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Ecosystems across the globe receive elevated inputs of nutrients, but the consequences of this for soil fungal guilds that mediate key ecosystem functions remain unclear. We find that nitrogen and phosphorus addition to 25 grasslands distributed across four continents promotes the relative abundance of fungal pathogens, suppresses mutualists, but does not affect saprotrophs. Structural equation models suggest that responses are often indirect and primarily mediated by nutrient-induced shifts in plant communities. Nutrient addition also reduces co-occurrences within and among fungal guilds, which could have important consequences for belowground interactions. Focusing only on plots that received no nutrient addition, soil properties influence pathogen abundance globally, whereas plant community characteristics influence mutualists, and climate influence saprotrophs. We show consistent, guild-level responses that enhance our ability to predict shifts in soil function related to anthropogenic eutrophication, which can have longer-term consequences for plant communities. Anthropogenic nutrient enrichment may drive shifts in soil microbial communities. Here, the authors analyse nitrogen and phosphorus addition effects on soil fungi in a distributed grassland experiment across four continents, finding promotion of pathogens, suppression of mutualists, and no shifts in saprotrophs.

Root-associated microbes play a key role in plant performance and productivity, making them important players in agroecosystems. So far, very few studies have assessed the impact of different farming systems on the root microbiota and it is still unclear whether agricultural intensification influences the structure and complexity of microbial communities. We investigated the impact of conventional, no-till, and organic farming on wheat root fungal communities using PacBio SMRT sequencing on samples collected from 60 farmlands in Switzerland. Organic farming harbored a much more complex fungal network with significantly higher connectivity than conventional and no-till farming systems. The abundance of keystone taxa was the highest under organic farming where agricultural intensification was the lowest. We also found a strong negative association ( R 2  = 0.366; P  < 0.0001) between agricultural intensification and root fungal network connectivity. The occurrence of keystone taxa was best explained by soil phosphorus levels, bulk density, pH, and mycorrhizal colonization. The majority of keystone taxa are known to form arbuscular mycorrhizal associations with plants and belong to the orders Glomerales , Paraglomerales , and Diversisporales . Supporting this, the abundance of mycorrhizal fungi in roots and soils was also significantly higher under organic farming. To our knowledge, this is the first study to report mycorrhizal keystone taxa for agroecosystems, and we demonstrate that agricultural intensification reduces network complexity and the abundance of keystone taxa in the root microbiome.

Soil microbes comprise a large portion of the genetic diversity on Earth and influence a large number of important ecosystem processes. Increasing atmospheric nitrogen (N) deposition represents a major global change driver; however, it is still debated whether the impacts of N deposition on soil microbial biomass and respiration are ecosystem-type dependent. Moreover, the extent of N deposition impacts on microbial composition remains unclear. Here we conduct a global meta-analysis using 1408 paired observations from 151 studies to evaluate the responses of soil microbial biomass, composition, and function to N addition. We show that nitrogen addition reduced total microbial biomass, bacterial biomass, fungal biomass, biomass carbon, and microbial respiration. Importantly, these negative effects increased with N application rate and experimental duration. Nitrogen addition reduced the fungi to bacteria ratio and the relative abundances of arbuscular mycorrhizal fungi and gram-negative bacteria and increased gram-positive bacteria. Our structural equation modeling showed that the negative effects of N application on soil microbial abundance and composition led to reduced microbial respiration. The effects of N addition were consistent across global terrestrial ecosystems. Our results suggest that atmospheric N deposition negatively affects soil microbial growth, composition, and function across all terrestrial ecosystems, with more pronounced effects with increasing N deposition rate and duration.

The publication of a large number of taxon names at all levels within the arbuscular mycorrhizal fungi (Glomeromycota) has resulted in conflicting systematic schemes and generated considerable confusion among biologists working with these important plant symbionts. A group of biologists with more than a century of collective experience in the systematics of Glomeromycota examined all available molecular–phylogenetic evidence within the framework of phylogenetic hypotheses, incorporating morphological characters when they were congruent. This study is the outcome, wherein the classification of Glomeromycota is revised by rejecting some new names on the grounds that they are founded in error and by synonymizing others that, while validly published, are not evidence-based. The proposed “consensus” will provide a framework for additional original research aimed at clarifying the evolutionary history of this important group of symbiotic fungi.

Arbuscular mycorrhizal fungi are asexual, obligately symbiotic fungi with unique morphology and genomic structure, which occupy a dual niche, that is, the soil and the host root. Consequently, the direct adoption of models for community assembly developed for other organism groups is not evident. In this paper we adapted modern coexistence and assembly theory to arbuscular mycorrhizal fungi. We review research on the elements of community assembly and coexistence of arbuscular mycorrhizal fungi, highlighting recent studies using molecular methods. By addressing several points from the individual to the community level where the application of modern community ecology terms runs into problems when arbuscular mycorrhizal fungi are concerned, we aim to account for these special circumstances from a mycocentric point of view. We suggest that hierarchical spatial structure of arbuscular mycorrhizal fungal communities should be explicitly taken into account in future studies. The conceptual framework we develop here for arbuscular mycorrhizal fungi is also adaptable for other host-associated microbial communities.

Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions 1 , 2 . To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sampling of fungal spores 3 . The vast majority of operational taxonomic units were detected within only one climatic zone, and the spatiotemporal patterns of species richness and community composition were mostly explained by annual mean air temperature. Tropical regions hosted the highest fungal diversity except for lichenized, ericoid mycorrhizal and ectomycorrhizal fungi, which reached their peak diversity in temperate regions. The sensitivity in climatic responses was associated with phylogenetic relatedness, suggesting that large-scale distributions of some fungal groups are partially constrained by their ancestral niche. There was a strong phylogenetic signal in seasonal sensitivity, suggesting that some groups of fungi have retained their ancestral trait of sporulating for only a short period. Overall, our results show that the hyperdiverse kingdom of fungi follows globally highly predictable spatial and temporal dynamics, with seasonality in both species richness and community composition increasing with latitude. Our study reports patterns resembling those described for other major groups of organisms, thus making a major contribution to the long-standing debate on whether organisms with a microbial lifestyle follow the global biodiversity paradigms known for macroorganisms 4 , 5 . Using a globally distributed standardized aerial sampling of fungal spores, we show that the hyperdiverse kingdom of fungi follows globally highly predictable spatial and temporal dynamics, with seasonality in both species richness and community composition increasing with latitude.

Forest management practices often severely affect forest ecosystem functioning. Tree removal by clearcutting is one such practice, producing severe impacts due to the total reduction of primary productivity. Here, we assessed changes to fungal community structure and decomposition activity in the soil, roots and rhizosphere of a Picea abies stand for a 2-year period following clearcutting compared to data from before tree harvest. We found that the termination of photosynthate flow through tree roots into soil is associated with profound changes in soil, both in decomposition processes and fungal community composition. The rhizosphere, representing an active compartment of high enzyme activity and high fungal biomass in the living stand, ceases to exist and starts to resemble bulk soil. Decomposing roots appear to separate from bulk soil and develop into hotspots of decomposition and important fungal biomass pools. We found no support for the involvement of ectomycorrhizal fungi in the decomposition of roots, but we found some evidence that root endophytic fungi may have an important role in the early stages of this process. In soil, activity of extracellular enzymes also decreased in the long term following the end of rhizodeposition by tree roots.

We investigated the interaction between fungal communities of soil and dead wood substrates. For this, we applied molecular species identification and stable isotope tracking to both soil and decaying wood in an unmanaged boreal Norway spruce-dominated stand. Altogether, we recorded 1990 operational taxonomic units, out of which more than 600 were shared by both substrates and 589 were found to exclusively inhabit wood. On average the soil was more species-rich than the decaying wood, but the species richness in dead wood increased monotonically along the decay gradient, reaching the same species richness and community composition as soil in the late stages. Decaying logs at all decay stages locally influenced the fungal communities from soil, some fungal species occurring in soil only under decaying wood. Stable isotope analyses suggest that mycorrhizal species colonising dead wood in the late decay stages actively transfer nitrogen and carbon between soil and host plants. Most importantly, Piloderma sphaerosporum and Tylospora sp. mycorrhizal species were highly abundant in decayed wood. Soil- and wood-inhabiting fungal communities interact at all decay phases of wood that has important implications in fungal community dynamics and thus nutrient transportation.

Findings of immense microbial diversity are at odds with observed functional redundancy, as competitive exclusion should hinder coexistence. Tradeoffs between dispersal and competitive ability could resolve this contradiction, but the extent to which they influence microbial community assembly is unclear. Because fungi influence the biogeochemical cycles upon which life on earth depends, understanding the mechanisms that maintain the richness of their communities is critically important. Here, we focus on ectomycorrhizal fungi, which are microbial plant mutualists that significantly affect global carbon dynamics and the ecology of host plants. Synthesizing theory with a decade of empirical research at our study site, we show that competition–colonization tradeoffs structure diversity in situ and that models calibrated only with empirically derived competition–colonization tradeoffs can accurately predict species–area relationships in this group of key eukaryotic microbes. These findings provide evidence that competition–colonization tradeoffs can sustain the landscape-scale diversity of microbes that compete for a single limiting resource.

Many forests are affected by chronic acid deposition, which can lower soil pH and limit the availability of nutrients such as phosphorus (P), but the response of mycorrhizal fungi to changes in soil pH and P availability and how this affects tree acquisition of nutrients is not well understood. Here, we describe an ecosystem-level manipulation in 72 plots, which increased pH and/or P availability across six forests in Ohio, USA. Two years after treatment initiation, mycorrhizal fungi on roots were examined with molecular techniques, including 454-pyrosequencing. Elevating pH significantly increased arbuscular mycorrhizal (AM) fungal colonization and total fungal biomass, and affected community structure of AM and ectomycorrhizal (EcM) fungi, suggesting that raising soil pH altered both mycorrhizal fungal communities and fungal growth. AM fungal taxa were generally negatively correlated with recalcitrant P pools and soil enzyme activity, whereas EcM fungal taxa displayed variable responses, suggesting that these groups respond differently to P availability. Additionally, the production of extracellular phosphatase enzymes in soil decreased under elevated pH, suggesting a shift in functional activity of soil microbes with pH alteration. Thus, our findings suggest that elevating pH increased soil P availability, which may partly underlie the mycorrhizal fungal responses we observed. Though decades of acidic deposition have contributed to reduce soil pH in forests worldwide, experimentally raising pH changes mycorrhizal fungi colonizing tree roots and alters phosphorus availability. Graphical Abstract Figure. Though decades of acidic deposition have contributed to reduce soil pH in forests worldwide, experimentally raising pH changes mycorrhizal fungi colonizing tree roots and alters phosphorus availability.