access to nutrients and defense against phytopathogenic fungi. In this context, factors such as plant assemblages and soil properties can impact the interaction between EMF and phytopathogenic fungi in forest soil. However, there is little understanding of how these fungal interactions evolve as forests move through succession stages. In this study, we used high-throughput sequencing to investigate fungal communities in young, intermediate, and old subtropical forests. At the genus level, EMF communities were dominated by Sebacina, Russula, and Lactarius, while Mycena was the most abundant genus in pathogenic fungal communities. The relative abundances of EMF and phytopathogenic fungi in different stages showed no significant difference with the regulation of different factors. We discovered that interactions between phytopathogenic fungi and EMF maintained a dynamic balance under the influence of the differences in soil quality attributed to each forest successional stage. The community composition of phytopathogenic fungi is one of the strong drivers in shaping EMF communities over successions. In addition, the EMF diversity was significantly related to plant diversity, and these relationships varied among successional stages. Despite the regulation of various factors, the positive relationship between the diversity of phytopathogenic fungi and EMF remained unchanged. However, there is no significant difference in the ratio of the abundance of EMF and phytopathogenic fungi over the course of successions. These results will advance our understanding of the biodiversity-ecosystem functioning during forest succession. KEY POINTS: •Community composition of both EMF and phytopathogenic fungi changed significantly over forest succession. •Phytopathogenic fungi is a key driver in shaping EMF community. •The effect of plant Shannon's diversity on EMF communities changed during the forest aging process.

Tree phylogeny predicts more than litter chemical components in explaining enzyme activities in forest leaf litter decomposition

Litter decomposition is an important process in ecosystem and despite recent research elucidating the significant influence of plant phylogeny on plant-associated microbial communities, it remains uncertain whether a parallel correlation exists between plant phylogeny and the community of decomposers residing in forest litter. In this study, we conducted a controlled litterbag experiment using leaf litter from ten distinct tree species in a central subtropical forest ecosystem in a region characterized by subtropical humid monsoon climate in China. The litterbags were placed in situ using a random experimental design and were collected after 12 months of incubation. Then, the litter chemical properties, microbial community composition and activities of enzyme related to the decomposition of organic carbon (C) and nitrogen (N) were assessed. Across all ten tree species, Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were identified as the predominant bacterial classes, while the primary fungal classes were Dothideomycetes, Sordariomycetes and Eurotiomycetes. Mantel test revealed significant correlations between litter chemical component and microbial communities, as well as enzyme activities linked to N and C metabolism. However, after controlling for plant phylogenetic distance in partial Mantel test, the relationships between litter chemical component and microbial community structure and enzyme activities were not significant. Random forest and structural equation modeling indicated that plant phylogenetic distance exerted a more substantial influence than litter chemical components on microbial communities and enzyme activities associated with the decomposition of leaf litter. In summary, plant phylogenic divergence was found to be a more influential predictor of enzyme activity variations than microbial communities and litter traits, which were commonly considered reliable indicators of litter decomposition and ecosystem function, thereby highlighting the previously underestimated significance of plant phylogeny in shaping litter microbial communities and enzyme activities associated with degradation processes in forest litter.

The influence of tree genus, phylogeny, and richness on the specificity, rarity, and diversity of ectomycorrhizal fungi

Partner specificity is a well-documented phenomenon in biotic interactions, yet the factors that determine specificity in plant-fungal associations remain largely unknown. By utilizing composite soil samples, we identified the predictors that drive partner specificity in both plants and fungi, with a particular focus on ectomycorrhizal associations. Fungal guilds exhibited significant differences in overall partner preference and avoidance, richness, and specificity to specific tree genera. The highest level of specificity was observed in root endophytic and ectomycorrhizal associations, while the lowest was found in arbuscular mycorrhizal associations. The majority of ectomycorrhizal fungal species showed a preference for one of their partner trees, primarily at the plant genus level. Specialist ectomycorrhizal fungi were dominant in belowground communities in terms of species richness and relative abundance. Moreover, all tree genera (and occasionally species) demonstrated a preference for certain fungal groups. Partner specificity was not related to the rarity of fungi or plants or environmental conditions, except for soil pH. Depending on the partner tree genus, specific fungi became more prevalent and relatively more abundant with increasing stand age, tree dominance, and soil pH conditions optimal for the partner tree genus. The richness of partner tree species and increased evenness of ectomycorrhizal fungi in multi-host communities enhanced the species richness of ectomycorrhizal fungi. However, it was primarily the partner-generalist fungi that contributed to the high diversity of ectomycorrhizal fungi in mixed forests.

Hexose/pentose ratio in rhizosphere exudates-mediated soil eutrophic/oligotrophic bacteria regulates the growth pattern of host plant in young apple-aromatic plant intercropping systems

Introduction

The positive effect of intercropping on host plant growth through plant-soil feedback has been established. However, the mechanisms through which intercropping induces interspecific competition remain unclear.

Methods

In this study, we selected young apple trees for intercropping with two companion plants: medium growth-potential Mentha haplocalyx Briq. (TM) and high growth-potential Ageratum conyzoides L. (TA) and conducted mixed intercropping treatment with both types (TMA) and a control treatment of monocropping apples (CT).

Results

Our findings revealed that TM increased the under-ground biomass of apple trees and TA and TMA decreased the above-ground biomass of apple trees, with the lowest above-ground biomass of apple trees in TA. The above- and under-ground biomass of intercrops in TA and TMA were higher than those in TM, with the highest in TA, suggesting that the interspecific competition was the most pronounced in TA. TA had a detrimental effect on the photosynthesis ability and antioxidant capacity of apple leaves, resulting in a decrease in above-ground apple biomass. Furthermore, TA led to a reduction in organic acids, alcohols, carbohydrates, and hydrocarbons in the apple rhizosphere soil (FRS) compared to those in both soil bulk (BS) and aromatic plant rhizosphere soil (ARS). Notably, TA caused an increase in pentose content and a decrease in the hexose/pentose (C6/C5) ratio in FRS, while ARS exhibited higher hexose content and a higher C6/C5 ratio. The changes in exudates induced by TA favored an increase in taxon members of Actinobacteria while reducing Proteobacteria in FRS compared to that in ARS. This led to a higher eutrophic/oligotrophic bacteria ratio relative to TM.

Discussion

This novel perspective sheds light on how interspecific competition, mediated by root exudates and microbial community feedback, influences plant growth and development.

The evolution of ectomycorrhizal symbiosis in the Late Cretaceous is a key driver of explosive diversification in Agaricomycetes

Ectomycorrhizal (EcM) symbiosis, a ubiquitous plant-fungus interaction in forests, evolved in parallel in fungi. Why the evolution of EcM fungi did not necessarily increase ecological opportunities for explosive diversification remains unclear. This study aimed to reveal the driving mechanism of the evolutionary diversification in the fungal class Agaricomycetes, specifically by testing whether the evolution of EcM symbiosis in the Late Cretaceous increased ecological opportunities. The historical character transitions of trophic state and fruitbody form were estimated based on phylogenies inferred from fragments of 89 single-copy genes. Moreover, five analyses were used to estimate the net diversification rates (speciation rate minus extinction rate). The results indicate that the unidirectional evolution of EcM symbiosis occurred 27 times, ranging in date from the Early Triassic to the Early Paleogene. The increased diversification rates appeared to occur intensively at the stem of EcM fungal clades diverging in the Late Cretaceous, coinciding with the rapid diversification of EcM angiosperms. By contrast, the evolution of fruitbody form was not strongly linked with the increased diversification rates. These findings suggest that the evolution of EcM symbiosis in the Late Cretaceous, supposedly with coevolving EcM angiosperms, was the key drive of the explosive diversification in Agaricomycetes.

Endophytic microbiota and ectomycorrhizal structure of Alnus glutinosa Gaertn. at saline and nonsaline forest sites

The tolerance of European alder (Alnus glutinosa Gaertn.) to soil salinity can be attributed to symbiosis with microorganisms at the absorptive root level. However, it is uncertain how soil salinity impacts microbial recruitment in the following growing season. We describe the bacterial and fungal communities in the rhizosphere and endosphere of A. glutinosa absorptive roots at three tested sites with different salinity level. We determined the morphological diversity of ectomycorrhizal (ECM) fungi, the endophytic microbiota in the rhizosphere, and the colonization of new absorptive roots in the following growing season. While bacterial diversity in the rhizosphere was higher than that in the absorptive root endosphere, the opposite was true for fungi. Actinomycetota, Frankiales, Acidothermus sp. and Streptomyces sp. were more abundant in the endosphere than in the rhizosphere, while Actinomycetota and Acidothermus sp. dominated at saline sites compared to nonsaline sites. Basidiomycota, Thelephorales, Russulales, Helotiales, Cortinarius spp. and Lactarius spp. dominated the endosphere, while Ascomycota, Hypocreales and Giberella spp. dominated the rhizosphere. The ECM symbioses formed by Thelephorales (Thelephora, Tomentella spp.) constituted the core community with absorptive roots in the spring and further colonized new root tips during the growing season. With an increase in soil salinity, the overall fungal abundance decreased, and Russula spp. and Cortinarius spp. were not present at all. Similarly, salinity also negatively affected the average length of the absorptive root. In conclusion, the endophytic microbiota in the rhizosphere of A. glutinosa was driven by salinity and season, while the ECM morphotype community was determined by the soil fungal community present during the growing season and renewed in the spring.

How do root fungi of Alnus nepalensis and Schima wallichii recover during succession of abandoned land?

Alnus nepalensis and Schima wallichii are native tree species accompanying succession in abandoned agricultural land in the middle mountainous region of central Nepal. To understand how root fungi recover during spontaneous succession, we analyzed the diversity and composition of arbuscular mycorrhizal (AM), ectomycorrhizal (ECM), and total fungi in tree fine roots from three land use types, short-term abandoned land (SA), long-term abandoned land (LA), and regenerated forest (RF) as a reference. Additionally, ECM morphotypes were examined. The results showed different speeds of succession in the studied fungal groups. While the change in the AM fungal community appears to be rapid and LA resembles the composition of RF, the total fungi in the abandoned land types are similar to each other but differed significantly from RF. Interestingly, the relative abundance of Archaeosporaceae followed a trend differing between the tree species (SA < LA in A. nepalensis, but SA > LA in S. wallichii). Unlike AM and total fungi, there was no significant difference in the ECM community of A. nepalensis between land use types, probably due to their low species diversity (9 ECM morphotypes, 31 ECM operational taxonomic units). However, Cortinarius sp. was significantly more abundant in RF than in the other land use types, whereas Alnicola, Tomentella, and Russula preferred young stages. Our results suggest that for both studied tree species the AM fungal succession could reach the stage of regenerated forest relatively fast. In the case of total fungi, because of hyperdiversity and composed of species specialized to a variety of environments and substrates, the transition was expected to be delayed in abandoned land where the vegetation was still developing and the ecosystem was not as complex as that found in mature forests.

Ectomycorrhizal community associated with Cedrus deodara in four urban forests of Nantong in East China

Ectomycorrhizal (ECM) fungi play fundamental roles in host plant growth and terrestrial ecosystems. Cedrus deodara is cultivated in several regions in China, has high ecological, economic and medicinal value, for its afforestation and providing timber and wood oil. Here, we investigated ECM colonization status of four urban C. deodara forests in Nantong, East China. We also characterized soil spore banks by conducting bioassay experiments using soils collected from these forests. In total, we identified 19 ECM fungal species, of which 13 species were found in mature forests and 9 species were identified in bioassay experiments, with only 3 species shared. Soil pH and available P content had significant effects on species occurrence in both mature trees and bioassay seedlings on local scales. ECM communities clearly (A = 0.391, p = 0.006) separated mature forests from spore banks. Thelephoracae was the richest family we detected associated with C. deodara, while Trichophaea sp. was the most dominant in mature forests, and Wilcoxina sp. was dominant in spore banks. ECM richness affected the growth of bioassay seedlings, especially after inoculation with 2 ECM species, promoting root growth, significantly (F = 3.028, p = 0.050), but it had no effects on shoots (F = 1.778, p = 0.177). No effect of inoculation rate was found on seedlings growth. To conserve this important tree species, the ECM fungi that are associated with it should be considered.

First report of the ectomycorrhizal fungal community associated with two herbaceous plants in Inner Mongolia, China

Ectomycorrhizal (EM) fungi play a vital role in ensuring plant health, plant diversity, and ecosystem function. However, the study on fungal diversity and community assembly of EM fungi associated with herbaceous plants remains poorly understood. Thus, in our study, Carex pediformis and Polygonum divaricatum in the subalpine meadow of central Inner Mongolia, China were selected for exploring EM fungal diversity and community assembly mechanisms by using llumina MiSeq sequencing of the fungal internal transcribed spacer 2 region (ITS2). We evaluated the impact of soil, climatic, and spatial variables on EM fungal diversity and community turnover. Deterministic vs. stochastic processes for EM fungal community assembly were quantified using β-Nearest taxon index scores. The results showed that a total of 70 EM fungal OTUs belonging to 21 lineages were identified, of which Tomentella-Thelephora, Helotiales1, Tricholoma, Inocybe, Wilcoxina were the most dominant EM fungal lineages. EM fungal communities were significantly different between the two herbaceous plants and among the two sampling sites, and this difference was mainly influenced by soil organic matter (OM) content and mean annual precipitation (MAP). The neutral community model (NCM) explained 45.7% of the variations in EM fungi community assembly. A total of 99.27% of the β-Nearest Taxa Index (βNTI) value was between -2 and 2. These results suggest that the dominant role of stochastic processes in shaping EM fungal community assembly. In addition, RC_bray values showed that ecological drift in stochastic processes dominantly determined community assembly of EM fungi. Overall, our study shed light on the EM fungal diversity and community assembly associated with herbaceous plants in the subalpine region of central Inner Mongolia for the first time, which provided a better understanding of the role of herbaceous EM fungi.

Novel Gene Rearrangement Pattern in Pachycrepoideus vindemmiae Mitochondrial Genome: New Gene Order in Pteromalidae (Hymenoptera: Chalcidoidea)

The mitochondrial genomes of Muscidifurax similadanacus, M. sinesensilla, Nasonia vitripennis, and Pachycrepoideus vindemmiae were sequenced to better understand the structural evolution of Pteromalidae mitogenomes. These newly sequenced mitogenomes all contained 37 genes. Nucleotide composition was AT-biased and the majority of the protein-coding genes exhibited a negative AT skew. All 13 protein-coding genes (PCGs) initiated with the standard start codon of ATN, excepted for nad1 of N. vitripennis, which started with TTG, and terminated with a typical stop codon TAA/TAG or an incomplete stop codon T. All transfer RNA (tRNA) genes were predicted to fold into the typical clover-leaf secondary structures, except for trnS1, which lacks the DHU arm in all species. In P. vindemmiae, trnR and trnQ lack the DHU arm and TΨC arm, respectively. Although most genes evolved under a strong purifying selection, the Ka/Ks value of the atp8 gene of P. vindemmiae was greater than 1, indicating putative positive selection. A novel transposition of trnR in P. vindemmiae was revealed, which was the first of this kind to be reported in Pteromalidae. Two kinds of datasets (PCG12 and AA) and two inference methods (maximum likelihood and Bayesian inference) were used to reconstruct a phylogenetic hypothesis for the newly sequenced mitogenomes of Pteromalidae and those deposited in GenBank. The topologies obtained recovered the monophyly of the three subfamilies included. Pachyneurinae and Pteromalinae were recovered as sister families, and both appeared sister to Sycophaginae. The pairwise breakpoint distances of mitogenome rearrangements were estimated to infer phylogeny among pteromalid species. The topology obtained was not totally congruent with those reconstructed using the ML and BI methods.

Differential distribution patterns and assembly processes of soil microbial communities under contrasting vegetation types at distinctive altitudes in the Changbai Mountain

Diversity patterns and community assembly of soil microorganisms are essential for understanding soil biodiversity and ecosystem processes. Investigating the impacts of environmental factors on microbial community assembly is crucial for comprehending the functions of microbial biodiversity and ecosystem processes. However, these issues remain insufficiently investigated in related studies despite their fundamental significance. The present study aimed to assess the diversity and assembly of soil bacterial and fungal communities to altitude and soil depth variations in mountain ecosystems by using 16S and ITS rRNA gene sequence analyses. In addition, the major roles of environmental factors in determining soil microbial communities and assembly processes were further investigated. The results showed a U-shaped pattern of the soil bacterial diversity at 0-10  cm soil depth along altitudes, reaching a minimum value at 1800 m, while the fungal diversity exhibited a monotonically decreasing trend with increasing altitude. At 10-20  cm soil depth, the soil bacterial diversity showed no apparent changes along altitudinal gradients, while the fungal Chao1 and phylogenetic diversity (PD) indices exhibited hump-shaped patterns with increasing altitude, reaching a maximum value at 1200 m. Soil bacterial and fungal communities were distinctively distributed with altitude at the same depth of soil, and the spatial turnover rates in fungi was greater than in bacteria. Mantel tests suggested soil physiochemical and climate variables significantly correlated with the β diversity of microbial community at two soil depths, suggesting both soil and climate heterogeneity contributed to the variation of bacterial and fungal community. Correspondingly, a novel phylogenetic null model analysis demonstrated that the community assembly of soil bacterial and fungal communities were dominated by deterministic and stochastic processes, respectively. The assembly processes of bacterial community were significantly related to the soil DOC and C:N ratio, while the fungal community assembly processes were significantly related to the soil C:N ratio. Our results provide a new perspective to assess the responses of soil microbial communities to variations with altitude and soil depth.

Primary succession of ectomycorrhizal fungi associated with Alnus sieboldiana on Izu-Oshima Island, Japan

The primary succession of ectomycorrhizal (ECM) fungi has been well described for Pinus and Salix, but the succession for other pioneer hosts is almost unknown. Here, we investigated ECM fungal communities of Alnus sieboldiana at different host growth stages in a primary successional volcanic site on Izu-Oshima Island, Japan. ECM root tips were collected from 120 host individuals, encompassing seedling, sapling, and mature tree stages. The taxonomic identity of the ECM fungi was determined based on rDNA internal transcribed spacer region sequences. Nine molecular taxonomic units were detected from a total of 807 root tips. The initial ECM fungal community on the pioneer seedlings was composed of only three species, where an undescribed Alpova species (Alpova sp.) was exclusively frequent. With host growth, other ECM fungal species were added to the communities, while the initial colonizers remained even at mature tree stages. Thus, the ECM fungal composition significantly changed along host growth stages and showed the nested community structure. Although most of the ECM fungi confirmed in this study had a broad Holarctic geographical distribution, the Alpova sp. had no previous records in other regions. These results suggest that a locally evolved Alpova sp. plays an essential role in the initial seedling establishment of A. sieboldiana at early successional volcanic sites.

Correlated evolution in an ectomycorrhizal host-symbiont system

Mechanisms of diversification in fungi are relatively poorly known. Many ectomycorrhizal symbionts show preference for particular host genera or families, so host-symbiont selection may be an important driver of fungal diversification in ectomycorrhizal systems. However, whether ectomycorrhizal hosts and symbionts show correlated evolutionary patterns remains untested, and it is unknown whether fungal specialisation also occurs in systems dominated by hosts from the same genus. We use metabarcoding of ectomycorrhizal fungi collected with hyphal ingrowth bags from Nothofagus forests across southern New Zealand to investigate host-symbiont specialisation and correlated evolution. We examine how ectomycorrhizal communities differ between host species and look for patterns of host-symbiont cophylogeny. We found substantial differences in ectomycorrhizal communities associated with different host taxa, particularly between hosts from different subgenera (Lophozonia and Fuscospora), but also between more closely related hosts. Twenty-four per cent of fungal taxa tested showed affiliations to particular hosts, and tests for cophylogeny revealed significant correlations between host relatedness and the fungal phylogeny that extended to substantial evolutionary depth. These results provide new evidence of correlated evolution in ectomycorrhizal systems, indicating that preferences among closely related host species may represent an important evolutionary driver for local lineage diversification in ectomycorrhizal fungi.

Global patterns in endemicity and vulnerability of soil fungi

Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms.

View from the Top: Insights into the Diversity and Community Assembly of Ectomycorrhizal and Saprotrophic Fungi along an Altitudinal Gradient in Chinese Boreal Larix gmelinii-Dominated Forests

The altitudinal patterns of soil fungi have attracted considerable attention; however, few studies have investigated the diversity and community assembly of fungal functional guilds along an altitudinal gradient. Here, we explored ectomycorrhizal (EcM) and saprotrophic (SAP) fungal diversity and community assembly along a 470 m vertical gradient (ranging from 830 to 1300 m) on Oakley Mountain, sampling bulk soils in the 0–10 cm and 10–20 cm soil layers of Larix gmelinii-dominated forests. Illumina MiSeq sequencing of the ITS genes was employed to explore the fungal community composition and diversity. The relative abundance of EcM and SAP fungi showed a divergent pattern along an altitudinal gradient, while we observed a consistent altitudinal tendency for EcM and SAP fungal diversity and community assembly. The diversity of both fungal guilds increased with increasing altitude. Altitude and soil moisture were the key factors affecting the community composition of both fungal guilds. In addition, the plant community composition significantly affected the EcM fungal community composition, whereas the dissolved organic nitrogen and ammonium nitrogen contents were the driving factors of SAP fungal community. Despite the effects of vegetation and soil factors, EcM and SAP fungal communities were mainly governed by stochastic processes (especially drift) at different altitudes and soil depths. These results shed new light on the ecology of different fungal functional guilds along an altitudinal gradient, which will provide a deeper understanding of the biogeography of soil fungi.

The Effect of Frankia and Hebeloma crustiliniforme on Alnus alnobetula subsp. Crispa Growing in Saline Soil

The mining of the oil sands region of Canada’s boreal forest creates disturbed land with elevated levels of salts. Understanding how native plants respond to salt stress is critical in reclaiming these lands. The native species, Alnus alnobetula subsp. crispa forms nitrogen-fixing nodules with Frankia, and ectomycorrhizae with a number of fungal species. These relationships may make the plant particularly well suited for restoring disturbed land. We inoculated A. alnobetula subsp. crispa with Frankia and Hebeloma crustiliniforme and exposed the plants to 0, 50, or 100 mM NaCl for seven weeks. Frankia-inoculated plants had increased biomass regardless of salt exposure, even though salt exposure reduced nitrogen fixation and reduced the efficiency of nitrogen-fixing nodules. The nitrogen-fixing symbiosis also decreased leaf stress and increased root phosphatase levels. This suggests that N-fixing plants not only have increased nitrogen nutrition but also have increased access to soil phosphorus. Mycorrhizae did not affect plant growth but did reduce nodule numbers and nodule efficiency. These results suggest that the nitrogen-fixing trait is more critical than mycorrhizae. While salt stress inhibits nitrogen-fixing symbiosis, plants still benefit from nitrogen fixation when exposed to salt.

Scale dependency of ectomycorrhizal fungal community assembly processes in Mediterranean mixed forests

The assembly of biological communities depends on deterministic and stochastic processes whose influence varies across spatial and temporal scales. Although ectomycorrhizal (ECM) fungi play a key role in forest ecosystems, our knowledge on ECM community assembly processes and their dependency on spatial scales is still scarce. We analysed the assembly processes operating on ECM fungal communities associated with Cistus albidus L. and Quercus spp. in Mediterranean mixed forests (Southern Spain), for which root tip ECM fungi were characterized by high-throughput sequencing. The relative contribution of deterministic and stochastic processes that govern the ECM fungal community assembly was inferred by using phylogenetic and compositional turnover descriptors across spatial scales. Our results revealed that stochastic processes had a significantly higher contribution than selection on root tip ECM fungal community assembly. The strength of selection decreased at the smallest scale and it was linked to the plant host identity and the environment. Dispersal limitation increased at finer scales, whilst drift showed the opposite pattern likely suggesting a main influence of priority effects on ECM fungal community assembly. This study highlights the potential of phylogeny to infer ECM fungal community responses and brings new insights into the ecological processes affecting the structure and dynamics of Mediterranean forests.

Global diversity and distribution of mushroom-inhabiting bacteria

Mushroom-forming fungi are important sources of food and medicine in many regions of the world, and their development and health are known to depend on various microbes. Recent studies have examined the structure of mushroom-inhabiting bacterial (MIB) communities and their association with local environmental variables, but global-scale diversity and determinants of these communities remain poorly understood. Here we examined the MIB global diversity and community composition in relation to climate, soil and host factors. We found a core global mushroom microbiome, accounting for 30% of sequence reads, while comprising a few bacterial genera such as Halomonas, Serratia, Bacillus, Cutibacterium, Bradyrhizobium and Burkholderia. Our analysis further revealed an important role of host phylogeny in shaping the communities of MIB, whereas the effects of climate and soil factors remained negligible. The results suggest that the communities of MIB and free-living bacteria are structured by contrasting community assembly processes and that fungal-bacterial interactions are an important determinant of MIB community structure.

The poly-extreme tolerant black yeasts are prevalent under high ultraviolet light and climatic seasonality across soils of global biomes

Black yeasts are among the most stress‐tolerant organisms of the planet, thriving under all types of terrestrial habitats and extreme environments. Yet, their global patterns and ecology remain far less studied, limiting our capacity to identify the main environmental drivers of these important organisms across biomes. To fill this knowledge gap, we analysed topsoils from 235 terrestrial ecosystems across and within globally distributed climate groups (i.e. dry, temperate and continental). We found that soils are important repositories of black yeasts, and that ultraviolet light, fine soil texture, and precipitation seasonality are the most consistent environmental factors associated with their diversity across biomes. Finally, we identified Exophiala and Cladophialophora as the most dominant black yeasts genera in soils across the globe. These findings provide novel evidence of global distribution of black yeasts and their key environmental predictors, giving new insights for speculating the evolution and spreading of these extreme‐tolerant organisms throughout both natural and human associated extreme environments.

Functional soil mycobiome across ecosystems

Fungi support a wide range of ecosystem processes such as decomposition of organic matter and plant-soil relationships. Yet, our understanding of the factors driving the metaproteome of fungal communities is still scarce. Here, we conducted a field survey including data on fungal biomass (by phospholipid fatty acids, PLFA), community composition (by metabarcoding of the 18S rRNA gene from extracted DNA) and functional profile (by metaproteomics) to investigate soil fungi and their relation to edaphic and environmental variables across three ecosystems (forests, grasslands, and shrublands) distributed across the globe. We found that protein richness of soil fungi was significantly higher in forests than in shrublands. Among a wide suite of edaphic and environmental variables, we found that soil carbon content and plant cover shaped evenness and diversity of fungal soil proteins while protein richness correlated to mean annual temperature and pH. Functions shifted from metabolism in forests to information processing and storage in shrublands. The differences between the biomes highlight the utility of metaproteomics to investigate functional microbiomes in soil. SIGNIFICANCE: Understanding the structure and the function of fungal communities and the driving factors is crucial to determine the contribution to ecosystem services of fungi and what effect future climate has. While there is considerable knowledge on the ecosystem processes provided by fungi such as decomposition of organic matter and plant-soil relationships, our understanding of the driving factors of the fungal metaproteome is scarce. Here we present the first estimates of fungal topsoil protein diversity in a wide range of soils across global biomes. We report taxonomic differences for genes delivered by amplicon sequencing of the 18S rRNA gene and differences of the functional microbiome based on metaproteomics. Both methods gave a complementary view on the fungal topsoil communities, unveiling both taxonomic and functional changes with changing environments. Such a comprehensive multi-omic analysis of fungal topsoil communities has never been performed before, to our knowledge.

High Fungal Diversity but Low Seasonal Dynamics and Ectomycorrhizal Abundance in a Mountain Beech Forest

Forests on steep slopes constitute a significant proportion of European mountain areas and are important as production and protection forests. This study describes the soil fungal community structure in a European beech-dominated mountain forest stands in the Northern Calcareous Alps and investigates how it is determined by season and soil properties. Samples were collected at high spatial resolution in an area of ca. 100 m × 700 m in May (spring) and August (summer). Illumina MiSeq high-throughput sequencing of the ITS2-region revealed distinct patterns for the soil fungal communities. In contrast to other studies from temperate European beech forest stands, Ascomycota dominated the highly diverse fungal community, while ectomycorrhizal fungi were of lower abundance. Russulaceae, which are often among the dominant ectomycorrhizal fungi associated with European beech, were absent from all samples. Potentially plant pathogenic fungi were more prevalent than previously reported. Only subtle seasonal differences were found between fungal communities in spring and summer. Especially, dominant saprotrophic taxa were largely unaffected by season, while slightly stronger effects were observed for ectomycorrhizal fungi. Soil characteristics like pH and organic carbon content, on the other hand, strongly shaped abundant taxa among the saprotrophic fungal community.

Phylogenetic relationships among false truffle genera of Paxillaceae-Alpova, Melanogaster, Neoalpova, and Paralpova, gen. nov

A phylogenetic analysis of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS), nuc rDNA 28S domains D1-D2 (28S), and the region between conserved domains 6 and 7 of RNA polymerase II second largest subunit (RPB2) from multiple species of Alpova and Melanogaster revealed four major clades, proposed here as distinct genera: Melanogaster, Alpova s. str. containing the type species A. cinnamomeus, Neoalpova for the species around N. rubescens, and the new genus Paralpova, proposed here for P. artikutzensis, sp. nov. Alpova, Neoalpova, and Paralpova form a monophyletic lineage of hypogeous fungi with a pseudoparenchymatic structure in their peridium (at least in the inner layer) that could be interpreted as a single genus, but they are separated due to distinct morphological and ecological traits. Alpova s. str. is employed for species strictly associated with Alnus, lacking a conspicuous odor, and producing relatively small basidiomata and basidiospores <10 µm long. Neoalpova and Paralpova occur under other hosts, present a conspicuous odor, have larger basidiomata and basidiospores than Alpova, and have a prosenchymatic peridiopellis. Finally, Paralpova is characterized by the yellowish gleba, monosporic or bisporic basidia, and basidiospores >15 µm long with a mean length/width ratio (Q_m) of <2.0. In addition, two new species of Neoalpova are proposed: N. arenicola, associated with Mediterranean forests in sandy soils and with spores slightly smaller and wider than those of N. rubescens, and N. montecchii, a cryptic species very similar to N. rubescens but for its putatively smaller peridiopellis elements and its genetic profile.

How Mycorrhizal Associations Influence Orchid Distribution and Population Dynamics

Orchid distribution and population dynamics are influenced by a variety of ecological factors and the formation of holobionts, which play key roles in colonization and ecological community construction. Seed germination, seedling establishment, reproduction, and survival of orchid species are strongly dependent on orchid mycorrhizal fungi (OMF), with mycorrhizal cheating increasingly observed in photosynthetic orchids. Therefore, changes in the composition and abundance of OMF can have profound effects on orchid distribution and fitness. Network analysis is an important tool for the study of interactions between plants, microbes, and the environment, because of the insights that it can provide into the interactions and coexistence patterns among species. Here, we provide a comprehensive overview, systematically describing the current research status of the effects of OMF on orchid distribution and dynamics, phylogenetic signals in orchid-OMF interactions, and OMF networks. We argue that orchid-OMF associations exhibit complementary and specific effects that are highly adapted to their environment. Such specificity of associations may affect the niche breadth of orchid species and act as a stabilizing force in plant-microbe coevolution. We postulate that network analysis is required to elucidate the functions of fungal partners beyond their effects on germination and growth. Such studies may lend insight into the microbial ecology of orchids and provide a scientific basis for the protection of orchids under natural conditions in an efficient and cost-effective manner.

Soil P reduces mycorrhizal colonization while favors fungal pathogens: observational and experimental evidence in Bipinnula (Orchidaceae)

Little is known about the soil factors influencing root-associated fungal communities in Orchidaceae. Limited evidence suggests that soil nutrients may modulate the association with orchid mycorrhizal fungi (OMF), but their influence on non-mycorrhizal fungi remains unexplored. To study how nutrient availability affects mycorrhizal and non-mycorrhizal fungi associated with the orchid Bipinnula fimbriata, we conducted a metagenomic investigation within a large population with variable soil conditions. Additionally, we tested the effect of phosphorus (P) addition on fungal communities and mycorrhizal colonization. Soil P negatively correlated with the abundance of OMF, but not with the abundance of non-mycorrhizal fungi. After fertilization, increments in soil P negatively affected mycorrhizal colonization; however, they had no effect on OMF richness or composition. The abundance and richness of pathotrophs were negatively related to mycorrhizal colonization and then, after fertilization, the decrease in mycorrhizal colonization correlated with an increase in pathogen richness. Our results suggest that OMF are affected by soil conditions differently from non-mycorrhizal fungi. Bipinnula fimbriata responds to fertilization by altering mycorrhizal colonization rather than by switching OMF partners in the short term, and the influence of nutrients on OMF is coupled with indirect effects on the whole fungal community and potentially on plant's health.

Ectomycorrhizal fungal communities associated with Larix gemelinii Rupr. in the Great Khingan Mountains, China

Larix gemelinii is an important tree species in the Great Khingan Mountains in Northeast China with a high economic and ecological value for its role in carbon sequestration and as a source of lumber and nuts. However, the ectomycorrhizal (EM) fungal diversity and community composition of this tree remain largely undefined. We examined EM fungal communities associated with L. gemelinii from three sites in the Great Khingan Mountains using Illumina Miseq to sequence the rDNA ITS2 region and evaluated the impact of spatial, soil, and climatic variables on the EM fungal community. A total of 122 EM fungal operational taxonomic units (OTUs) were identified from 21 pooled-root samples, and the dominant EM fungal lineages were /tricholoma, /tomentella-thelephora, /suillus-rhizopogon, and /piloderma. A high proportion of unique EM fungal OTUs were present; some abundant OTUs largely restricted to specific sites. EM fungal richness and community assembly were significantly correlated with spatial distance and climatic and soil variables, with mean annual temperature being the most important predictor for fungal richness and geographic distance as the largest determinant for community turnover. Our findings indicate that L. gemelinii has a rich and distinctive EM fungal community contributing to our understanding of the montane EM fungal community structure from the perspective of a single host plant that has not been previously reported.

Diversity and community structure of ectomycorrhizal fungi in Pinus thunbergii coastal forests bordering the Yellow Sea of China

Ectomycorrhizas play a fundamental role in the function of forest ecosystems, being essential for plant nutrition absorption and soil quality. Many afforestation and reforestation programmes have begun to recover and maintain coastal forests in China, using pine species including Pinus thunbergii. We investigated the ectomycorrhizal colonization status of P. thunbergii in coastal pine forests of the Yellow Sea of China. We identified a total of 53 ectomycorrhizal fungal species in 74 soil samples collected from three sites and found that Thelephoraceae (10 spp.) and Russulaceae (8 spp.) were the most species-rich ectomycorrhizal fungal lineages. Russula sp. 1 was the most abundant species, accounting for 15.3% of the total ectomycorrhizal tips identified. Most of the remaining species were rare. At this small scale, host identity had no significant effect on the ectomycorrhizal fungal community composition (A = 0.036, P = 0.258), but sampling sites did (A = 0.135, P = 0.041). In addition, Na⁺ and K⁺ content and soil pH had significant effects on the ectomycorrhizal fungal community. The ectomycorrhizal fungal community associated with different host plants will become an important new direction for research, as ectomycorrhiza may have the potential to improve host capacity to establish in salt-stressed environments. This will provide a theoretical basis and technical support for saline soil reforestation and rehabilitation using pine species with compatible, native ectomycorrhizal fungi in Yellow Sea coastal areas.

Fungal Diversity and Community Assembly of Ectomycorrhizal Fungi Associated With Five Pine Species in Inner Mongolia, China

Ectomycorrhizal (EM) fungi play vital roles in ensuring host plants’ health, plant diversity, and the functionality of the ecosystem. However, EM fungal diversity, community composition, and underlying assembly processes in Inner Mongolia, China, where forests are typically semiarid and cold-temperate zones, attract less attention. In this study, we investigated EM fungal communities from 63 root samples of five common pine plants in Inner Mongolia across 1,900 km using Illumina Miseq sequencing of the fungal internal transcribed spacer 2 region. We evaluated the impact of host plant phylogeny, soil, climatic, and spatial variables on EM fungal diversity and community turnover. Deterministic vs. stochastic processes for EM fungal community assembly were quantified using β-nearest taxon index scores. In total, we identified 288 EM fungal operational taxonomic units (OTUs) belonging to 31 lineages, of which the most abundant lineages were Tomentella–Thelephora, Wilcoxina, Tricholoma, and Suillus–Rhizopogon. Variations in EM fungal OTU richness and community composition were significantly predicted by host phylogeny, soil (total nitrogen, phosphorus, nitrogen–phosphorus ratio, and magnesium), climate, and spatial distance, with the host plant being the most important factor. β-nearest taxon index demonstrated that both deterministic and stochastic processes jointly determined the community assembly of EM fungi, with the predominance of stochastic processes. At the Saihanwula site selected for preference analysis, all plant species (100%) presented significant preferences for EM fungi, 54% of abundant EM fungal OTUs showed significant preferences for host plants, and 26% of pairs of plant species and abundant fungal OTUs exhibited remarkably strong preferences. Overall, we inferred that the high diversity and distinctive community composition of EM fungi associated with natural pine species in Inner Mongolia and the stochastic processes prevailed in determining the community assembly of EM fungi. Our study shed light on the diversity and community assembly of EM fungi associated with common pine species in semiarid and cold temperate forests in Inner Mongolia, China, for the first time and provided a better understanding of the ecological processes underlying the community assembly of mutualistic fungi.

Tree Species Richness and Neighborhood Effects on Ectomycorrhizal Fungal Richness and Community Structure in Boreal Forest

Tree species identity is one of the key factors driving ectomycorrhizal (EcM) fungal richness and community composition in boreal and temperate forest ecosystems, but little is known about the influence of tree species combinations and their neighborhood effects on EcM communities. To advance our understanding of host plant effects on EcM fungi, the roots of silver birch, Scots pine, and Norway spruce were analyzed using high-throughput sequencing across mature boreal forest exploratory plots of monocultures and two- and three-species mixtures in Finland. Our analyses revealed that tree species identity was an important determinant of EcM fungal community composition, but tree species richness had no significant influence on EcM fungal richness and community composition. We found that EcM fungal community composition associated with spruce depends on neighboring tree species. Our study suggests that at a regional-scale tree species identity is the primary factor determining community composition of root-associated EcM fungi alongside with tree species composition effects on EcM fungal community of spruce in mixed stands.

Seasonal Changes in Pinus tabuliformis Root-Associated Fungal Microbiota Drive N and P Cycling in Terrestrial Ecosystem

In terrestrial ecosystems, mycorrhizal roots play a key role in the cycling of soil carbon (C) and other nutrients. The impact of environmental factors on the mycorrhizal fungal community has been well studied; however, the seasonal variations in the root-associated fungal microbiota affected by environmental changes are less clear. To improve the understanding of how environmental factors shape the fungal microbiota in mycorrhizal roots, seasonal changes in Pinus tabuliformis root-associated fungi were investigated. In the present study, the seasonal dynamics of edaphic properties, soil enzymatic activities, root fungal colonization rates, and root-associated fungal microbiota in P. tabuliformis forests were studied across four seasons during a whole year to reveal their correlations with environmental changes. The results indicate that the soil functions, such as the enzymatic activities related to nitrogen (N) and phosphorus (P) degradation, were varied with the seasonal changes in microclimate factors, resulting in a significant fluctuation of edaphic properties. In addition, the ectomycorrhizal fungal colonization rate in the host pine tree roots increased during warm seasons (summer and autumn), while the fungal colonization rate of dark septate endophyte was declined. Moreover, the present study indicates that the fungal biomass increased in both the pine roots and rhizospheric soils during warm seasons, while the fungal species richness and diversity decreased. While the Basidiomycota and Ascomycota were the two dominant phyla in both root and soil fungal communities, the higher relative abundance of Basidiomycota taxa presented in warm seasons. In addition, the fungal microbial network complexity declined under the higher temperature and humidity conditions. The present study illustrates that the varieties in connectivity between the microbial networks and in functional taxa of root-associated fungal microbiota significantly influence the soil ecosystem functions, especially the N and P cycling.

Metabarcoding on both environmental DNA and RNA highlights differences between fungal communities sampled in different habitats

In recent years, metabarcoding has become a key tool to describe microbial communities from natural and artificial environments. Thanks to its high throughput nature, metabarcoding efficiently explores microbial biodiversity under different conditions. It can be performed on environmental (e)DNA to describe so-called total microbial community, or from environmental (e)RNA to describe active microbial community. As opposed to total microbial communities, active ones exclude dead or dormant organisms. For what concerns Fungi, which are mostly filamentous microorganisms, the relationship between DNA-based (total) and RNA-based (active) communities is unclear. In the present study, we evaluated the consequences of performing metabarcoding on both soil and wood-extracted eDNA and eRNA to delineate molecular operational taxonomic units (MOTUs) and differentiate fungal communities according to the environment they originate from. DNA and RNA-based communities differed not only in their taxonomic composition, but also in the relative abundances of several functional guilds. From a taxonomic perspective, we showed that several higher taxa are globally more represented in either “active” or “total” microbial communities. We also observed that delineation of MOTUs based on their co-occurrence among DNA and RNA sequences highlighted differences between the studied habitats that were overlooked when all MOTUs were considered, including those identified exclusively by eDNA sequences. We conclude that metabarcoding on eRNA provides original functional information on the specific roles of several taxonomic or functional groups that would not have been revealed using eDNA alone.

Regional-Scale In-Depth Analysis of Soil Fungal Diversity Reveals Strong pH and Plant Species Effects in Northern Europe

Soil microbiome has a pivotal role in ecosystem functioning, yet little is known about its build-up from local to regional scales. In a multi-year regional-scale survey involving 1251 plots and long-read third-generation sequencing, we found that soil pH has the strongest effect on the diversity of fungi and its multiple taxonomic and functional groups. The pH effects were typically unimodal, usually both direct and indirect through tree species, soil nutrients or mold abundance. Individual tree species, particularly Pinus sylvestris, Picea abies, and Populus x wettsteinii, and overall ectomycorrhizal plant proportion had relatively stronger effects on the diversity of biotrophic fungi than saprotrophic fungi. We found strong temporal sampling and investigator biases for the abundance of molds, but generally all spatial, temporal and microclimatic effects were weak. Richness of fungi and several functional groups was highest in woodlands and around ruins of buildings but lowest in bogs, with marked group-specific trends. In contrast to our expectations, diversity of soil fungi tended to be higher in forest island habitats potentially due to the edge effect, but fungal richness declined with island distance and in response to forest fragmentation. Virgin forests supported somewhat higher fungal diversity than old non-pristine forests, but there were no differences in richness between natural and anthropogenic habitats such as parks and coppiced gardens. Diversity of most fungal groups suffered from management of seminatural woodlands and parks and thinning of forests, but especially for forests the results depended on fungal group and time since partial harvesting. We conclude that the positive effects of tree diversity on overall fungal richness represent a combined niche effect of soil properties and intimate associations.

Alien ectomycorrhizal plants differ in their ability to interact with co-introduced and native ectomycorrhizal fungi in novel sites

Alien plants represent a potential threat to environment and society. Understanding the process of alien plants naturalization is therefore of primary importance. In alien plants, successful establishment can be constrained by the absence of suitable fungal partners. Here, we used 42 independent datasets of ectomycorrhizal fungal (EcMF) communities associated with alien Pinaceae and Eucalyptus spp., as the most commonly introduced tree species worldwide, to explore the strategies these plant groups utilize to establish symbioses with EcMF in the areas of introduction. We have also determined the differences in composition of EcMF communities associated with alien ectomycorrhizal plants in different regions. While alien Pinaceae introduced to new regions rely upon association with co-introduced EcMF, alien Eucalyptus often form novel interactions with EcMF species native to the region where the plant was introduced. The region of origin primarily determines species composition of EcMF communities associated with alien Pinaceae in new areas, which may largely affect invasion potential of the alien plants. Our study shows that alien ectomycorrhizal plants largely differ in their ability to interact with co-introduced and native ectomycorrhizal fungi in sites of introduction, which may potentially affect their invasive potential.

Blind spots in global soil biodiversity and ecosystem function research

Soils harbor a substantial fraction of the world's biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil taxa and ecosystem functioning data across soil macroecological studies and 17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.

Successional trajectory of bacterial communities in soil are shaped by plant-driven changes during secondary succession

This study investigated the potential role of a nitrogen-fixing early-coloniser Alnus Nepalensis D. Don (alder) in driving the changes in soil bacterial communities during secondary succession. We found that bacterial diversity was positively associated with alder growth during course of ecosystem development. Alder development elicited multiple changes in bacterial community composition and ecological networks. For example, the initial dominance of actinobacteria within bacterial community transitioned to the dominance of proteobacteria with stand development. Ecological networks approximating species associations tend to stabilize with alder growth. Janthinobacterium lividum, Candidatus Xiphinematobacter and Rhodoplanes were indicator species of different growth stages of alder. While the growth stages of alder has a major independent contribution to the bacterial diversity, its influence on the community composition was explained conjointly by the changes in soil properties with alder. Alder growth increased trace mineral element concentrations in the soil and explained 63% of variance in the Shannon-diversity. We also found positive association of alder with late-successional Quercus leucotrichophora (Oak). Together, the changes in soil bacterial community shaped by early-coloniser alder and its positive association with late-successional oak suggests a crucial role played by alder in ecosystem recovery of degraded habitats.

Host plant phylogeny and geographic distance strongly structure Betulaceae-associated ectomycorrhizal fungal communities in Chinese secondary forest ecosystems

Environmental filtering and dispersal limitation are two of the primary drivers of community assembly in ecosystems, but their effects on ectomycorrhizal (EM) fungal communities associated with wide ranges of Betulaceae taxa at a large scale are poorly documented. In this study, we examined EM fungal communities associated with 23 species from four genera (Alnus, Betula, Carpinus and Corylus) of Betulaceae in Chinese secondary forest ecosystems, using Illumina MiSeq sequencing of the ITS2 region. Effects of host plant phylogeny, soil, climate and geographic distance on EM fungal community were explored. In total, we distinguished 1738 EM fungal operational taxonomic units (OTUs) at a 97% sequence similarity level. The EM fungal communities of Alnus had significantly lower OTU richness than those associated with the other three plant genera. The EM fungal OTU richness was significantly affected by geographic distance, host plant phylogeny, soil and climate. The EM fungal community composition was significantly influenced by host plant phylogeny (12.1% of variation explained in EM fungal community), geographic distance (7.7%), soil (4.6%) and climate (1.1%). This finding highlights that environmental filtering linked to host plant phylogeny and dispersal limitation strongly influence EM fungal communities associated with Betulaceae plants in Chinese secondary forest ecosystems.

Virus population structure in the ectomycorrhizal fungi Lactarius rufus and L. tabidus at two forest sites in Southern Finland

Lactarius fungi belong to the Russulaceae family and have an important ecological role as ectomycorrhizal symbionts of coniferous and deciduous trees. Two Lactarius species, L. tabidus and L. rufus have been shown to harbor bisegmented dsRNA viruses belonging to an unclassified virus group including the mutualistic Curvularia thermal tolerance virus (CThTV). In this study, we characterized the first complete genome sequences of these viruses designated as Lactarius tabidus RNA virus 1 (LtRV1) and Lactarius rufus RNA virus 1 (LrRV1), both of which included two genome segments of 2241 and 2049 bp. We also analyzed spatial distribution and sequence diversity of the viruses in sixty host strains at two forest sites, and showed that the viruses are species-specific at sites where both host species co-occur. We also found that single virus isolates inhabited several different conspecific host strains, and were involved in persistent infections during up to eight years.

Ectomycorrhizal Fungi: Participation in Nutrient Turnover and Community Assembly Pattern in Forest Ecosystems

Ectomycorrhizal fungi (EcMF) are involved in soil nutrient cycling in forest ecosystems. These fungi can promote the uptake of nutrients (e.g., nitrogen (N) and phosphorus (P)) and water by host plants, as well as facilitate host plant growth and resistance to stresses and diseases, thereby maintaining the aboveground primary productivity of forest ecosystems. Moreover, EcMF can acquire the carbon (C) sources needed for their growth from the host plants. The nutrient regulation mechanisms of EcMF mainly include the decay of soil organic matter via enzymatic degradation, nonenzymatic mechanism (Fenton chemistry), and priming effects, which in turn promote C and N cycling. At the same time, EcMF can secrete organic acids and phosphatases to improve the availability of soil P, or increase mycelium inputs to facilitate plant acquisition of P. The spatiotemporal distribution of EcMF is influenced by a combination of historical factors and contemporary environmental factors. The community of EcMF is associated with various factors, such as climate change, soil conditions, and host distribution. Under global climate change, investigating the relationships between the nutrient cycling functions of EcMF communities and their distribution patterns under various spatiotemporal scales is conducive to more accurate assessments of the ecological effects of EcMF on the sustainable development of forest.

Co-occurring Fungal Functional Groups Respond Differently to Tree Neighborhoods and Soil Properties Across Three Tropical Rainforests in Panama

Abiotic and biotic drivers of co-occurring fungal functional guilds across regional-scale environmental gradients remain poorly understood. We characterized fungal communities using Illumina sequencing from soil cores collected across three Neotropical rainforests in Panama that vary in soil properties and plant community composition. We classified each fungal OTU into different functional guilds, namely plant pathogens, saprotrophs, arbuscular mycorrhizal (AM), or ectomycorrhizal (ECM). We measured soil properties and nutrients within each core and determined the tree community composition and richness around each sampling core. Canonical correspondence analyses showed that soil pH and moisture were shared potential drivers of fungal communities for all guilds. However, partial the Mantel tests showed different strength of responses of fungal guilds to composition of trees and soils. Plant pathogens and saprotrophs were more strongly correlated with soil properties than with tree composition; ECM fungi showed a stronger correlation with tree composition than with soil properties; and AM fungi were correlated with soil properties, but not with trees. In conclusion, we show that co-occurring fungal guilds respond differently to abiotic and biotic environmental factors, depending on their ecological function. This highlights the joint role that abiotic and biotic factors play in determining composition of fungal communities, including those associated with plant hosts.

Ectomycorrhizal fungus-associated determinants jointly reflect ecological processes in a temperature broad-leaved mixed forest

Ectomycorrhizal (ECM) fungi are closely related to vegetation compositions, edaphic properties, and site-specific processes. However, the coevolutionary mechanisms underlying the spatial distributions in floristic and ECM fungal composition in the context of biotic adaptations and abiotic variances remain unclear. We combine a total of 25 ECM fungus-associated environmental variables to impose three types of composite scores and then quantify the environmental gradients of geographical site, soil chemical property and vegetation functional trait across 122 grids of 20 m × 20 m in a 25-hm² forest plot. Significant dissimilarities in vegetational and ECM fungal abundance and composition existed along the above environmental gradients. Specifically, a contrasting floristic distribution (e.g., Betula platyphylla vs. Tilia mandshurica) existed between the northeastern and southwestern areas and was closely related to the nutrient and moisture gradients (with high levels in the west and low levels in the east). Furthermore, the ECM fungal communities were more abundant in the nutrient-poor and low-moisture environments than in the nutrient-rich and high-moisture environments, and the mixed-forest in the middle-gradient sites between the northeastern and southwestern areas harbored the highest ECM fungal diversity. These findings suggest that predictable within-site vegetation succession is closely related to ECM-associated determinants and the natural spatial heterogeneity of edaphic properties at a local scale.

Community Assembly of Endophytic Fungi in Ectomycorrhizae of Betulaceae Plants at a Regional Scale

The interaction between aboveground and belowground biotic communities drives community assembly of plants and soil microbiota. As an important component of belowground microorganisms, root-associated fungi play pivotal roles in biodiversity maintenance and community assembly of host plants. The Betulaceae plants form ectomycorrhizae with soil fungi and widely distribute in various ecosystems. However, the community assembly of endophytic fungi in ectomycorrhizae is less investigated at a large spatial scale. Here, we examined the endophytic fungal communities in ectomycorrhizae of 22 species in four genera belonging to Betulaceae in Chinese forest ecosystems, using Illumina Miseq sequencing of internal transcribed spacer 2 amplicons. The relative contribution of host phylogeny, climate and soil (environmental filtering) and geographic distance (dispersal limitation) on endophytic fungal community was disentangled. In total, 2,106 endophytic fungal operational taxonomic units (OTUs) were obtained at a 97% sequence similarity level, dominated by Leotiomycetes, Agaricomycetes, Eurotiomycetes, and Sordariomycetes. The endophytic fungal OTU richness was significantly related with host phylogeny, geographic distance, soil and climate. The endophytic fungal community composition was significantly affected by host phylogeny (19.5% of variation explained in fungal community), geographic distance (11.2%), soil (6.1%), and climate (1.4%). This finding suggests that environmental filtering by plant and abiotic variables coupled with dispersal limitation linked to geographic distance determines endophytic fungal community assembly in ectomycorrhizae of Betulaceae plants, with host phylogeny being a stronger determinant than other predictor variables at the regional scale.

Biogeographic Patterns of Ectomycorrhizal Fungal Communities Associated With Castanopsis sieboldii Across the Japanese Archipelago

Biogeographic patterns in ectomycorrhizal (ECM) fungal communities and their drivers have been elucidated, including effects of host tree species and abiotic (climatic and edaphic) conditions. At these geographic scales, genotypic diversity and composition of single host tree species change with spatial and environmental gradients, reflecting their historical dispersal events. However, whether the host genotypes can be associated with the biogeographic patterns of ECM communities remains unclear. We investigated the biogeographic pattern of ECM fungal community associated with the single host species Castanopsis sieboldii (Fagaceae), whose genotypic diversity and composition across the Japanese archipelago has already been evaluated. ECM communities were investigated in 12 mature Castanopsis-dominated forests covering almost the entire distribution range of C. sieboldii, and we quantified the effect of host genotypes on the biogeographic pattern of ECM fungal communities. Richness and community composition of ECM fungi changed with latitude and longitude; these biogeographic changes of ECM community were significantly correlated with host genotypic variables. Quantitative analyses showed a higher relative explanatory power of climatic and spatial variables than that of host genotypic variables for the biogeographic patterns in the ECM community. Our results suggest historical events of host dispersal can affect the biogeographic patterns of the ECM fungal community, while their explanation power was lower than that for climatic filtering and/or fungal dispersal.

A meta-analysis of global fungal distribution reveals climate-driven patterns

The evolutionary and environmental factors that shape fungal biogeography are incompletely understood. Here, we assemble a large dataset consisting of previously generated mycobiome data linked to specific geographical locations across the world. We use this dataset to describe the distribution of fungal taxa and to look for correlations with different environmental factors such as climate, soil and vegetation variables. Our meta-study identifies climate as an important driver of different aspects of fungal biogeography, including the global distribution of common fungi as well as the composition and diversity of fungal communities. In our analysis, fungal diversity is concentrated at high latitudes, in contrast with the opposite pattern previously shown for plants and other organisms. Mycorrhizal fungi appear to have narrower climatic tolerances than pathogenic fungi. We speculate that climate change could affect ecosystem functioning because of the narrow climatic tolerances of key fungal taxa.

The authors assemble and analyse previously generated mycobiome data linked to geographical locations across the world. They describe the distribution of fungal taxa and show that climate is an important driver of fungal biogeography and that fungal diversity appears to be concentrated at high latitudes.

Fungal Endophytes of Alnus incana ssp. rugosa and Alnus alnobetula ssp. crispa and Their Potential to Tolerate Heavy Metals and to Promote Plant Growth

Soil contamination by metals is of particular interest, given that their retention times within the profile can be indefinite. Thus, phytostabilization can be viewed as a means of limiting metal toxicity in soils. Due to their ability to grow on contaminated soils, alders have repeatedly been used as key species in phytostabilization efforts. Alder ability to grow on contaminated sites stems, in part, from its association with microbial endophytes. This work emphasizes the fungal endophytes populations associated with Alnus incana ssp. rugosa and Alnus alnobetula ssp. crispa (previously A. viridis ssp. crispa) under a phytostabilization angle. Fungal endophytes were isolated from alder trees that were growing on or near disturbed environments; their tolerances to Cu, Ni, Zn, and As, and acidic pH (4.3, 3, and 2) were subsequently assessed. Cryptosporiopsis spp. and Rhizoscyphus spp. were identified as fungal endophytes of Alnus for the first time. When used as inoculants for alder, some isolates promoted plant growth, while others apparently presented antagonistic relationships with the host plant. This study reports the first step in finding the right fungal endophytic partners for two species of alder used in phytostabilization of metal-contaminated mining sites.

Mycorrhizal types differ in ecophysiology and alter plant nutrition and soil processes

Mycorrhizal fungi benefit plants by improved mineral nutrition and protection against stress, yet information about fundamental differences among mycorrhizal types in fungi and trees and their relative importance in biogeochemical processes is only beginning to accumulate. We critically review and synthesize the ecophysiological differences in ectomycorrhizal, ericoid mycorrhizal and arbuscular mycorrhizal symbioses and the effect of these mycorrhizal types on soil processes from local to global scales. We demonstrate that guilds of mycorrhizal fungi display substantial differences in genome-encoded capacity for mineral nutrition, particularly acquisition of nitrogen and phosphorus from organic material. Mycorrhizal associations alter the trade-off between allocation to roots or mycelium, ecophysiological traits such as root exudation, weathering, enzyme production, plant protection, and community assembly as well as response to climate change. Mycorrhizal types exhibit differential effects on ecosystem carbon and nutrient cycling that affect global elemental fluxes and may mediate biome shifts in response to global change. We also note that most studies performed to date have not been properly replicated and collectively suffer from strong geographical sampling bias towards temperate biomes. We advocate that combining carefully replicated field experiments and controlled laboratory experiments with isotope labelling and -omics techniques offers great promise towards understanding differences in ecophysiology and ecosystem services among mycorrhizal types.