Tomáš Větrovský

Ultramafic substrates impose severe edaphic stress characterised by metal toxicity, nutrient imbalance, and extreme microclimatic conditions, creating spatially fragmented habitats that can shape evolutionary and ecological dynamics of associated organisms. Together with climatic variation, such factors may also influence the structure of holobiont communities of lichenized fungi. Here we investigated the ultramafic specialist lichen Solenopsora liparina across its entire range. We contextualized its symbiotic associations using calcicolous congeners ( S. candicans and S. cesatii ), as ecological reference taxa representing contrasting substrate-associated lineages within the sampled dataset, to assess how climatic filtering acting within a specialised edaphic niche structures symbiotic partner diversity and composition. Photobionts and endolichenic fungi displayed climate-associated compositional turnover and lineage-level diversity. Variation in the composition of these symbionts was most strongly associated with precipitation during the warmest quarter and, in photobionts, with altitude and temperature seasonality. In photobionts, dominant lineages differed in their relative occurrence among host taxa, whereas low-abundance lineages were broadly shared across samples within the dataset. Despite this turnover, alpha diversity remained generally stable across environmental gradients, indicating that climatic variation most strongly affects community composition rather than within-sample diversity. The results are consistent with a model of mixed host- and substrate- associated symbiont assembly, in which dominant photobiont lineages exhibit host- or substrate-linked preferences, whereas low-abundance associates show weaker specificity and broader ecological overlap across environmental and host contexts. Overall, the findings indicate that climatic factors structure the composition of symbiotic partners without strongly altering their overall diversity, while variation among host taxa is reflected in lineage turnover of dominant symbionts. The persistence of the ultramafic specialist lichen S. liparina thus appears to rely on flexible, compositionally dynamic symbiotic associations shaped by climatic variation within a spatially and edaphically constrained niche, rather than obligate partner specificity. Substrate effects are interpreted here as host-associated lineage patterns rather than independently quantified drivers. More broadly, the results suggest that climatic variation can in some cases strongly influence symbiotic assembly within environmentally extreme and spatially heterogeneous systems. Substrate specialisation provides the ecological context in which such interactions occur. Together, the findings highlight the importance of climatic variation in shaping symbiotic assembly within an edaphically specialised system, emphasizing that patterns associated with host and substrate context are expressed mainly through lineage turnover rather than wholesale community replacement.

Summary: 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.

Summary: 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.

Summary: 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.

The nuclear ribosomal DNA Internal Transcribed Spacer (ITS) region is used as a universal fungal barcode marker, but often lacks a significant DNA barcoding gap between sister taxa. Here we tested the reliability of protein coding low‐copy genes as alternative barcode markers. Mock communities of three unrelated agaric genera (Dermoloma, Hodophilus, and Russula) representing lineages of closely related species were sequenced by the Illumina platform targeting the ITS1, ITS2, the second largest subunit of RNA polymerase II gene (rpb2) and the transcription elongation factor 1‐alpha gene (ef1‐α) regions. Species representation and their relative abundances were similar across all tested barcode regions, despite a lower copy number in protein coding markers. ITS1 and ITS2 required more sophisticated sequence filtering because they produced a high number of chimeric sequences requiring reference‐based chimera removal and had a higher number of sequence variants per species. Although clustering of filtered ITS sequences resulted in an average higher number of correctly clustered units at optimal similarity thresholds, these thresholds varied substantially among genera. Best‐fitted thresholds of low‐copy markers were more consistent across genera but frequently lacked species resolution due to low intraspecific variability. At some thresholds, we observed multiple species lumped together, and at the same time, species split into multiple partial clusters, which should be taken into consideration when assessing the best clustering thresholds and taxonomic identity of clusters. To achieve the best taxonomic resolution and improve species detection, we recommend combining different markers and applying additional reference‐based sorting of clusters. The current availability of rpb2 and ef1‐α reference sequences in public databases is far from being complete for all fungal groups, but a combined marker approach can be used for group‐specific studies that can build reference data for their own purposes.

Fluctuating conditions drive adaptive evolution, yet understanding how genomes evolve under stable conditions over extended periods remains a major challenge, since most research on microbial evolution relies on short-term experiments or phylogenetic comparisons. The Movile Cave, isolated from external influences 5.5 million years, offers a unique opportunity to explore microbial evolution under prolonged environmental stability. Here, we analyzed metagenome-assembled genomes from this cave, revealing that prokaryotes exhibit lower gene diversity and higher levels of pseudogenization compared to those from non-isolated environments, mainly affecting housekeeping functions involved in translation. Functional redundancy across genomes remained comparable to related habitats. Our results suggest that pseudogenization may serve as a fine-tuning mechanism to reduce excess redundancy. Although horizontal gene transfer is limited overall, the cave virome seems to contribute to microbial adaptation through the transfer of auxiliary metabolic genes. Movile microorganisms harbor fewer phage-defense systems than counterparts in related environments, suggesting a long-term adaptation to a relatively stable virosphere. Our findings indicate that prolonged isolation under stable selective pressures does not necessarily lead to major genomic divergence, but rather promotes adaptive gene loss. This study provides key insights into how long-term stability shapes microbial genome evolution and ecosystem function.

Summary: Gradients in species diversity across elevations and latitudes have fascinated biologists for decades. While these gradients have been well documented for macroorganisms, there is limited consensus about their universality, shape and drivers for microorganisms, such as fungi, despite the importance of fungal diversity for ecosystem functions and services. We conducted a comprehensive survey of fungal species richness in forests across 17 elevational transects along a latitudinal gradient covering the continental scale of Europe. Diversity patterns along elevational and latitudinal gradients differed among fungal ecological guilds. Diversity of saprotrophs declined with elevation while ectomycorrhizal (ECM) fungal diversity peaked in mid‐elevations. Moreover, the diversity of root endophytic fungi increased with latitude but did not change with elevation. Bayesian species distribution modeling suggests that fungal diversity is structured by deterministic rather than stochastic drivers. Importantly, ECM fungal diversity pattern persists even after accounting for the effects of environmental conditions. These results suggest that environmental conditions differentially shape the diversity of fungal guilds along elevational and latitudinal gradients, but this goes beyond soil and climatic factors in the case of ECM fungi. This study paves the way toward a better understanding of fungal diversity gradients across elevations and latitudes, with possible implications for macroecological theory, conservation and management.

Summary: Arbuscular mycorrhizal (AM) fungi are crucial mutualistic symbionts of the majority of plant species, with essential roles in plant nutrient uptake and stress mitigation. The importance of AM fungi in ecosystems contrasts with our limited understanding of the patterns of AM fungal biogeography and the environmental factors that drive those patterns. This article presents a release of a newly developed global AM fungal dataset (GlobalAMFungi database, https://globalamfungi.com) that aims to reduce this knowledge gap. It contains almost 50 million observations of Glomeromycotinian AM fungal amplicon DNA sequences across almost 8500 samples with geographical locations and additional metadata obtained from 100 original studies. The GlobalAMFungi database is built on sequencing data originating from AM fungal taxon barcoding regions in: i) the small subunit rRNA (SSU) gene; ii) the internal transcribed spacer 2 (ITS2) region; and iii) the large subunit rRNA (LSU) gene. The GlobalAMFungi database is an open source and open access initiative that compiles the most comprehensive atlas of AM fungal distribution. It is designed as a permanent effort that will be continuously updated by its creators and through the collaboration of the scientific community. This study also documented applicability of the dataset to better understand ecology of AM fungal taxa.