Climate is a major driver of fungal species distributions and community composition, yet disentangling the effects of climate-mediated changes in dominant vegetation from other climatic effects remains a key challenge. To separate climatic effects mediated by dominant vegetation from other climatic effects on soil fungal communities, we analyzed soil fungal communities from eight European altitudinal gradients including sites with homogeneous and heterogeneous dominant vegetation. We combined community-level analyses with species-level hierarchical modeling to assess how different fungal ecological guilds respond to climate. Our results reveal clear contrasts among fungal ecological guilds. Ectomycorrhizal fungi showed significantly higher community turnover along the climatic gradient than any other group and responded only weakly to changes in dominant vegetation, whereas plant pathogens, root endophytes, and saprotrophic fungi showed consistently stronger responses under heterogeneous vegetation. The realized climatic niche of ectomycorrhizal fungi therefore appears only weakly constrained by dominant vegetation, whereas the distributions of plant pathogens, root endophytes, and saprotrophic fungi are more strongly associated with climate-mediated vegetation change. Together, our findings demonstrate that fungal guilds differ markedly in the pathways through which climate shapes their distributions.

Ericoid mycorrhizal (ErM) fungi play a crucial role across terrestrial ecosystems, forming mutualistic symbiosis with Ericaceae and contributing to soil organic matter dynamics. However, compared to other fungal groups, their biogeography remains unknown. Here, we combined several analytical approaches to analyze a newly compiled, large-scale dataset comprising 39 163 soil samples and more than 13 million ITS rRNA sequences assigned to ErM fungi. Specifically, we asked: What are the global patterns of ErM fungal species richness and relative abundance (out of all fungi) and their predictors, and how is the distribution of ErM fungi associated with soil carbon content at the global scale? We show that ErM fungi reach their highest species richness in very high latitudes. Soil chemistry is a stronger predictor of ErM fungal species richness than climate or ericoid vegetation cover. The relative abundance of ErM fungi is highest in soils with high surface carbon content, supporting their proposed role in soil carbon storage. Furthermore, we predict that climate change will reduce ErM fungal abundance across 38% of the land cover of their current global distribution. Our study shows distinct biogeographic patterns of ErM fungi compared with arbuscular and ectomycorrhizal fungi and indicates the vulnerability of ErM fungi to climate change.

Arbuscular mycorrhizal (AM) fungal taxa differ in their life-history strategies, including their preferential association with intraradical vs extraradical compartments. We introduce the arbuscular mycorrhizal root-soil association index (AMF-RSI), a novel quantitative index describing the relative association of AM fungi with root vs soil compartments, corresponding to the previously proposed rhizophilic and edaphophilic AM fungi. The AMF-RSI was calculated from metabarcoding data compiled in the GlobalAMFungi database using Hierarchical Modeling of Species Communities and was subsequently applied to assess shifts in AM fungal community traits driven by soil disturbance caused by tillage. We assessed 301 AM fungal taxa and found that AMF-RSI was strongly conserved at the genus level. While the majority of AM fungal taxa from families Archaeosporaceae, Diversisporaceae and Paraglomeraceae exhibited preferential association with soil, taxa within Glomeraceae exhibited high variability in edaphophilic vs rhizophilic strategies. AMF-RSI values predicted AM fungal community responses to soil disturbance, with rhizophilic taxa being more prevalent in tilled soils. The AMF-RSI represents a new quantitative trait distinguishing preferential association of AM fungi with intraradical vs extraradical compartments (edaphophilic vs rhizophilic life-history strategies). Applied at the community level, it provides a tool for characterizing shifts in AM fungal communities in response to environmental conditions.

Coniferous forest soils represent a globally important carbon sink, where the microbiome is essential for carbon flux between tree roots, rhizosphere, litter and soil. Soil habitats, such as roots, rhizosphere, bulk soil and litter differ in physicochemical properties and composition of highly specialized microbial communities, whose activity reflects the seasonality of temperature and tree activity of these mid- to high-latitude biomes. Here we present a multi-omic dataset encompassing 160 samples collected from four coniferous forest soil habitats in the Czech Republic and Norway, sampled in early summer, late summer, early winter and late winter that characterize the composition, genomic potential and activity of tree roots and microbiome. For each sample, we provide metabarcoding-based composition of bacterial, fungal and eukaryotic communities, results of shotgun DNA sequencing (metagenomes) and shotgun RNA sequencing (metatranscriptomes) illustrating the functional potential and activity within habitats. This dataset enables analyses of the temporal variation of taxonomic composition, functional potential and transcription across seasons in a temperate and boreal coniferous forest.

Alien trees reshape belowground fungal communities, but the factors governing the balance between mutualists and pathogens remain unclear. We tested whether residence time, mycorrhizal type, and biogeographical origin shape this balance, and whether alien stands differ from native vegetation. We sampled soils beneath 73 alien tree species in 48 chateau parks and native stands. Using ITS2 metabarcoding with guild assignment, we quantified ectomycorrhizal (ECM) and pathogen fungi and analysed predictors with multivariate models and binomial GLMMs, accounting for spatial structure and covariates. Symbiotic fungal community composition varied with origin, phylogenetic group and mycorrhizal type. With increasing residence time, ECM alien trees showed higher ECM fungal richness and relative abundance; whereas, contrary to enemy accumulation expectations, pathogen richness and relative abundance declined. Alien arbuscular mycorrhizal (AM) trees harboured more pathogens than ECM trees. Alien tree assemblages had a lower ECM fungal share, twice the pathogen relative richness, and threefold higher pathogen relative abundance than native assemblages. Residence time and mycorrhizal type are primary filters shaping belowground trajectories of alien trees, with biogeographical origin patterning community composition. Elevated pathogen loads in alien stands highlight spillover risks to neighbouring vegetation, informing risk assessment and monitoring of alien tree plantings.

High-throughput sequencing of the Internal Transcribed Spacer (ITS) regions is the primary method for estimating fungal diversity from environmental DNA. However, reliance solely on ITS markers is complicated by its high variability in sequence length and the presence of multiple variants within a single genome, which can bias diversity estimates. This study compares the performance of the ITS1 and ITS2 molecular markers with five alternative markers targeting protein-coding genes using a defined mock community of 413 fungal species from 32 orders. We show that none of the markers provided a reliable estimate of fungal diversity and two failed to produce sufficient data. While the ITS2 marker showed the highest proportion of individual species detections at 75.3%, a multi-marker approach significantly improved this result. Combining the top three markers (ITS1, ITS2 and elongation factor 1-alpha gene) increased this number to 92.2%. This approach also provided a crucial corrective for relative sequence abundance (RSA) estimates, as combining markers helps to offset the individual biases of each of them resulting in a more balanced picture of the community composition. Although the ITS region remains a cornerstone in fungal metabarcoding studies, we recommend combining both ITS1 and ITS2 markers with at least one alternative DNA marker to achieve more accurate species richness and RSA estimates. The broader application of these alternative markers will depend on the continued development of comprehensive, curated reference databases.

Deadwood fungi are extremely diverse and crucial for carbon turnover in forests. To achieve multifunctional forests, we need to better understand the relationships between diversity, management, and ecosystem processes. We tested the effects of forest structure, i.e. canopy cover and deadwood enrichment, on fungal diversity and mass loss of European beech and Scots pine. We additionally assessed the effects of fungal diversity on mass loss. We expected deadwood enrichment to better explain fungal diversity, while canopy cover, alongside fungal diversity, would best explain mass loss. Overall, host tree species was more important than forest structure in explaining diversity. Beech fungal diversity was higher under closed canopies, while pine fungal diversity increased with some types of deadwood enrichment. Surprisingly, beech mass loss was higher in stands without deadwood enrichment, but also where tree crowns were added. Pine mass loss was not affected by forest structure. Effects of fungal diversity on mass loss were significantly related to fungal community composition in pine. Our findings emphasize the need for diverse tree hosts at the forest landscape-scale. However, contrasting diversity and decomposition effects between host trees indicate that stand-scale management strategies should be tailored to tree species to maintain diversity and decomposition processes.

Soil pollution by heavy metals (HMs) poses a major threat to soil quality and human health, with mining and smelting industries identified as key sources. Soils around smelters are often considered polluted hotspots, being generally unsuitable for agricultural activities. Although many studies have identified microbial taxa able to survive in such environments, most have focused on relatively low HM concentrations. The purpose of the study was to assess the ecological risk and to evaluate the diversity and structural shifts in microbial communities, as well as to predict key metabolic pathways associated with HM resistance in soils near Pb-Zn smelter in Bulgaria. The soils ranged from low-risk to disastrous, with cadmium (Cd) identified as the primary contributor to soil toxicity. High-throughput sequencing of 16S rRNA and ITS amplicons revealed widespread dominance of the phyla Proteobacteria, Actinobacteriota and Acidobacteriota, and Ascomycota, with the prevailing classes Acidobacteriae, Chloroflexia, and Eurotiomycetes, indicating their high tolerance to HMs. Functional predictions suggested enrichment of key pathways in the most polluted soils related to HM resistance, including efflux systems and detoxifying enzymes. These results highlight the necessity of integrating soil microbial indicators into agricultural management strategies to ensure safe food production.

The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiome studies in a standardized and machine-actionable manner. Based on input from 248 researchers spanning 28 countries, we provide detailed guidance, including comparisons with STORMS, and case studies that demonstrate the usage of the STREAMS guidelines. STREAMS, like STORMS, will be a living community resource updated by the Consortium with consensus-building input of the broader community.

Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.

Mycorrhizal fungi are ecosystem engineers that sustain plant life and help regulate Earth's biogeochemical cycles[1-3]. However, in contrast to plants and animals, the global distribution of mycorrhizal fungal biodiversity is largely unknown, which limits our ability to monitor and protect key underground ecosystems[4,5]. Here we trained machine-learning algorithms on a global dataset of 25,000 geolocated soil samples comprising >2.8 billion fungal DNA sequences. We predicted arbuscular mycorrhizal and ectomycorrhizal fungal richness and rarity across terrestrial ecosystems. On the basis of these predictions, we generated high-resolution, global-scale maps and identified key reservoirs of highly diverse and endemic mycorrhizal communities. Intersecting protected areas with mycorrhizal hotspots indicated that less than 10% of predicted mycorrhizal richness hotspots currently exist in protected areas. Our results describe a largely hidden component of Earth's underground ecosystems and can help identify conservation priorities, set monitoring benchmarks and create specific restoration plans and land-management strategies.

Decomposition is a crucial process in terrestrial ecosystems, driving nutrient cycling and carbon storage dynamics. Considering the amount of fungal necromass produced in soils annually, its decomposition represents an important nutrient recycling process. Understanding the decomposition dynamics and associated microbial communities of fungal necromass is essential for elucidating ecosystem functioning, especially in environmentally sensitive regions such as the Arctic tundra, which remain under-explored. In a three-year field experiment conducted in the Svalbard archipelago, we investigated the decomposition of two types of fungal necromass with differing biochemical properties. We studied the decomposition rate, changes in chemical composition, and the succession of fungal and bacterial communities associated with the decaying fungal necromass. We discovered that up to 20% of fungal necromass remained even after three years of decomposition, indicating that the decomposition process was incomplete. Our results indicate the crucial role of Pseudogymnoascus in decomposing low-quality, highly melanized necromass with a high C:N ratio in Arctic soils, underscoring its importance in carbon cycling in the Arctic tundra. Notably, we observed dynamic changes in bacterial communities, with increasing richness over time and a shift from copiotrophic to oligotrophic species specializing in decomposing recalcitrant material. Our study indicates the strong potential that fungal necromass can play in carbon sequestration of arctic soils and reveals the distinct dynamics between rather stable fungal and rapidly changing bacterial communities associated with the decomposing fungal necromass in the Arctic tundra. These findings enhance our understanding of microbial succession during decomposition in extreme environments and highlight the potentially differing roles of fungi and bacteria in these processes.