Environment and host as large-scale controls of ectomycorrhizal fungi

Deterministic assembly of grassland soil microbial communities driven by climate warming amplifies soil carbon loss

Perturbations in soil microbial communities caused by climate warming are expected to have a strong impact on biodiversity and future climate-carbon (C) feedback, especially in vulnerable habitats that are highly sensitive to environmental change. Here, we investigate the impact of four-year experimental warming on soil microbes and C cycling in the Loess Hilly Region of China. The results showed that warming led to soil C loss, mainly from labile C, and this C loss is associated with microbial response. Warming significantly decreased soil bacterial diversity and altered its community structure, especially increasing the abundance of heat-tolerant microorganisms, but had no effect on fungi. Warming also significantly increased the relative importance of homogeneous selection and decreased "drift" of bacterial and fungal communities. Moreover, warming decreased bacterial network stability but increased fungal network stability. Notably, the magnitude of soil C loss was significantly and positively correlated with differences in bacterial community characteristics under ambient and warming conditions, including diversity, composition, network stability, and community assembly. This result suggests that microbial responses to warming may amplify soil C loss. Combined, these results provide insights into soil microbial responses and C feedback in vulnerable ecosystems under climate warming scenarios.

Ectomycorrhizal fungi are more sensitive to high soil nitrogen levels in forests exposed to nitrogen deposition

Ectomycorrhizal fungi are essential for nitrogen (N) cycling in many temperate forests and responsive to anthropogenic N addition, which generally decreases host carbon (C) allocation to the fungi. In the boreal region, however, ectomycorrhizal fungal biomass has been found to correlate positively with soil N availability. Still, responses to anthropogenic N input, for instance through atmospheric deposition, are commonly negative. To elucidate whether variation in N supply affects ectomycorrhizal fungi differently depending on geographical context, we investigated ectomycorrhizal fungal communities along fertility gradients located in two nemo-boreal forest regions with similar ranges in soil N : C ratios and inorganic N availability but contrasting rates of N deposition. Ectomycorrhizal biomass and community composition remained relatively stable across the N gradient with low atmospheric N deposition, but biomass decreased and the community changed more drastically with increasing N availability in the gradient subjected to higher rates of N deposition. Moreover, potential activities of enzymes involved in ectomycorrhizal mobilisation of organic N decreased as N availability increased. In forests with low external input, we propose that stabilising feedbacks in tree-fungal interactions maintain ectomycorrhizal fungal biomass and communities even in N-rich soils. By contrast, anthropogenic N input seems to impair ectomycorrhizal functions.

Maintenance of host specialisation gradients in ectomycorrhizal symbionts

Many fungi that form ectomycorrhizas exhibit a degree of host specialisation, and individual trees are frequently colonised by communities of mycorrhizal fungi comprising species that fall on a gradient of specialisation along genetic, functional and taxonomic axes of variation. By contrast, arbuscular mycorrhizal fungi exhibit little specialisation. Here, we propose that host tree root morphology is a key factor that gives host plants fine-scale control over colonisation and therefore opportunities for driving specialisation and speciation of ectomycorrhizal fungi. A gradient in host specialisation is likely driven by four proximate mechanistic 'filters' comprising partner availability, signalling recognition, competition for colonisation, and symbiotic function (trade, rewards and sanctions), and the spatially restricted colonisation seen in heterorhizic roots enables these mechanisms, especially symbiotic function, to be more effective in driving the evolution of specialisation. We encourage manipulation experiments that integrate molecular genetics and isotope tracers to test these mechanisms, alongside mathematical simulations of eco-evolutionary dynamics in mycorrhizal symbioses.

Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution

Research on mycorrhizal symbiosis has been slowed by a lack of established study systems. To address this challenge, we have been developing Suillus, a widespread ecologically and economically relevant fungal genus primarily associated with the plant family Pinaceae, into a model system for studying ectomycorrhizal (ECM) associations. Over the last decade, we have compiled extensive genomic resources, culture libraries, a phenotype database, and protocols for manipulating Suillus fungi with and without their tree partners. Our efforts have already resulted in a large number of publicly available genomes, transcriptomes, and respective annotations, as well as advances in our understanding of mycorrhizal partner specificity and host communication, fungal and plant nutrition, environmental adaptation, soil nutrient cycling, interspecific competition, and biological invasions. Here, we highlight the most significant recent findings enabled by Suillus, present a suite of protocols for working with the genus, and discuss how Suillus is emerging as an important model to elucidate the ecology and evolution of ECM interactions.

Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems

Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.

Local Community Assembly Mechanisms and the Size of Species Pool Jointly Explain the Beta Diversity of Soil Fungi

Fungi play vital regulatory roles in terrestrial ecosystems. Local community assembly mechanisms, including deterministic and stochastic processes, as well as the size of regional species pools (gamma diversity), typically influence overall soil microbial community beta diversity patterns. However, there is limited evidence supporting their direct and indirect effects on beta diversity of different soil fungal functional groups in forest ecosystems. To address this gap, we collected 1606 soil samples from a 25-ha subtropical forest plot in southern China. Our goal was to determine the direct effects and indirect effects of regional species pools on the beta diversity of soil fungi, specifically arbuscular mycorrhizal (AM), ectomycorrhizal (EcM), plant-pathogenic, and saprotrophic fungi. We quantified the effects of soil properties, mycorrhizal tree abundances, and topographical factors on soil fungal diversity. The beta diversity of plant-pathogenic fungi was predominantly influenced by the size of the species pool. In contrast, the beta diversity of EcM fungi was primarily driven indirectly through community assembly processes. Neither of them had significant effects on the beta diversity of AM and saprotrophic fungi. Our results highlight that the direct and indirect effects of species pools on the beta diversity of soil functional groups of fungi can significantly differ even within a relatively small area. They also demonstrate the independent and combined effects of various factors in regulating the diversities of soil functional groups of fungi. Consequently, it is crucial to study the fungal community not only as a whole but also by considering different functional groups within the community.

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.

Fungal community composition predicts forest carbon storage at a continental scale

Forest soils harbor hyper-diverse microbial communities which fundamentally regulate carbon and nutrient cycling across the globe. Directly testing hypotheses on how microbiome diversity is linked to forest carbon storage has been difficult, due to a lack of paired data on microbiome diversity and in situ observations of forest carbon accumulation and storage. Here, we investigated the relationship between soil microbiomes and forest carbon across 238 forest inventory plots spanning 15 European countries. We show that the composition and diversity of fungal, but not bacterial, species is tightly coupled to both forest biotic conditions and a seven-fold variation in tree growth rates and biomass carbon stocks when controlling for the effects of dominant tree type, climate, and other environmental factors. This linkage is particularly strong for symbiotic endophytic and ectomycorrhizal fungi known to directly facilitate tree growth. Since tree growth rates in this system are closely and positively correlated with belowground soil carbon stocks, we conclude that fungal composition is a strong predictor of overall forest carbon storage across the European continent.

Three new species in Russula subsection Xerampelinae supported by genealogical and phenotypic coherence

Xerampelinae is a subsection composed of species of ectomycorrhizal fungi belonging to the hyperdiverse and cosmopolitan genus Russula (Russulales). Species of Xerampelinae are recognized by their fishy or shrimp odor, browning context, and a green reaction to iron sulfate. However, species delimitation has traditionally relied on morphology and analysis of limited molecular data. Prior taxonomic work in Xerampelinae has led to the description of as many as 59 taxa in Europe and 19 in North America. Here we provide the first multilocus phylogeny of European and North American members based on two nrDNA loci and two protein-coding genes. The resulting phylogeny supports the recognition of 17 species-rank Xerampelinae clades; however, higher species richness (~23) is suggested by a more inclusive nuclear rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) analysis. Phylogenetic and morphological analyses support three new species with restricted geographic distributions: R. lapponica, R. neopascua, and R. olympiana. We confirm that the European species R. subrubens is present in North America and the North American species R. serissima (previously known as R. favrei) is present in Europe. Most other Xerampelinae appear restricted to either North America or Eurasia, which indicates a high degree of regional endemism; this includes R. xerampelina, a name widely applied to North American taxa, but a species restricted to Eurasia.

Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe

Trees interact with a multitude of microbes through their roots and root symbionts such as mycorrhizal fungi and root endophytes. Here, we explore the role of fungal root symbionts as predictors of the soil and root-associated microbiomes of widespread broad-leaved trees across a European latitudinal gradient. Our results suggest that, alongside factors such as climate, soil, and vegetation properties, root colonization by ectomycorrhizal, arbuscular mycorrhizal, and dark septate endophytic fungi also shapes tree-associated microbiomes. Notably, the structure of root and soil microbiomes across our sites is more strongly and consistently associated with dark septate endophyte colonization than with mycorrhizal colonization and many abiotic factors. Root colonization by dark septate endophytes also has a consistent negative association with the relative abundance and diversity of nutrient cycling genes. Our study not only indicates that root-symbiotic interactions are an important factor structuring soil communities and functions in forest ecosystems, but also that the hitherto less studied dark septate endophytes are likely to be central players in these interactions.

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.

Protecting the invisible: Establishing guideline values for copper toxicity to marine microbiomes

Understanding the rapid responses of marine microbiomes to environmental disturbances is paramount for supporting early assessments of harm to high-value ecosystems, such as coral reefs. Yet, management guidelines aimed at protecting aquatic life from environmental pollution remain exclusively defined for organisms at higher trophic levels. In this study, 16S rRNA gene amplicon sequencing was applied in conjunction with propidium monoazide for cell-viability assessment as a sensitive tool to determine taxon- and community-level changes in a seawater microbial community under copper (Cu) exposure. Bayesian model averaging was used to establish concentration-response relationships to evaluate the effects of copper on microbial composition, diversity, and richness for the purpose of estimating microbiome Hazard Concentration (mHCx) values. Predicted mHC5 values at which a 5 % change in microbial composition, diversity, and richness occurred were 1.05, 0.72, and 0.38 μg Cu L-1, respectively. Threshold indicator taxa analysis was applied across the copper concentrations to identify taxon-specific change points for decreasing taxa. These change points were then used to generate a Prokaryotic Sensitivity Distribution (PSD), from which mHCxdec values were derived for copper, suitable for the protection of 99, 95, 90, and 80 % of the marine microbiome. The mHC5dec guideline value of 0.61 μg Cu L-1, protective of 95 % of the marine microbial community, was lower than the equivalent Australian water quality guideline value based on eukaryotic organisms at higher trophic levels. This suggests that marine microbial communities might be more vulnerable, highlighting potential insufficiencies in their protection against copper pollution. The mHCx values proposed here provide approaches to quantitatively assess the effects of contaminants on microbial communities towards the inclusion of prokaryotes in future water quality guidelines.

Mycorrhizal C/N ratio determines plant-derived carbon and nitrogen allocation to symbiosis

Carbon allocation of trees to ectomycorrhizas is thought to shape forest nutrient cycling, but the sink activities of different fungal taxa for host resources are unknown. Here, we investigate fungal taxon-specific differences in naturally composed ectomycorrhizal (EM) communities for plant-derived carbon and nitrogen. After aboveground dual labeling of young beech with 15N and 13C, ectomycorrhizas formed with different fungal taxa exhibit strong differences in label enrichment. Secondary Ion Mass Spectrometry (SIMS) imaging of nitrogen in cross sections of ectomycorrhizas demonstrates plant-derived 15N in both root and fungal structures. Isotope enrichment in ectomycorrhizas correlates with that in the corresponding ectomycorrhiza-attached lateral root, supporting fungal taxon-specific N and C fluxes in ectomycorrhizas. The enrichments with 13C and 15N in the symbiosis decrease with increasing C/N ratio of ectomycorrhizas, converging to zero at high C/N. The relative abundances of EM fungal species on roots are positively correlated with 13C enrichment, demonstrating higher fitness of stronger than of less C-demanding symbioses. Overall, our results support that differences among the C/N ratios in ectomycorrhizas formed with different fungal species regulate the supply of the symbioses with host-derived carbon and provide insights on functional traits of ectomycorrhizas, which are important for major ecosystem processes.

Above- and belowground fungal biodiversity of Populus trees on a continental scale

Understanding drivers of terrestrial fungal communities over large scales is an important challenge for predicting the fate of ecosystems under climate change and providing critical ecological context for bioengineering plant-microbe interactions in model systems. We conducted an extensive molecular and microscopy field study across the contiguous United States measuring natural variation in the Populus fungal microbiome among tree species, plant niche compartments and key symbionts. Our results show clear biodiversity hotspots and regional endemism of Populus-associated fungal communities explained by a combination of climate, soil and geographic factors. Modelling climate change impacts showed a deterioration of Populus mycorrhizal associations and an increase in potentially pathogenic foliar endophyte diversity and prevalence. Geographic differences among these symbiont groups in their sensitivity to environmental change are likely to influence broader forest health and ecosystem function. This dataset provides an above- and belowground atlas of Populus fungal biodiversity at a continental scale.

The Ectomycorrhizal Fungi and Soil Bacterial Communities of the Five Typical Tree Species in the Junzifeng National Nature Reserve, Southeast China

To explore the contribution of microorganisms to forest ecosystem function, we studied the ectomycorrhizal (ECM) fungal and soil bacterial community of the five typical tree species (Pinus massoniana, PM; Castanopsis carlesii, CC; Castanopsis eyrei, CE; Castanopsis fargesii, CF; and Keteleeria cyclolepis, KC) at the Junzifeng National Nature Reserve. The results indicated that the ECM fungal and soil bacterial diversity of CC and CF was similar, and the diversity rates of CC and CF were higher than those of PM, CE, and KC. Cenococcum geophilum and unclassified_Cortinariaceae II were the most prevalent occurring ECM fungi species in the five typical tree species, followed by unclassified_Cortinariaceae I and Lactarius atrofuscus. In bacteria, the dominant bacterial genera were Acidothermus, Bradyrhizobium, Acidibacter, Candidatus_Solibacter, Candidatus_Koribacter, Roseiarcus, and Bryobacter. EMF fungi and soil bacteria were correlated with edaphic factors, especially the soil pH, TP, and TK, caused by stand development. The results show that the community characteristics of ECM fungi and bacteria in the typical tree species of the Junzifeng National Nature Reserve reflect the critical role of soil microorganisms in stabilizing forest ecosystems.

Diversity and biogeography of plant phyllosphere bacteria are governed by latitude-dependent mechanisms

Predicting and managing the structure and function of plant microbiomes requires quantitative understanding of community assembly and predictive models of spatial distributions at broad geographic scales. Here, we quantified the relative contribution of abiotic and biotic factors to the assembly of phyllosphere bacterial communities, and developed spatial distribution models for keystone bacterial taxa along a latitudinal gradient, by analyzing 16S rRNA gene sequences from 1453 leaf samples taken from 329 plant species in China. We demonstrated a latitudinal gradient in phyllosphere bacterial diversity and community composition, which was mostly explained by climate and host plant factors. We found that host-related factors were increasingly important in explaining bacterial assembly at higher latitudes while nonhost factors including abiotic environments, spatial proximity and plant neighbors were more important at lower latitudes. We further showed that local plant-bacteria associations were interconnected by hub bacteria taxa to form metacommunity-level networks, and the spatial distribution of these hub taxa was controlled by hosts and spatial factors with varying importance across latitudes. For the first time, we documented a latitude-dependent importance in the driving factors of phyllosphere bacteria assembly and distribution, serving as a baseline for predicting future changes in plant phyllosphere microbiomes under global change and human activities.

Unveiling the Diversity of Hydnum in the Republic of Korea with One New Species, Hydnum paucispinum

Hydnum is a genus of ectomycorrhizal fungi belonging to the Hydnaceae family. It is widely distributed across different regions of the world, including North America, Europe, and Asia; however, some of them showed disjunct distributions. In recent years, with the integration of molecular techniques, the taxonomy and classification of Hydnum have undergone several revisions and advancements. However, these changes have not yet been applied in the Republic of Korea. In this study, we conducted an integrated analysis combining the morphological and molecular analyses of 30 specimens collected over a period of approximately 10 years in the Republic of Korea. For molecular analysis, the sequence data of the internal transcribed spacer (ITS) region, the large subunit of nuclear ribosomal RNA gene (nrLSU), and a portion of translation elongation factor 1-α (TEF1) were employed as molecular markers. Through this study, we identified eight species that had previously not been reported to occur in the Republic of Korea, including one new species, Hydnum paucispinum. A taxonomic key and detailed descriptions of the eight Hydnum species are provided in this study.

Mycorrhizal Fungal Diversity Associated with Six Understudied Ectomycorrhizal Trees in the Republic of Korea

Mycorrhizal fungi are key components of forest ecosystems and play essential roles in host health. The host specificity of mycorrhizal fungi is variable and the mycorrhizal fungi composition for the dominant tree species is largely known but remains unknown for the less common tree species. In this study, we collected soil samples from the roots of six understudied ectomycorrhizal tree species from a preserved natural park in the Republic of Korea over four seasons to investigate the host specificity of mycorrhizal fungi in multiple tree species, considering the abiotic factors. We evaluated the mycorrhizal fungal composition in each tree species using a metabarcoding approach. Our results revealed that each host tree species harbored unique mycorrhizal communities, despite close localization. Most mycorrhizal taxa belonged to ectomycorrhizal fungi, but a small proportion of ericoid mycorrhizal fungi and arbuscular mycorrhizal fungi were also detected. While common mycorrhizal fungi were shared between the plant species at the genus or higher taxonomic level, we found high host specificity at the species/OTU (operational taxonomic unit) level. Moreover, the effects of the seasons and soil properties on the mycorrhizal communities differed by tree species. Our results indicate that mycorrhizal fungi feature host-specificity at lower taxonomic levels.

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.

Ectomycorrhizal diversity, taxon-specific traits and root N uptake in temperate beech forests

Roots of forest trees are colonized by a diverse spectrum of ectomycorrhizal (EM) fungal species differing in their nitrogen (N) acquisition abilities. Here, we hypothesized that root N gain is the result of EM fungal diversity or related to taxon-specific traits for N uptake. To test our hypotheses, we traced ¹⁵ N enrichment in fine roots, coarse roots and taxon-specific ectomycorrhizas in temperate beech forests in two regions and three seasons, feeding 1 mM NH₄ NO₃ labelled with either ¹⁵ NH₄ ⁺ or ¹⁵ NO₃ ^- . We morphotyped > 45 000 vital root tips and identified 51 of 53 detected EM species by sequencing. EM root tips exhibited strong, fungal taxon-specific variation in ¹⁵ N enrichment with higher NH₄ ⁺ than NO₃ ^- enrichment. The translocation of N into the upper parts of the root system increased with increasing EM fungal diversity. Across the growth season, influential EM species predicting root N gain were not identified, probably due to high temporal dynamics of the species composition of EM assemblages. Our results support that root N acquisition is related to EM fungal community-level traits and highlight the importance of EM diversity for tree N nutrition.

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.

Applying molecular and genetic methods to trees and their fungal communities

Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.

Forest microbiome and global change

Forests influence climate and mitigate global change through the storage of carbon in soils. In turn, these complex ecosystems face important challenges, including increases in carbon dioxide, warming, drought and fire, pest outbreaks and nitrogen deposition. The response of forests to these changes is largely mediated by microorganisms, especially fungi and bacteria. The effects of global change differ among boreal, temperate and tropical forests. The future of forests depends mostly on the performance and balance of fungal symbiotic guilds, saprotrophic fungi and bacteria, and fungal plant pathogens. Drought severely weakens forest resilience, as it triggers adverse processes such as pathogen outbreaks and fires that impact the microbial and forest performance for carbon storage and nutrient turnover. Nitrogen deposition also substantially affects forest microbial processes, with a pronounced effect in the temperate zone. Considering plant-microorganism interactions would help predict the future of forests and identify management strategies to increase ecosystem stability and alleviate climate change effects. In this Review, we describe the impact of global change on the forest ecosystem and its microbiome across different climatic zones. We propose potential approaches to control the adverse effects of global change on forest stability, and present future research directions to understand the changes ahead.

Advancing research on ectomycorrhizal fungal adaptation with landscape genomics

Ectomycorrhizal (ECM) fungi serve key functions in forest ecosystems by supplying water and nutrients to tree hosts, yet mutualistic plant-fungi interactions are jeopardised by environmental alterations. Here, we discuss the great potential and current limitations of landscape genomics in investigating signatures of local adaptation in natural populations of ECM fungi.

Discrepancies of fungi and plants in the pattern of beta-diversity with environmental gradient imply a comprehensive community assembly rule

Beta-diversity partitioning has shown that the nestedness component is developed with environmental stress in a variety of taxa. However, soil fungal community may maintain its turnover components in contrast to the development of plants' nestedness component, and the potential causes remain unclear. To investigate the process of species turnover of soil fungi along a stress gradient in the Arctic, we divided species turnover component into sub-components: βsim_hete and βsim_homo representing species turnover with and without a change in the guilds, respectively. The results indicate that fungal communities maintain their turnover components, unlike plant communities; however, their βsim_hete increased under stressful conditions. Additionally, GDM analysis showed that βsim_hete was mainly explained by stress gradient and plant nestedness, suggesting that the functionality of soil fungi was ecologically filtered by environmental stress and plant community structure. The discordant trend of beta-diversity values between plant and fungi (i.e. development of plant nestedness and maintenance of fungal turnover) is possibly not caused by different assembly rules working in parallel on the two taxa, but according to an ecological rule that reflects plant-fungal interaction.

On the significance of long-term trends in tree-ring N isotopes - The interplay of soil conditions and regional NOx emissions

As anthropogenic nitrogen (N) emissions have been rising for decades, it is critical to develop natural archives that help understand how natural processes were modified in the past. Tree-ring δ¹⁵N values may represent such an indicator but its validity as faithful record of N cycling changes is still debated. Here we produce long-tree-ring δ¹⁵N series for five white spruce stands from two boreal regions submitted to moderate industrial N inputs. The obtained δ¹⁵N series show sharp differences among stands, even from the same region, despite the fact that they show similar increases in intrinsic water use efficiency (iWUE), a proxy for foliar strategies derived from δ¹³C values. The statistical modeling of these series and the basal area increment (BAI) of the trees allow to suggest that the mechanisms controlling the isotopic fractionation of N assimilated by tree rings are decoupled from the foliar strategies under the anthropogenic N emissions. The iWUE trends mainly reflect rise of pCO₂ and changes in air quality. The long-term δ¹⁵N trends echo different biogeochemical processes responding to N deposition due to distinct original soil pH at the various sites. We contend that tree-ring δ¹⁵N series can record changes in the forest N cycle, but their rigorous interpretation requires laborious work, particularly an understanding of the biogeochemistry in the soil immediately around the investigated trees. "Seek simplicity and distrust it", Alfred North Whitehead.

Tree mycorrhizal association types control biodiversity-productivity relationship in a subtropical forest

Mycorrhizae are symbiotic associations between terrestrial plants and fungi in which fungi obtain nutrients in exchange for plant photosynthates. However, it remains unclear how different types of mycorrhizae affect their host interactions and productivity. Using a long-term experiment with a diversity gradient of arbuscular (AM) and ectomycorrhizal (EcM) tree species, we show that the type of mycorrhizae critically controls the effect of diversity on productivity. With increasing diversity, the net primary production of AM trees increased, but EcM trees decreased, largely because AM trees are more effective in acquiring nitrogen and phosphorus. Specifically, with diversity increase, AM trees enhance both nutrient resorption and litter decomposition, while there was a trade-off between litter decomposability and nutrient resorption in EcM trees. These results provide a mechanistic understanding of why AM trees using a different nutrient acquisition strategy from EcM trees can dominate in subtropical forests and at the same time their diversity enhances productivity.

Identifying thresholds of nitrogen enrichment for substantial shifts in arbuscular mycorrhizal fungal community metrics in a temperate grassland of northern China

Nitrogen (N) enrichment poses threats to biodiversity and ecosystem stability, while arbuscular mycorrhizal (AM) fungi play important roles in ecosystem stability and functioning. However, the ecological impacts, especially thresholds of N enrichment potentially causing AM fungal community shifts have not been adequately characterized. Based on a long-term field experiment with nine N addition levels ranging from 0 to 50 g N m^-2  yr^-1 in a temperate grassland, we characterized the community response patterns of AM fungi to N enrichment. Arbuscular mycorrhizal fungal biomass continuously decreased with increasing N addition levels. However, AM fungal diversity did not significantly change below 20 g N m^-2  yr^-1 , but dramatically decreased at higher N levels, which drove the AM fungal community to a potentially unstable state. Structural equation modeling showed that the decline in AM fungal biomass could be well explained by soil acidification, whereas key driving factors for AM fungal diversity shifted from soil nitrogen : phosphorus (N : P) ratio to soil pH with increasing N levels. Different aspects of AM fungal communities (biomass, diversity and community composition) respond differently to increasing N addition levels. Thresholds for substantial community shifts in response to N enrichment in this grassland ecosystem are identified.

Do ectomycorrhizal exploration types reflect mycelial foraging strategies?

Ectomycorrhizal exploration types are commonly assumed to denote spatial foraging patterns and resource-related niches of extraradical mycelia. However, empirical evidence of the consistency of foraging strategies within exploration types is lacking. Here, we analysed ectomycorrhizal foraging patterns by incubating root-excluding ingrowth mesh bags filled with six different substrates in mature Picea abies forests. High-throughput sequencing was used to characterise ectomycorrhizal fungal communities in the mesh bags and on adjacent fine roots after one growing season. Contrary to expectations, many ectomycorrhizal genera of exploration types that are thought to produce little extraradical mycelium colonised ingrowth bags extensively, whereas genera commonly associated with ample mycelial production occurred sparsely in ingrowth bags relative to their abundance on roots. Previous assumptions about soil foraging patterns of exploration types do not seem to hold. Instead, we propose that variation in the proliferation of extraradical mycelium is related to intergeneric differences in mycelial longevity and the mobility of targeted resources.

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.

Arbuscular mycorrhizal fungi enhance photosynthesis and drought tolerance by regulating MAPK genes expressions of Populus simonii × P. nigra

Arbuscular mycorrhizal fungi (AMF) promote plants to absorb more water and nutrients and improve their stress resistance. As the main signal transducer, the mitogen-activated protein kinase (MAPK) cascade plays a vital role in drought stress. However, how the MAPK family genes of mycorrhizal plants respond to stress is still not clear. Our study analyzed physiological indexes and expression profiles of MAPK family genes of Populus simonii × P. nigra under two inoculation treatments (inoculated with or without Rhizophagus irregularis) and two water conditions (well-watered or drought stress). The results showed that the stronger photosynthesis of mycorrhizal plants may be mediated by MAPK genes induced by AMF. Mycorrhizal plants showed lower oxidative damage and drought sensitivity. Mycorrhiza downregulated the expression of PsnMAPK7-2, PsnMAPK16-1, PsnMAPK19-2, and PsnMAPK20-2 which negatively regulate drought tolerance and induced specific PsnMAPKs in roots which activate transcription factors to regulate downstream gene expressions, enhancing drought tolerance. This is the first time to identify part of the MAPK gene family of P. simonii × P. nigra at the genome level and study MAPK genes in mycorrhizal forest trees. This is helpful to understand the function of the MAPK gene family in response to drought of mycorrhizal plants and lays a foundation for afforestation by using mycorrhizal saplings.

Community Assembly of Fungi and Bacteria along Soil-Plant Continuum Differs in a Zoige Wetland

Distinct plant associated microbiomes live in rhizosphere soil, roots, and leaves. However, the differences in community assembly of fungi and bacteria along soil-plant continuum are less documented in ecosystems. We examined fungal and bacterial communities associated with leaves, roots, and rhizosphere soil of the dominant arbuscular mycorrhizal (AM) plants Taraxacum mongolicum and Elymus nutans and non-AM plant Carex enervis in the Zoige Wetland by using high throughput sequencing techniques. The operational taxonomic unit (OTU) richness of fungi and bacteria was significantly higher in rhizosphere soil than in roots and leaves, and their community compositions were significantly different in the rhizosphere soil, roots, and leaves in each plant species. The co-occurrence network analysis revealed that the sensitive fungal and bacterial OTUs with various taxonomic positions were mainly clustered into different modules according to rhizosphere soil, roots, and leaves in each plant species. Along the soil-plant continuum, the rhizosphere soil pool contributed more source on bacterial than on fungal communities in roots and leaves of the three plant species, and more source on bacterial and fungal communities in leaves of T. mongolicum and E. nutans compared with C. enervis. Furthermore, the root pool contributed more source on bacterial than on fungal communities in leaves of T. mongolicum and E. nutans but not that of C. enervis. This study highlights that the host plant selection intensity is higher in fungal than in bacterial communities in roots and leaves from rhizosphere soil in each plant species, and differs in fungal and bacterial communities along the soil-plant continuum in AM plants T. mongolicum and E. nutans and non-AM plant C. enervis in the Zoige Wetland. IMPORTANCE Elucidating the community microbiome assemblage alone the soil-plant continuum will help to better understand the biodiversity maintenance and ecosystem functioning. Here, we examined the fungal and bacterial communities in rhizosphere soil, roots, and leaves of two dominant AM plants and a non-AM plant in Zoige Wetland. We found that along the soil - plant continuum, host plant selection intensity is higher in fungal than in bacterial communities in roots and leaves from rhizosphere soil in each plant species, and differs in fungal and bacterial communities in the AM- and non-AM plants. This is the first report provides evidence of different assembly patterns of fungal and bacterial communities along the soil-plant continuum in the AM- and non-AM plants in the Zoige Wetland.

Soil nutrients and plant diversity affect ectomycorrhizal fungal community structure and functional traits across three subalpine coniferous forests

The symbiotic relationship between ectomycorrhizal fungi (EMF) and the roots of host plants is significantly important in regulating the health and stability of ecosystems, especially of those such as the climate warming affected subalpine forest ecosystems. Therefore, from the coniferous forest systems located in the Southern Qinghai-Tibetan Plateau, root tips from three forest tree species: Pinus wallichiana, Abies spectabilis and Picea spinulosa, were collected to look for the local causes of EMF community composition and diversity patterns. The EMF colonization rate, diversity and taxonomic community structure were determined by morphotyping and sanger sequencing of the fungal ITS gene from the root tip samples. Soil exploration types were identified based on the morphologies of the ectomycorrhizas, coupled with soil properties analysis and plant diversity survey. Contrasting patterns of EMF community and functional diversity were found across the studied three forests types dominated by different coniferous tree species. In terms of associations between soil and EMF properties, the total phosphorus (TP) and nitrate (NO₃⁻) contents in soil negatively correlated with the colonization rate and the Shannon diversity index of EMF in contrast to the positive relationship between TP and EMF richness. The soil total nitrogen (TN), ammonium (NH₄⁺) and plant diversity together caused 57.6% of the total variations in the EMF taxonomic community structure at the three investigated forest systems. Whereas based on the soil exploration types alone, NH₄⁺ and TN explained 74.2% of variance in the EMF community structures. Overall, the findings of this study leverage our understanding of EMF dynamics and local influencing factors in coniferous forests dominated by different tree species within the subalpine climatic zone.

Defending Earth's terrestrial microbiome

Microbial life represents the majority of Earth's biodiversity. Across disparate disciplines from medicine to forestry, scientists continue to discover how the microbiome drives essential, macro-scale processes in plants, animals and entire ecosystems. Yet, there is an emerging realization that Earth's microbial biodiversity is under threat. Here we advocate for the conservation and restoration of soil microbial life, as well as active incorporation of microbial biodiversity into managed food and forest landscapes, with an emphasis on soil fungi. We analyse 80 experiments to show that native soil microbiome restoration can accelerate plant biomass production by 64% on average, across ecosystems. Enormous potential also exists within managed landscapes, as agriculture and forestry are the dominant uses of land on Earth. Along with improving and stabilizing yields, enhancing microbial biodiversity in managed landscapes is a critical and underappreciated opportunity to build reservoirs, rather than deserts, of microbial life across our planet. As markets emerge to engineer the ecosystem microbiome, we can avert the mistakes of aboveground ecosystem management and avoid microbial monocultures of single high-performing microbial strains, which can exacerbate ecosystem vulnerability to pathogens and extreme events. Harnessing the planet's breadth of microbial life has the potential to transform ecosystem management, but it requires that we understand how to monitor and conserve the Earth's microbiome.

Biogeographic history of a large clade of ectomycorrhizal fungi, the Russulaceae, in the Neotropics and adjacent regions

The biogeography of neotropical fungi remains poorly understood. Here, we reconstruct the origins and diversification of neotropical lineages in one of the largest clades of ectomycorrhizal fungi in the globally widespread family Russulaceae. We inferred a supertree of 3285 operational taxonomic units, representing worldwide internal transcribed spacer sequences. We reconstructed biogeographic history and diversification and identified lineages in the Neotropics and adjacent Patagonia. The ectomycorrhizal Russulaceae have a tropical African origin. The oldest lineages in tropical South America, most with African sister groups, date to the mid-Eocene, possibly coinciding with a boreotropical migration corridor. There were several transatlantic dispersal events from Africa more recently. Andean and Central American lineages mostly have north-temperate origins and are associated with North Andean uplift and the general north-south biotic interchange across the Panama isthmus, respectively. Patagonian lineages have Australasian affinities. Diversification rates in tropical South America and other tropical areas are lower than in temperate areas. Neotropical Russulaceae have multiple biogeographic origins since the mid-Eocene involving dispersal and co-migration. Discontinuous distributions of host plants may explain low diversification rates of tropical lowland ectomycorrhizal fungi. Deeply diverging neotropical fungal lineages need to be better documented.

50 Years of Cumulative Open-Source Data Confirm Stable and Robust Biodiversity Distribution Patterns for Macrofungi

Fungi are a hyper-diverse kingdom that contributes significantly to the regulation of the global carbon and nutrient cycle. However, our understanding of the distribution of fungal diversity is often hindered by a lack of data, especially on a large spatial scale. Open biodiversity data may provide a solution, but concerns about the potential spatial and temporal bias in species occurrence data arising from different observers and sampling protocols challenge their utility. The theory of species accumulation curves predicts that the cumulative number of species reaches an asymptote when the sampling effort is sufficiently large. Thus, we hypothesize that open biodiversity data could be used to reveal large-scale macrofungal diversity patterns if these datasets are accumulated long enough. Here, we tested our hypothesis with 50 years of macrofungal occurrence records in Norway and Sweden that were downloaded from the Global Biodiversity Information Facility (GBIF). We first grouped the data into five temporal subsamples with different cumulative sampling efforts (i.e., accumulation of data for 10, 20, 30, 40 and 50 years). We then predicted the macrofungal diversity and distribution at each subsample using the maximum entropy (MaxEnt) species distribution model. The results revealed that the cumulative number of macrofungal species stabilized into distinct distribution patterns with localized hotspots of predicted macrofungal diversity with sampling efforts greater than approximately 30 years. Our research demonstrates the utility and importance of the long-term accumulated open biodiversity data in studying macrofungal diversity and distribution at the national level.

Seasonal Succession and Temperature Response Pattern of a Microbial Community in the Yellow Sea Cold Water Mass

Explaining the temporal dynamics of marine microorganisms is critical for predicting their changing pattern under environmental disturbances. Although the effect of temperature on microbial seasonality has been widely studied, the phylogenetic structure of the temperature response pattern and the extent to which temperature shift leads to disruptive community changes are still unclear. Here, we explored the microbial seasonal dynamics in the Yellow Sea Cold Water Mass (YSCWM) that occurs in summer and disappears in winter and tested the temperature thresholds and phylogenetic coherence in response to temperature change. The existence of YSCWM generates strong temperature gradients in summer and confers little temperature change during seasonal transition, thus representing a unique intermediate state. The microbial community of YSCWM is more similar to that in the previous YSCWM in winter than that outside YSCWM. Temperature alone explains >50% of the community variation, suggesting that a temperature shift can induce a nearly seasonality-level community variance in summer. Persistence of most previous winter YSCWM inhabitants in YSCWM leads to conservation in predicted functional potentials and cooccurrence patterns, indicating a decisive role of temperature in maintaining functionality. Evaluation of the temperature threshold reveals that a small temperature change can lead to significant community turnover, with most taxa negatively responding to an elevation in temperature. The temperature response pattern is phylogenetically structured, and closely related taxa show an incohesive response. Our study provides novel insights into microbial seasonality and into how marine microorganisms respond to temperature fluctuations. IMPORTANCE Microbial seasonality is driven by a set of covarying factors including temperature. There is still a lack of understanding of the details of the phylogenetic structure and susceptibility of microbial communities in response to temperature variation. Through examination of the microbial community in a seasonally occurring summer cold water mass, which experiences little temperature change during seasonal transition, we show here that the cold water mass leads to nearly seasonality-level variations in community composition and predicted functional profile in summer. Moreover, massive community turnover occurs within a small temperature shift, with most taxa decreasing in abundance in response to increased temperature, and contrasting response patterns are observed between phylogenetically closely related taxa. These results suggest temperature as the fundamental factor over other covarying factors in structuring microbial seasonality, providing important insights into the variation mode of the microbial community under temperature disturbances.

Strategic roadmap to assess forest vulnerability under air pollution and climate change

Although it is an integral part of global change, most of the research addressing the effects of climate change on forests have overlooked the role of environmental pollution. Similarly, most studies investigating the effects of air pollutants on forests have generally neglected the impacts of climate change. We review the current knowledge on combined air pollution and climate change effects on global forest ecosystems and identify several key research priorities as a roadmap for the future. Specifically, we recommend (1) the establishment of much denser array of monitoring sites, particularly in the South Hemisphere; (2) further integration of ground and satellite monitoring; (3) generation of flux-based standards and critical levels taking into account the sensitivity of dominant forest tree species; (4) long-term monitoring of N, S, P cycles and base cations deposition together at global scale; (5) intensification of experimental studies, addressing the combined effects of different abiotic factors on forests by assuring a better representation of taxonomic and functional diversity across the ~73,000 tree species on Earth; (6) more experimental focus on phenomics and genomics; (7) improved knowledge on key processes regulating the dynamics of radionuclides in forest systems; and (8) development of models integrating air pollution and climate change data from long-term monitoring programs.

Fungal communities in soils under global change

Soil fungi play indispensable roles in all ecosystems including the recycling of organic matter and interactions with plants, both as symbionts and pathogens. Past observations and experimental manipulations indicate that projected global change effects, including the increase of CO₂ concentration, temperature, change of precipitation and nitrogen (N) deposition, affect fungal species and communities in soils. Although the observed effects depend on the size and duration of change and reflect local conditions, increased N deposition seems to have the most profound effect on fungal communities. The plant-mutualistic fungal guilds - ectomycorrhizal fungi and arbuscular mycorrhizal fungi - appear to be especially responsive to global change factors with N deposition and warming seemingly having the strongest adverse effects. While global change effects on fungal biodiversity seem to be limited, multiple studies demonstrate increases in abundance and dispersal of plant pathogenic fungi. Additionally, ecosystems weakened by global change-induced phenomena, such as drought, are more vulnerable to pathogen outbreaks. The shift from mutualistic fungi to plant pathogens is likely the largest potential threat for the future functioning of natural and managed ecosystems. However, our ability to predict global change effects on fungi is still insufficient and requires further experimental work and long-term observations. Citation: Baldrian P, Bell-Dereske L, Lepinay C, Větrovský T, Kohout P (2022). Fungal communities in soils under global change. Studies in Mycology 103: 1-24. doi: 10.3114/sim.2022.103.01.

Seedling ectomycorrhization is central to conifer forest restoration: a case study from Kashmir Himalaya

Over the past few decades, many countries have attempted to carry out forest landscape restoration over millions of hectares of degraded land. Such efforts, however, have met with limited success because of several factors, including a lack of adequate emphasis on ectomycorrhization of the nursery seedlings. A similar scenario is seen in the Kashmir Himalaya, where the natural regeneration of degraded forests is poor despite ample restoration efforts by forest managers. To overcome this challenge, we identified two promising ectomycorrhizal species, namely Clitocybe nuda and Cortinarius distans, for their use in ectomycorrhization of seedlings of three common conifers, namely Abies pindrow, Cedrus deodara, and Picea smithiana. Laboratory studies were carried out to investigate the requirements for optimum mycelial growth of these ectomycorrhizal fungi. Best ECM mycelial growth was obtained in the basic MMN medium containing glucose as the source of carbon and nitrogen in ammonium form. C. distans showed higher growth than C. nuda across all the treatments and also proved significantly more effective in enhancing the survival and growth of the conifer host plant seedlings. The present study resulted in standardizing the requirements for mass inoculum production of the two mycobionts which could help in successful forest restoration programmes.

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.

Canopy and Understory Nitrogen Addition Alters Organic Soil Bacterial Communities but Not Fungal Communities in a Temperate Forest

Atmospheric nitrogen (N) deposition is known to alter soil microbial communities, but how canopy and understory N addition affects soil bacterial and fungal communities in different soil layers remains poorly understood. Conducting a 6-year canopy and understory N addition experiment in a temperate forest, we showed that soil bacterial and fungal communities in the organic layer exhibited different responses to N addition. The main effect of N addition decreased soil bacterial diversity and altered bacterial community composition in the organic layer, but not changed fungal diversity and community composition in all layers. Soil pH was the main factor that regulated the responses of soil bacterial diversity and community composition to N addition, whereas soil fungal diversity and community composition were mainly controlled by soil moisture and nutrient availability. In addition, compared with canopy N addition, the understory N addition had stronger effects on soil bacterial Shannon diversity and community composition but had a weaker effect on soil bacteria richness in the organic soil layer. Our study demonstrates that the bacterial communities in the organic soil layer were more sensitive than the fungal communities to canopy and understory N addition, and the conventional method of understory N addition might have skewed the effects of natural atmospheric N deposition on soil bacterial communities. This further emphasizes the importance of considering canopy processes in future N addition studies and simultaneously evaluating soil bacterial and fungal communities in response to global environmental changes.

Coupling of plant and mycorrhizal fungal diversity: its occurrence, relevance, and possible implications under global change

First principles predict that diversity at one trophic level often begets diversity at other levels, suggesting plant and mycorrhizal fungal diversity should be coupled. Local-scale studies have shown positive coupling between the two, but the association is less consistent when extended to larger spatial and temporal scales. These inconsistencies are likely due to divergent relationships of different mycorrhizal fungal guilds to plant diversity, scale dependency, and a lack of coordinated sampling efforts. Given that mycorrhizal fungi play a central role in plant productivity and nutrient cycling, as well as ecosystem responses to global change, an improved understanding of the coupling between plant and mycorrhizal fungal diversity across scales will reduce uncertainties in predicting the ecosystem consequences of species gains and losses.

Atmospheric pollution, soil nutrients and climate effects on Mucoromycota arbuscular mycorrhizal fungi

Fine root endophyte mycorrhizal fungi in the Endogonales (Mucoromycota arbuscular mycorrhizal fungi, M‐AMF) are now recognized as at least as important globally as Glomeromycota AMF (G‐AMF), yet little is known about the environmental factors which influence M‐AMF diversity and colonization, partly because they typically only co‐colonize plants with G‐AMF. Wild populations of Lycopodiella inundata predominantly form mycorrhizas with M‐AMF and therefore allow focussed study of M‐AMF environmental drivers. Using microscopic examination and DNA sequencing we measured M‐AMF colonization and diversity over three consecutive seasons and modelled interactions between these response variables and environmental data. Significant relationships were found between M‐AMF colonization and soil S, P, C:N ratio, electrical conductivity, and the previously overlooked micronutrient Mn. Estimated N deposition was negatively related to M‐AMF colonization. Thirty‐nine Endogonales Operational Taxonomic Units (OTUs) were identified in L. inundata roots, a greater diversity than previously recognized in this plant. Endogonales OTU richness correlated negatively with soil C:N while community composition was mostly influenced by soil P. This study provides first evidence that M‐AMF have distinct ecological preferences in response to edaphic variables also related to air pollution. Future studies require site‐level atmospheric pollution monitoring to guide critical load policy for mycorrhizal fungi in heathlands and grasslands.

Preferential associations of soil fungal taxa under mixed compositions of eastern American tree species

Soil fungi are vital to forest ecosystem function, in part through their role mediating tree responses to environmental factors, as well as directly through effects on resource cycling. While the distribution of soil fungi can vary with abiotic factors, plant species identity is also known to affect community composition. However, the particular influence that a plant will have on its soil microbiota remains difficult to predict. Here, we paired amplicon sequencing and enzymatic assays to assess soil fungal composition and function under three tree species, Quercus rubra, Betula nigra, and Acer rubrum, planted individually and in all combinations in a greenhouse. We observed that fungal communities differed between each of the individual planted trees, suggesting at least some fungal taxa may associate preferentially with these tree species. Additionally, fungal community composition under mixed-tree plantings broadly differed from the individual planted trees, suggesting mixing of these distinct soil fungal communities. The data also suggest that there were larger enzymatic activities in the individual plantings as compared to all mixed-tree plantings which may be due to variations in fungal community composition. This study provides further evidence of the importance of tree identity on soil microbiota and functional changes to forest soils.

Forest tree growth is linked to mycorrhizal fungal composition and function across Europe

Most trees form symbioses with ectomycorrhizal fungi (EMF) which influence access to growth-limiting soil resources. Mesocosm experiments repeatedly show that EMF species differentially affect plant development, yet whether these effects ripple up to influence the growth of entire forests remains unknown. Here we tested the effects of EMF composition and functional genes relative to variation in well-known drivers of tree growth by combining paired molecular EMF surveys with high-resolution forest inventory data across 15 European countries. We show that EMF composition was linked to a three-fold difference in tree growth rate even when controlling for the primary abiotic drivers of tree growth. Fast tree growth was associated with EMF communities harboring high inorganic but low organic nitrogen acquisition gene proportions and EMF which form contact versus medium-distance fringe exploration types. These findings suggest that EMF composition is a strong bio-indicator of underlying drivers of tree growth and/or that variation of forest EMF communities causes differences in tree growth. While it may be too early to assign causality or directionality, our study is one of the first to link fine-scale variation within a key component of the forest microbiome to ecosystem functioning at a continental scale.

Molecular-Based Diversity Studies and Field Surveys Are Not Mutually Exclusive: On the Importance of Integrated Methodologies in Mycological Research

Understanding and describing the diversity of living organisms is a great challenge. Fungi have for a long time been, and unfortunately still are, underestimated when it comes to taxonomic research. The foundations were laid by the first mycologists through field observations. These important fundamental works have been and remain vital reference works. Nevertheless, a non-negligible part of the studied funga escaped their attention. Thanks to modern developments in molecular techniques, the study of fungal diversity has been revolutionized in terms of tools and knowledge. Despite a number of disadvantages inherent to these techniques, traditional field-based inventory work has been increasingly superseded and neglected. This perspective aims to demonstrate the central importance of field-based research in fungal diversity studies, and encourages researchers not to be blinded by the sole use of molecular methods.