Spatial analysis of ectomycorrhizal fungi reveals that root tip communities are structured by competitive interactions

Abundances of ectomycorrhizal exploration types show the type-dependent temporal dynamics over the seasons-a controlled growth container experiment

Ectomycorrhizas are ubiquitous symbiotic associations between host trees and soil fungi. While the seasonal changes of the taxonomic community structure of ectomycorrhizal fungi have been studied extensively, the temporal dynamics of ectomycorrhizal exploration types which have been proposed for elucidating the functional roles of ectomycorrhizas have not been fully examined. The purpose of the study is to test the hypothesis of whether the abundance of the exploration types in the hosts with different phenology shows different temporal patterns over the seasons. Two host species, deciduous Quercus acutissima and evergreen Q. glauca, were planted in growth containers with natural forest soils and were grown in single or combined species treatment, under similar environmental conditions and in shared soil spore banks of the ectomycorrhizal fungi. The ectomycorrhizal exploration types that occurred on these two host species in two different treatments were observed for two growing seasons. The observed exploration types, namely contact, short-distance, and long-distance type as well as the overall abundance of the ectomycorrhizas showed distinct temporal patterns although no specific response to the host seasonal phenology was found. The abundances of the contact type showed no relation to the seasons whereas those of the short- and the long-distance type increased with time. The formation of the long-distance type was strongly influenced by the host species treatments while that of the other two types was not so. Therefore, the different exploration types demonstrate distinct temporal patterns depending on the types but no specific seasonal responses.

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.

Fungal Fight Club: phylogeny and growth rate predict competitive outcomes among ectomycorrhizal fungi

Ectomycorrhizal fungi are among the most prevalent fungal partners of plants and can constitute up to one-third of forest microbial biomass. As mutualistic partners that supply nutrients, water, and pathogen defense, these fungi impact host plant health and biogeochemical cycling. Ectomycorrhizal fungi are also extremely diverse, and the community of fungal partners on a single plant host can consist of dozens of individuals. However, the factors that govern competition and coexistence within these communities are still poorly understood. In this study, we used in vitro competitive assays between five ectomycorrhizal fungal strains to examine how competition and pH affect fungal growth. We also tested the ability of evolutionary history to predict the outcomes of fungal competition. We found that the effects of pH and competition on fungal performance varied extensively, with changes in growth media pH sometimes reversing competitive outcomes. Furthermore, when comparing the use of phylogenetic distance and growth rate in predicting competitive outcomes, we found that both methods worked equally well. Our study further highlights the complexity of ectomycorrhizal fungal competition and the importance of considering phylogenetic distance, ecologically relevant traits, and environmental conditions in predicting the outcomes of these interactions.

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.

Exploring fine-scale assembly of ectomycorrhizal fungal communities through phylogenetic and spatial distribution analyses

Ectomycorrhizal fungi (EMF) form symbiotic relationship with the roots of host plants. EMF communities are composed of highly diverse species; however, how they are assembled has been a long-standing question. In this study, we investigated from a phylogenetic perspective how EMF communities assemble on Pinus densiflora seedlings at different spatial scales (i.e., seedling scale and root tip scale). P. densiflora seedlings were collected from different habitats (i.e., disturbed areas and mature forests), and their EMF communities were investigated by morphotype sequencing and next-generation sequencing (NGS). To infer assembly mechanisms, phylogenetic relatedness within the community (i.e., phylogenetic structure) was estimated and spatial distribution of EMF root tips was analyzed. The EMF communities on pine seedlings were largely different between the two habitats. Phylogenetically restricted lineages (Amphinema, /suillus-rhizopogon) were abundant in the disturbed areas, whereas species from diverse lineages were abundant in the mature forests (Russula, Sebacina, /tomentella-thelephora, etc.). In the disturbed areas, phylogenetically similar EMF species were aggregated at the seedling scale, suggesting that disturbance acts as a powerful abiotic filter. However, phylogenetically similar species were spatially segregated from each other at the root tip scale, indicating limiting similarity. In the mature forest seedlings, no distinct phylogenetic signals were detected at both seedling and root tip scale. Collectively, our results suggest that limiting similarity may be an important assembly mechanism at the root tip scale and that assembly mechanisms can vary across habitats and spatial scales.

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.

Niche partitioning in an assemblage of granivorous rodents, and the challenge of community-level conservation

Coexistence of competing species in the same foraging guild has long puzzled ecologists. In particular, how do small subordinate species persist with larger dominant competitors? This question becomes particularly important when conservation interventions, such as reintroduction or translocation, become necessary for the smaller species. Exclusion of dominant competitors might be necessary to establish populations of some endangered species. Ultimately, however, the goal should be to conserve whole communities. Determining how subordinate species escape competitive exclusion in intact communities could inform conservation decisions by clarifying the ecological conditions and processes required for coexistence at local or regional scales. We tested for spatial and temporal partitioning among six species of native, granivorous rodents using null models, and characterized the microhabitat of each species using resource-selection models. We found that the species’ nightly activity patterns are aggregated temporally but segregated spatially. As expected, we found clear evidence that the larger-bodied kangaroo rats drive spatial partitioning, but we also found species-specific microhabitat associations, which suggests that habitat heterogeneity is part of what enables these species to coexist. Restoration of natural disturbance regimes that create habitat heterogeneity, and selection of translocation sites without specific competitors, are among the management recommendations to consider in this case. More generally, this study highlights the need for a community-level approach to conservation and the usefulness of basic ecological data for guiding management decisions.

Spheres of Influence: Host Tree Proximity and Soil Chemistry Shape rRNA, but Not DNA, Communities of Symbiotic and Free-Living Soil Fungi in a Mixed Hardwood-Conifer Forest

Host and symbiont diversity are inextricably linked across partnerships and ecosystems, with degree of partner reliance governing the strength of this correlation. In many forest soils, symbiotic ectomycorrhizal fungi coexist and compete with free-living saprotrophic fungi, with the outcomes of these interactions shaping resource availability and competitive outcomes for the trees aboveground. Traditional approaches to characterizing these communities rely on DNA sequencing of a ribosomal precursor RNA gene (the internal transcribed spacer region), but directly sequencing the precursor rRNA may provide a more functionally relevant perspective on the potentially active fungal communities. Here, we map ectomycorrhizal and saprotrophic soil fungal communities through a mixed hardwood-conifer forest to assess how above- and belowground diversity linkages compare across these differently adapted guilds. Using highly spatially resolved transects (sampled every 2 m) and well-mapped stands of varying host tree diversity, we sought to understand the relative influence of symbiosis versus environment in predicting fungal diversity measures. Canopy species in this forest included two oaks (Quercus agrifolia and Quercus douglasii) and one pine (Pinus sabiniana). At the scale of our study, spatial turnover in rRNA-based communities was much more predictable from measurable environmental attributes than DNA-based communities. And while turnover of ectomycorrhizal fungi and saprotrophs were predictable by the presence and abundance of different canopy species, they both responded strongly to soil nutrient characteristics, namely pH and nitrogen availability, highlighting the niche overlap of these coexisting guilds and the strong influence of aboveground plants on belowground fungal communities.

Management After Windstorm Affects the Composition of Ectomycorrhizal Symbionts of Regenerating Trees but Not Their Mycorrhizal Networks

Due to ongoing climate change, forests are expected to face significant disturbances more frequently than in the past. Appropriate management is intended to facilitate forest regeneration. Because European temperate forests mostly consist of trees associated with ectomycorrhizal (ECM) fungi, understanding their role in these disturbances is important to develop strategies to minimize their consequences and effectively restore forests. Our aim was to determine how traditional (EXT) and nonintervention (NEX) management in originally Norway spruce (Picea abies) forests with an admixture of European larch (Larix decidua) affect ECM fungal communities and the potential to interconnect different tree species via ECM networks 15 years after a windstorm. Ten plots in NEX and 10 plots in EXT with the co-occurrences of Norway spruce, European larch, and silver birch (Betula pendula) were selected, and a total of 57 ECM taxa were identified using ITS sequencing from ECM root tips. In both treatments, five ECM species associated with all the studied tree species dominated, with a total abundance of approximately 50% in the examined root samples. Because there were no significant differences between treatments in the number of ECM species associated with different tree species combinations in individual plots, we concluded that the management type did not have a significant effect on networking. However, management significantly affected the compositions of ECM symbionts of Norway spruce and European larch but not those of silver birch. Although this result is explained by the occurrence of seedlings and ECM propagules that were present in the original forest, the consequences are difficult to assess without knowledge of the ecology of different ECM symbionts.

Effects of Field Fumigation and Inoculation With the Pecan Truffle (Tuber lyonii) on the Fungal Community of Pecan (Carya illinoinensis) Seedlings Over 5 Years

Truffle fungi are esteemed for their aromatic qualities and are among the most widely cultivated edible ectomycorrhizal fungi. Here we document a successful method for establishing Tuber lyonii, the pecan truffle, on pecan (Carya illinoinensis) seedlings in a field setting. We assessed the impacts of soil fumigation and varying concentrations of truffle spore inoculum on the ectomycorrhizal fungal and the complete fungal communities as well as the colonization of T. lyonii on pecan roots at three nurseries in Georgia, United States. To identify fungal communities on pecan seedlings, we performed high-throughput amplicon sequencing of the fungal ITS1 rDNA region. Our 5-year long field experiment demonstrates that fumigation and inoculation together resulted in the highest persistence of T. lyonii on pecan roots. While fungal OTU numbers fluctuated over the years of our experiments, there was no statistical support to demonstrate diversification of communities when Shannon diversity metrics were used. However, we did find that older seedlings were less likely to be dominated by T. lyonii compared to younger ones, suggesting successional changes in the fungal community over time. This suggests that transplanting inoculated seedlings after 2 or 3 years post-inoculation is optimal for future truffle propagation efforts. Our results demonstrate that T. lyonii can be established in situ with methods that are compatible with current pecan nursery industry practices and that fungal communities on pecan seedlings vary depending on the experimental treatments used during planting. While the pecan truffle is not yet widely cultivated, our results provide insights for future large-scale cultivation of this and perhaps other Tuber species.

Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities

Fungi form diverse communities and play essential roles in many terrestrial ecosystems, yet there are methodological challenges in taxonomic and phylogenetic placement of fungi from environmental sequences. To address such challenges, we investigated spatiotemporal structure of a fungal community using soil metabarcoding with four different sequencing strategies: short-amplicon sequencing of the ITS2 region (300-400 bp) with Illumina MiSeq, Ion Torrent Ion S5 and PacBio RS II, all from the same PCR library, as well as long-amplicon sequencing of the full ITS and partial LSU regions (1200-1600 bp) with PacBio RS II. Resulting community structure and diversity depended more on statistical method than sequencing technology. The use of long-amplicon sequencing enables construction of a phylogenetic tree from metabarcoding reads, which facilitates taxonomic identification of sequences. However, long reads present issues for denoising algorithms in diverse communities. We present a solution that splits the reads into shorter homologous regions prior to denoising, and then reconstructs the full denoised reads. In the choice between short and long amplicons, we suggest a hybrid approach using short amplicons for sampling breadth and depth, and long amplicons to characterize the local species pool for improved identification and phylogenetic analyses.

A non-linear effect of the spatial structure of the soil ectomycorrhizal spore bank on the performance of pine seedlings

The spatial structure of the environment is known to affect ecological processes. Unlike the spatial structure of negative interactions, such as competition and predation, the role of spatial structure in positive interaction has received less attention. We tested how the spatial structure of spores of ectomycorrhizal fungi (EMF) in the soil affects the growth of Aleppo pine (Pinus halepensis) seedlings. Spores were spatially distributed at four different levels of patchiness (1 patch, 4 patches, 8 patches and complete mixing) in 4 L pots (all pots received the same total amount of spores). Based on previous findings, we hypothesized that plant performance would gradually increase from the single patch treatment to the complete mixing. However, we found a non-linear response to patchiness. Specifically, plants were largest in the single patch and complete mixing while those in the 4 and 8 patch treatments were the smallest. This non-monotonic response, which might be the result of spatially determined colonization timing or community composition, suggests that the spatial structure of EMF spores has a complex effect on seedling growth.

Location, but not defensive genotype, determines ectomycorrhizal community composition in Scots pine (Pinus sylvestris L.) seedlings

For successful colonization of host roots, ectomycorrhizal (EM) fungi must overcome host defense systems, and defensive phenotypes have previously been shown to affect the community composition of EM fungi associated with hosts. Secondary metabolites, such as terpenes, form a core part of these defense systems, but it is not yet understood whether variation in these constitutive defenses can result in variation in the colonization of hosts by specific fungal species.We planted seedlings from twelve maternal families of Scots pine (Pinus sylvestris) of known terpene genotype reciprocally in the field in each of six sites. After 3 months, we characterized the mycorrhizal fungal community of each seedling using a combination of morphological categorization and molecular barcoding, and assessed the terpene chemodiversity for a subset of the seedlings. We examined whether parental genotype or terpene chemodiversity affected the diversity or composition of a seedling's mycorrhizal community.While we found that terpene chemodiversity was highly heritable, we found no evidence that parental defensive genotype or a seedling's terpene chemodiversity affected associations with EM fungi. Instead, we found that the location of seedlings, both within and among sites, was the only determinant of the diversity and makeup of EM communities.These results show that while EM community composition varies within Scotland at both large and small scales, variation in constitutive defensive compounds does not determine the EM communities of closely cohabiting pine seedlings. Patchy distributions of EM fungi at small scales may render any genetic variation in associations with different species unrealizable in field conditions. The case for selection on traits mediating associations with specific fungal species may thus be overstated, at least in seedlings.

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.

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.

The dominance of Suillus species in ectomycorrhizal fungal communities on Larix gmelinii in a post-fire forest in the Russian Far East

Wildfires can negatively affect ectomycorrhizal (EM) fungal communities. However, potential shifts in community structures due to wildfires have rarely been evaluated in the forests of eastern Eurasia, where surface fires are frequent. We investigated EM fungal communities in a Larix gmelinii-dominated forest that burned in 2003 in Zeya, in the Russian Far East. A total of 120 soil samples were collected from burned and adjacent unburned forest sites. The EM fungal root tips were morphotyped and internal transcribed spacer (ITS) sequences were obtained for fungal identification. We detected 147 EM fungal operational taxonomic units, and EM fungal richness was 25% lower at the burned site than at the unburned site. EM fungal composition was characterized by the occurrence of disturbance-adapted fungi (Amphinema and Wilcoxina) at the burned site and late-successional fungi (Lactarius, Russula and Cortinarius) at the unburned site. These findings suggest that the EM fungal communities did not recover to pre-fire levels 16 years after the fire. Suillus species were the dominant EM fungi on L. gmelinii, with greater richness and frequency at the burned site. Both Larix and Suillus exhibit adaptive traits to quickly colonize fire-disturbed habitats. Frequent surface fires common to eastern Eurasia are likely to play important roles in maintaining Larix forests, concomitantly with their closely associated EM fungi.

Abundant fungi adapt to broader environmental gradients than rare fungi in agricultural fields

Soil communities are intricately linked to ecosystem functioning, and a predictive understanding of how communities assemble in response to environmental change is of great ecological importance. Little is known about the assembly processes governing abundant and rare fungal communities across agro-ecosystems, particularly with regard to their environmental adaptation. By considering abundant and rare taxa, we tested the environmental thresholds and phylogenetic signals for ecological preferences of fungal communities across complex environmental gradients to reflect their environmental adaptation, and explored the factors influencing their assembly based on the large-scale soil survey in agricultural fields across eastern China. We found that the abundant taxa exhibited remarkably broader response thresholds and stronger phylogenetic signals for the ecological preferences across environmental gradients compared to the rare taxa. Neutral processes played a key role in shaping the abundant subcommunity compared to the rare subcommunity. Null model analysis revealed that the abundant subcommunity was less clustered phylogenetically and governed primarily by dispersal limitation, while homogeneous selection was the major assembly process in the rare subcommunity. Soil available sulfur was the major factor mediating the balance between stochastic and deterministic processes of both the abundant and rare subcommunities, as indicated by an increase in stochasticity with higher available sulfur concentration. Based on macroecological spatial scale datasets, our study revealed the potential broader environmental adaptation of abundant fungal taxa compared to rare fungal taxa, and identified the factors mediating their distinct community assembly processes in agricultural fields. These results contribute to our understanding of the mechanisms underlying the generation and maintenance of fungal diversity in response to global environmental change.

In vitro evidence of root colonization suggests ecological versatility in the genus Mycena

The root-associated habit has evolved on numerous occasions in different fungal lineages, suggesting a strong evolutionary pressure for saprotrophic fungi to switch to symbiotic associations with plants. Species within the ubiquitous, saprotrophic genus Mycena are frequently major components in molecular studies of root-associated fungal communities, suggesting that an evaluation of their trophic status is warranted. Here, we report on interactions between a range of Mycena species and the plant Betula pendula. In all, 17 Mycena species were inoculated onto B. pendula seedlings. Physical interactions between hyphae and fine roots were examined using differential staining and fluorescence microscopy. Physiological interactions were investigated using ¹⁴ C and ³² P to show potential transfer between symbionts. All Mycena species associated closely with fine roots, showing hyphal penetration into the roots, which in some cases were intracellular. Seven species formed mantle-like structures around root tips, but none formed a Hartig net. Mycena pura and Mycena galopus both enhanced seedling growth, with M. pura showing significant transfer of ³² P to the seedlings. Our results support the view that several Mycena species can associate closely with plant roots and some may potentially occupy a transitional state between saprotrophy and biotrophy.

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.

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.

Notes, outline and divergence times of Basidiomycota

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

JF. Large-scale insect outbreak homogenizes the spatial structure of ectomycorrhizal fungal communities

Ectomycorrhizal fungi (plant symbionts) are diverse and exist within spatially variable communities that play fundamental roles in the functioning of terrestrial ecosystems. However, the underlying ecological mechanisms that maintain and regulate the spatial structuring of ectomycorrhizal fungal communities are both complex and remain poorly understood. Here, we use a gradient of mountain pine beetle (Dendroctonus ponderosae) induced tree mortality across eleven stands in lodgepole pine (Pinus contorta) forests of western Canada to investigate: (i) the degree to which spatial structure varies within this fungal group, and (ii) how these patterns may be driven by the relative importance of tree mortality from changes in understory plant diversity, productivity and fine root biomass following tree death. We found that the homogeneity of the ectomycorrhizal fungal community increased with increasing tree death, aboveground understory productivity and diversity. Whereas, the independent effect of fine root biomass, which declined along the same gradient of tree mortality, increased the heterogeneity of the ectomycorrhizal fungal community. Together, our results demonstrate that large-scale biotic disturbance homogenizes the spatial patterns of ectomycorrhizal fungal communities.

Context dependency, co-introductions, novel mutualisms, and host shifts shaped the ectomycorrhizal fungal communities of the alien tree Eucalyptus globulus

The identity and relevance of the ectomycorrhizal (ECM) fungal partners of Eucalyptus globulus was investigated in NW Spain, to detect which symbionts mainly support its invasiveness. Root tips of E. globulus and of three common native plant species (Quercus robur, Pinus pinaster and Halimium lasianthum) were collected in eucalypt plantations, Q. robur forests, P. pinaster plantations and shrublands. Fungal taxonomical identity was ascertained by use of rDNA and direct sequencing. We studied diversity, composition and colonization rate of the ECM fungal communities of E. globulus to determine if fungal assemblages are host specific (i.e. similar in different habitats) or more dependent on the neighbourhood context. We also identified the type of associations formed (i.e. co-introductions, familiar or novel associations). Twenty-six ECM taxa were associated with E. globulus. Most of them engaged in novel associations with eucalypts, whereas only three fungal species were co-introduced Australian aliens. Eucalypt fungal richness, diversity and colonization rate differed between habitats, being higher in native oak forests, whereas in shrublands E. globulus showed the lowest colonization rate and diversity. The Australian fungus Descolea maculata dominated the eucalypt fungal assemblage and also spread to the native host plants, in all the habitats, posing the risk of further co-invasion.

A single ectomycorrhizal plant root system includes a diverse and spatially structured fungal community

Although only a relatively small proportion of plant species form ectomycorrhizae with fungi, it is crucial for growth and survival for a number of widespread woody plant species. Few studies have attempted to investigate the fine scale spatial structure of entire root systems of adult ectomycorrhizal (EcM) plants. Here, we use the herbaceous perennial Bistorta vivipara to map the entire root system of an adult EcM plant and investigate the spatial structure of its root-associated fungi. All EcM root tips were sampled, mapped and identified using a direct PCR approach and Sanger sequencing of the internal transcribed spacer region. A total of 32.1% of all sampled root tips (739 of 2302) were successfully sequenced and clustered into 41 operational taxonomic units (OTUs). We observed a clear spatial structuring of the root-associated fungi within the root system. Clusters of individual OTUs were observed in the younger parts of the root system, consistent with observations of priority effects in previous studies, but were absent from the older parts of the root system. This may suggest a succession and fragmentation of the root-associated fungi even at a very fine scale, where competition likely comes into play at different successional stages within the root system.

The effects of co-colonising ectomycorrhizal fungi on mycorrhizal colonisation and sporocarp formation in Laccaria japonica colonising seedlings of Pinus densiflora

Forest trees are colonised by different species of ectomycorrhizal (ECM) fungi that interact competitively or mutualistically with one another. Most ECM fungi can produce sporocarps. To date, the effects of co-colonising fungal species on sporocarp formation in ECM fungi remain unknown. In this study, we examined host plant growth, mycorrhizal colonisation, and sporocarp formation when roots of Pinus densiflora are colonised by Laccaria japonica and three other ECM fungal species (Cenococcum geophilum, Pisolithus sp., and Suillus luteus). Sporocarp numbers were recorded throughout the experimental period. The biomass, photosynthetic rate, and mycorrhizal colonisation rate of the seedlings were also measured at 45 days, 62 days, and 1 year after seedlings were transplanted. Results indicated that C. geophilum and S. luteus may negatively impact mycorrhizal colonisation and sporocarp formation in L. japonica. Sporocarp formation in L. japonica was positively correlated with conspecific mycorrhizal colonisation but negatively correlated with the biomass of seedlings of P. densiflora. The co-occurring ECM fungi largely competed with L. japonica, resulting in various effects on mycorrhizal colonisation and sporocarp formation in L. japonica. A variety of mechanisms may be involved in the competitive interactions among the different ECM fungal species, including abilities to more rapidly colonise root tips, acquire soil nutrients, or produce antibiotics. These mechanisms need to be confirmed in further studies.

Diversity and taxonomy of Tricholoma species from Yunnan, China, and notes on species from Europe and North America

Although taxonomic knowledge on Tricholoma (Agaricales, Basidiomycota) is fairly comprehensive in northwest Europe, knowledge of the global diversity and distribution of Tricholoma spp. is still sparse. In this study, the diversity and distribution of some Tricholoma spp. are analyzed by morphological and molecular methods based on 70 collections from Yunnan, China, 45 from central Europe, 32 from Colorado, USA, 9 from Japan, and 3 from Ukraine. A Holarctic distribution is suggested for several species, based on collections and nuc rDNA internal transcribed spacer ITS1-5.8S-ITS2 (ITS) sequences. Six species new to science are formally described from Yunnan: five in existing sections, Tricholoma forteflavescens, T. olivaceoluteolum, T. melleum, T. olivaceum, and T. sinoportentosum, and one, T. muscarioides, in the newly described section Muscaria alongside several previously described species. Additional putatively new species cannot be formally described because they lack sufficient material. Tricholoma foliicola is recognized as a species of the genus Gerhardtia.

Host Phylogeny Is a Major Determinant of Fagaceae-Associated Ectomycorrhizal Fungal Community Assembly at a Regional Scale

Environmental filtering (niche process) and dispersal limitation (neutral process) are two of the primary forces driving community assembly in ecosystems, but how these processes affect the Fagaceae-associated ectomycorrhizal (EM) fungal community at regional scales is so far poorly documented. We examined the EM fungal communities of 61 plant species in six genera belonging to the Fagaceae distributed across Chinese forest ecosystems (geographic distance up to ∼3,757 km) using Illumina Miseq sequencing of ITS2 sequences. The relative effects of environmental filtering (e.g., host plant phylogeny, soil and climate) and dispersal limitation (e.g., spatial distance) on the EM fungal community were distinguished using multiple models. In total, 2,706 operational taxonomic units (OTUs) of EM fungi, corresponding to 54 fungal lineages, were recovered at a 97% sequence similarity level. The EM fungal OTU richness was significantly affected by soil pH and nutrients and by host phylogeny. The EM fungal community composition was significantly influenced by combinations of host phylogeny, spatial distance, soil and climate. Furthermore, host phylogeny had the greatest effect on EM fungal community. The study suggests that the assembly of the EM fungal community is governed by both environmental filtering and dispersal limitation, with host effect being the most important determinant at the regional scale.

Adaptive root foraging strategies along a boreal-temperate forest gradient

The tree root-mycorhizosphere plays a key role in resource uptake, but also in the adaptation of forests to changing environments. The adaptive foraging mechanisms of ectomycorrhizal (EcM) and fine roots of Picea abies, Pinus sylvestris and Betula pendula were evaluated along a gradient from temperate to subarctic boreal forest (38 sites between latitudes 48°N and 69°N) in Europe. Variables describing tree resource uptake structures and processes (absorptive fine root biomass and morphology, nitrogen (N) concentration in absorptive roots, extramatrical mycelium (EMM) biomass, community structure of root-associated EcM fungi, soil and rhizosphere bacteria) were used to analyse relationships between root system functional traits and climate, soil and stand characteristics. Absorptive fine root biomass per stand basal area increased significantly from temperate to boreal forests, coinciding with longer and thinner root tips with higher tissue density, smaller EMM biomass per root length and a shift in soil microbial community structure. The soil carbon (C) : N ratio was found to explain most of the variability in absorptive fine root and EMM biomass, root tissue density, N concentration and rhizosphere bacterial community structure. We suggest a concept of absorptive fine root foraging strategies involving both qualitative and quantitative changes in the root-mycorrhiza-bacteria continuum along climate and soil C : N gradients.

Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera

BACKGROUND

Within the root endosphere, fungi are known to be important for plant nutrition and resistance to stresses. However, description and understanding of the rules governing community assembly in the fungal fraction of the plant microbiome remains scarce.

METHODS

We used an innovative DNA- and RNA-based analysis of co-extracted nucleic acids to reveal the complexity of the fungal community colonizing the roots of an Agrostis stolonifera population. The normalized RNA/DNA ratio, designated the 'mean expression ratio', was used as a functional trait proxy. The link between this trait and phylogenetic relatedness was measured using the Blomberg's K statistic.

RESULTS

Fungal communities were highly diverse. Only ∼1.5% of the 635 OTUs detected were shared by all individuals, however these accounted for 33% of the sequence number. The endophytic fungal communities in plant roots exhibit phylogenetic clustering that can be explained by a plant host effect acting as environmental filter. The 'mean expression ratio' displayed significant but divergent phylogenetic signals between fungal phyla.

DISCUSSION

These results suggest that environmental filtering by the host plant favours the co-existence of related and similar OTUs within the Basidiomycota community assembly, whereas the Ascomycota and Glomeromycota communities seem to be impacted by competitive interactions which promote the co-existence of phylogenetically related but ecologically dissimilar OTUs.

Local-scale spatial structure and community composition of orchid mycorrhizal fungi in semi-natural grasslands

Orchid mycorrhizal (OrM) fungi play a crucial role in the ontogeny of orchids, yet little is known about how the structure of OrM fungal communities varies with space and environmental factors. Previous studies suggest that within orchid patches, the distance to adult orchids may affect the abundance of OrM fungi. Many orchid species grow in species-rich temperate semi-natural grasslands, the persistence of which depends on moderate physical disturbances, such as grazing and mowing. The aim of this study was to test whether the diversity, structure and composition of OrM fungal community are influenced by the orchid patches and management intensity in semi-natural grasslands. We detected putative OrM fungi from 0 to 32 m away from the patches of host orchid species (Orchis militaris and Platanthera chlorantha) in 21 semi-natural calcareous grasslands using pyrosequencing. In addition, we assessed different ecological conditions in semi-natural grasslands but primarily focused on the effect of grazing intensity on OrM fungal communities in soil. We found that investigated orchid species were mostly associated with Ceratobasidiaceae and Tulasnellaceae and, to a lesser extent, with Sebacinales. Of all the examined factors, the intensity of grazing explained the largest proportion of variation in OrM fungal as well as total fungal community composition in soil. Spatial analyses showed limited evidence for spatial clustering of OrM fungi and their dependence on host orchids. Our results indicate that habitat management can shape OrM fungal communities, and the spatial distribution of these fungi appears to be weakly structured outside the orchid patches.

Phylogenetic and functional traits of ectomycorrhizal assemblages in top soil from different biogeographic regions and forest types

Ectomycorrhizal (EM) fungal taxonomic, phylogenetic, and trait diversity (exploration types) were analyzed in beech and conifer forests along a north-to-south gradient in three biogeographic regions in Germany. The taxonomic community structures of the ectomycorrhizal assemblages in top soil were influenced by stand density and forest type, by biogeographic environmental factors (soil physical properties, temperature, and precipitation), and by nitrogen forms (amino acids, ammonium, and nitrate). While α-diversity did not differ between forest types, β-diversity increased, leading to higher γ-diversity on the landscape level when both forest types were present. The highest taxonomic diversity of EM was found in forests in cool, moist climate on clay and silty soils and the lowest in the forests in warm, dry climate on sandy soils. In the region with higher taxonomic diversity, phylogenetic clustering was found, but not trait clustering. In the warm region, trait clustering occurred despite neutral phylogenetic effects. These results suggest that different forest types and favorable environmental conditions in forests promote high EM species richness in top soil presumably with both high functional diversity and phylogenetic redundancy, while stressful environmental conditions lead to lower species richness and functional redundancy.

Change in soil fungal community structure driven by a decline in ectomycorrhizal fungi following a mountain pine beetle (Dendroctonus ponderosae) outbreak

Western North American landscapes are rapidly being transformed by forest die-off caused by mountain pine beetle (Dendroctonus ponderosae), with implications for plant and soil communities. The mechanisms that drive changes in soil community structure, particularly for the highly prevalent ectomycorrhizal fungi in pine forests, are complex and intertwined. Critical to enhancing understanding will be disentangling the relative importance of host tree mortality from changes in soil chemistry following tree death. Here, we used a recent bark beetle outbreak in lodgepole pine (Pinus contorta) forests of western Canada to test whether the effects of tree mortality altered the richness and composition of belowground fungal communities, including ectomycorrhizal and saprotrophic fungi. We also determined the effects of environmental factors (i.e. soil nutrients, moisture, and phenolics) and geographical distance, both of which can influence the richness and composition of soil fungi. The richness of both groups of soil fungi declined and the overall composition was altered by beetle-induced tree mortality. Soil nutrients, soil phenolics and geographical distance influenced the community structure of soil fungi; however, the relative importance of these factors differed between ectomycorrhizal and saprotrophic fungi. The independent effects of tree mortality, soil phenolics and geographical distance influenced the community composition of ectomycorrhizal fungi, while the community composition of saprotrophic fungi was weakly but significantly correlated with the geographical distance of plots. Taken together, our results indicate that both deterministic and stochastic processes structure soil fungal communities following landscape-scale insect outbreaks and reflect the independent roles tree mortality, soil chemistry and geographical distance play in regulating the community composition of soil fungi.

An assessment of ectomycorrhizal fungal communities in Tasmanian temperate high-altitude Eucalyptus delegatensis forest reveals a dominance of the Cortinariaceae

Fungal diversity of Australian eucalypt forests remains underexplored. We investigated the ectomycorrhizal (EcM) fungal community characteristics of declining temperate eucalypt forests in Tasmania. Within this context, we explored the diversity of EcM fungi of two forest types in the northern highlands in the east and west of the island. We hypothesised that EcM fungal community richness and composition would differ between forest type but that the Cortinariaceae would be the dominant family irrespective of forest type. We proposed that EcM richness would be greater in the wet sclerophyll forest than the dry sclerophyll forest type. Using both sporocarps and EcM fungi from root tips amplified by PCR and sequenced in the rDNA ITS region, 175 EcM operational taxonomic units were identified of which 97 belonged to the Cortinariaceae. The Cortinariaceae were the most diverse family, in both the above and below ground communities. Three distinct fungal assemblages occurred within the wet and dry sclerophyll forest types and two geographic regions that were studied, although this pattern did not remain when only the root tip data were analysed. EcM sporocarp richness was unusually higher than root tip richness and EcM richness did not significantly differ among forest types. The results are discussed in relation to the importance of the Cortinariaceae and the drivers of EcM fungal community composition within these forests.

Competition-function tradeoffs in ectomycorrhizal fungi

Background. The extent to which ectomycorrhizal fungi mediate primary production, carbon storage, and nutrient remineralization in terrestrial ecosystems depends upon fungal community composition. However, the factors that govern community composition at the root system scale are not well understood. Here, we explore a potential tradeoff between ectomycorrhizal fungal competitive ability and enzymatic function. Methods. We grew Pinus muricata (Bishop Pine) seedlings in association with ectomycorrhizal fungi from three different genera in a fully factorial experimental design. We measured seedling growth responses, ectomycorrhizal abundance, and the root tip activity of five different extracellular enzymes involved in the mobilization of carbon and phosphorus. Results. We found an inverse relationship between competitiveness, quantified based on relative colonization levels, and enzymatic activity. Specifically, Thelephora terrestris, the dominant fungus, had the lowest enzyme activity levels, while Suillus pungens, the least dominant fungus, had the highest. Discussion. Our results identify a tradeoff between competition and function in ectomycorrhizal fungi, perhaps mediated by the competing energetic demands associated with competitive interactions and enzymatic production. These data suggest that mechanisms such as active partner maintenance by host trees may be important to maintaining "high-quality" ectomycorrhizal fungal partners in natural systems.

Competition-function tradeoffs in ectomycorrhizal fungi

Background. The extent to which ectomycorrhizal fungi mediate primary production, carbon storage, and nutrient remineralization in terrestrial ecosystems depends upon fungal community composition. However, the factors that govern community composition at the root system scale are not well understood. Here, we explore a potential tradeoff between ectomycorrhizal fungal competitive ability and enzymatic function. Methods. We grew Pinus muricata (Bishop Pine) seedlings in association with ectomycorrhizal fungi from three different genera in a fully factorial experimental design. We measured seedling growth responses, ectomycorrhizal abundance, and the root tip activity of five different extracellular enzymes involved in the mobilization of carbon and phosphorus. Results. We found an inverse relationship between competitiveness, quantified based on relative colonization levels, and enzymatic activity. Specifically, Thelephora terrestris, the dominant fungus, had the lowest enzyme activity levels, while Suillus pungens, the least dominant fungus, had the highest. Discussion. Our results identify a tradeoff between competition and function in ectomycorrhizal fungi, perhaps mediated by the competing energetic demands associated with competitive interactions and enzymatic production. These data suggest that mechanisms such as active partner maintenance by host trees may be important to maintaining "high-quality" ectomycorrhizal fungal partners in natural systems.