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Belowground biota can deeply influence plant invasion. The presence of appropriate soil mutualists can act as a driver to enable plants to colonize new ranges. We reviewed the species of ectomycorrhizal fungi (EMF) that facilitate pine establishment in both native and non-native ranges, and that are associated with their invasion into nonforest settings. We found that one particular group of EMF, suilloid fungi, uniquely drive pine invasion in the absence of other EMF. Although the association with other EMF is variable, suilloid EMF are always associated with invasive pines, particularly at early invasion, when invasive trees are most vulnerable. We identified five main ecological traits of suilloid fungi that may explain their key role at pine invasions: their long-distance dispersal capacity, the establishment of positive biotic interactions with mammals, their capacity to generate a resistant spore bank, their rapid colonization of roots and their long-distance exploration type. These results suggest that the identity of mycorrhizal fungi and their ecological interactions, rather than simply the presence of compatible fungi, are key to the understanding of plant invasion processes and their success or failure. Particularly for pines, their specific association with suilloid fungi determines their invasion success in previously uninvaded ecosystems.

Ectomycorrhizal fungi (EMF) represent one of the major guilds of symbiotic fungi associated with roots of forest trees, where they function to improve plant nutrition and fitness in exchange for plant carbon. Many groups of EMF exhibit preference or specificity for different plant host genera; a good example is the genus Suillus, which grows in association with the conifer family Pinaceae. We investigated genetics of EMF host-specificity by cross-inoculating basidiospores of five species of Suillus onto ten species of Pinus, and screened them for their ability to form ectomycorrhizae. Several Suillus spp. including S. granulatus, S. spraguei, and S. americanus readily formed ectomycorrhizae (compatible reaction) with white pine hosts (subgenus Strobus), but were incompatible with other pine hosts (subgenus Pinus). Metatranscriptomic analysis of inoculated roots reveals that plant and fungus each express unique gene sets during incompatible vs. compatible pairings. The Suillus-Pinus metatranscriptomes utilize highly conserved gene regulatory pathways, including fungal G-protein signaling, secretory pathways, leucine-rich repeat and pathogen resistance proteins that are similar to those associated with host-pathogen interactions in other plant-fungal systems. Metatranscriptomic study of the combined Suillus-Pinus transcriptome has provided new insight into mechanisms of adaptation and coevolution of forest trees with their microbial community, and revealed that genetic regulation of ectomycorrhizal symbiosis utilizes universal gene regulatory pathways used by other types of fungal-plant interactions including pathogenic fungal-host interactions.

Identifying the ecological processes that structure communities and the consequences for ecosystem function is a central goal of ecology. The recognition that fungi, bacteria, and viruses control key ecosystem functions has made microbial communities a major focus of this field. Because many ecological processes are apparent only at particular spatial or temporal scales, a complete understanding of the linkages between microbial community, environment, and function requires analysis across a wide range of scales. Here, we map the biological and functional geography of soil fungi from local to continental scales and show that the principal ecological processes controlling community structure and function operate at different scales. Similar to plants or animals, most soil fungi are endemic to particular bioregions, suggesting that factors operating at large spatial scales, like dispersal limitation or climate, are the first-order determinants of fungal community structure in nature. By contrast, soil extracellular enzyme activity is highly convergent across bioregions and widely differing fungal communities. Instead, soil enzyme activity is correlated with local soil environment and distribution of fungal traits within the community. The lack of structure–function relationships for soil fungal communities at continental scales indicates a high degree of functional redundancy among fungal communities in global biogeochemical cycles.

Host-specific mortality driven by natural enemies is a widely discussed mechanism for explaining plant diversity. In principle, populations of plant species can be regulated by distinct host-specific natural enemies that have weak or nonexistent effects on heterospecific competitors, preventing any single species from becoming dominant and thus promoting diversity. Two of the first steps in exploring the role of natural enemies in diversity regulation are to (1) identify potential enemies and (2) evaluate their levels of host specificity by determining if interactions between any one host and its enemy have equivalent survival impacts on co-occurring host species. We developed a bioinformatics framework to evaluate impacts of potential pathogens on seedling survival, for both single and multiple infections. Importantly, we consider scenarios not only if there are specialist pathogens for each plant, but also when generalist pathogens have differential effects on multiple host species, and when co-infection has species-specific effects. We then applied this analytical framework to a field experiment using molecular techniques to detect potential fungal pathogens on co-occurring tree seedling hosts. Combinatorial complexity created by 160 plant-fungus interactions was reduced to eight combinations that affect seedling survival. Potential fungal pathogens had broad host ranges, but seedling species were each regulated by different combinations of fungi or by generalist fungi that had differential effects on multiple plant species. Soil moisture can have the potential to shift the nature of the interactions in some plant-fungal combinations from neutral to detrimental. Reassessing the assumption of single-enemy-single-host interactions broadens the mechanisms through which natural enemies can influence plant diversity.

Purpose Wildfire, an increasing disturbance in peatlands, could dramatically change carbon stocks and reshape plant/microbial communities, with long-lasting effects on peatland functions. Soil fungi are important in controlling the belowground carbon and nutrient cycling in peatlands; however, the impact of altered fire regimes on these fungi is still unclear. Methods We assessed fungal abundance, composition, and diversity across four soil depths (0–5 cm, 6–10 cm, 11–15 cm, 16–20 cm) under low-severity and high-severity fire in a subtropical peatland in the southeastern USA. Results Low-severity fire significantly increased fungal Shannon diversity and saprotrophic fungi in the 0–5 cm soil layer immediately after fire and then retracted within 2 years. This pattern was not observed below 5 cm soils. The dominant fungal class − Archaeorhizomycetes declined initially and then returned to pre-low-severity fires levels at 0–5 cm depths. Time since low-severity fire was a primary driver of fungal composition in the 0–10 cm soil depth, while spatial distance among sites affected the deeper soils (11–20 cm). The fungal Shannon diversity failed to recover in the unburned state even 30 years after high-severity fire, especially in 6–20 cm soil layers. Stratification patterns of the fungal community were diminished by high-severity fire. Soil properties (either phenolics or carbon) were the primary drivers in shaping fungal community reassembly after high-severity fire across all soil depths. Conclusion Collectively, the fungal communities seem to be highly resilient to low-severity fire, but not to high-severity fire in the shrub-dominated coastal peatlands.

• While there has been significant progress characterizing the ‘symbiotic toolkit’ of ectomycorrhizal (ECM) fungi, how host specificity may be encoded into ECM fungal genomes remains poorly understood. • We conducted a comparative genomic analysis of ECM fungal host specialists and generalists, focusing on the specialist genus Suillus. Global analyses of genome dynamics across 46 species were assessed, along with targeted analyses of three classes of molecules previously identified as important determinants of host specificity: small secreted proteins (SSPs), secondary metabolites (SMs) and G-protein coupled receptors (GPCRs). • Relative to other ECM fungi, including other host specialists, Suillus had highly dynamic genomes including numerous rapidly evolving gene families and many domain expansions and contractions. Targeted analyses supported a role for SMs but not SSPs or GPCRs in Suillus host specificity. Phylogenomic-based ancestral state reconstruction identified Larix as the ancestral host of Suillus, with multiple independent switches between white and red pine hosts. • These results suggest that like other defining characteristics of the ECM lifestyle, host specificity is a dynamic process at the genome level. In the case of Suillus, both SMs and pathways involved in the deactivation of reactive oxygen species appear to be strongly associated with enhanced host specificity.

Soil bacteria regulate wetland biogeochemical processes, yet little is known about controls over their distribution and abundance. Bacteria in North Carolina swamps and bogs differ greatly from Florida Everglades fens, where communities studied were unexpectedly similar along a nutrient enrichment gradient. Bacterial composition and diversity corresponded strongly with soil pH, land use, and restoration status, but less to nutrient concentrations, and not with wetland type or soil carbon. Surprisingly, wetland restoration decreased bacterial diversity, a response opposite to that in terrestrial ecosystems. Community level patterns were underlain by responses of a few taxa, especially the Acidobacteria and Proteobacteria, suggesting promise for bacterial indicators of restoration and trophic status.

The extramatrical mycelia (EMM) of ectomycorrhizal fungi make up a large proportion of the microbial diversity and biomass in temperate forest soils. Thus, their response to elevated CO₂ can have large effects on plant nutrient acquisition and carbon movement through forests. Here, the effects of CO₂ and nitrogen (N) fertilization on EMM biomass and community structure in Pinus taeda forest plots were examined using sand-filled mesh bags buried in the field, the contents of which were analyzed by phospholipid fatty acid (PLFA) and DNA sequencing. A total of 2138 sequences comprising 295 taxa were recovered; most (83.5%) were from ectomycorrhizal fungal taxa. No biomass increase was detected in elevated CO₂ plots relative to control plots, but individual taxa responded to both CO₂ and N fertilization, four of the six most abundant taxa were less frequent in N-fertilized plots. Thelephoroid and athelioid taxa were both frequent and abundant as EMM, and thelephoroid richness was extremely high. Russula and Cortinariaceae taxa were less abundant and boletoid taxa were more abundant as EMM relative to ectomycorrhizas. The EMM community, sampled across seasons and years, was dynamic with a high degree of interspecific variation in response to CO₂ enrichment and N fertilization.

Ecologists have long acknowledged the importance of seed banks; yet, despite the fact that many plants rely on mycorrhizal fungi for survival and growth, the structure of ectomycorrhizal (ECM) fungal spore banks remains poorly understood. The primary goal of this study was to assess the geographic structure in pine‐associated ECM fungal spore banks across the North American continent. Soils were collected from 19 plots in forests across North America. Fresh soils were pyrosequenced for fungal internal transcribed spacer (ITS) amplicons. Adjacent soil cores were dried and bioassayed with pine seedlings, and colonized roots were pyrosequenced to detect resistant propagules of ECM fungi. The results showed that ECM spore banks correlated strongly with biogeographic location, but not with the identity of congeneric plant hosts. Minimal community overlap was found between resident ECM fungi vs those in spore banks, and spore bank assemblages were relatively simple and dominated by Rhizopogon, Wilcoxina, Cenococcum, Thelephora, Tuber, Laccaria and Suillus. Similar to plant seed banks, ECM fungal spore banks are, in general, depauperate, and represent a small and rare subset of the mature forest soil fungal community. Yet, they may be extremely important in fungal colonization after large‐scale disturbances such as clear cuts and forest fires.