Structure and function of the global topsoil microbiome.

Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities1-4. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.

Short-term responses of the soil microbiome and its environment indicate an uncertain future of restored peatland forests.

Restoring peatland ecosystems involves significant uncertainty due to complex ecological and socio-economic feedbacks as well as alternative stable ecological states. The primary aim of this study was to investigate to what extent the natural functioning of drainage-affected peat soils can be restored, and to examine role of soil microbiota in this recovery process. To address these questions, a large-scale before-after-control-impact (BACI) experiment was conducted in drained peatland forests in Estonia. The restoration treatments included ditch closure and partial tree cutting to raise the water table and restore stand structure. Soil samples and environmental data were collected before and 3-4 years after the treatments; the samples were subjected to metabarcoding to assess fungal and bacterial communities and analysed for their chemical properties. The study revealed some indicators of a shift toward the reference state (natural mixotrophic bog-forests): the spatial heterogeneity in soil fungi and bacteria increased, as well as the relative abundance of saprotrophic fungi; while nitrogen content in the soil decreased significantly. However, a general stability of other physico-chemical properties (including pH remaining elevated by ca. one unit) and annual fluctuations in the microbiome suggested that soil recovery will remain incomplete and patchy for decades. The main implication is the necessity to manage hydrologically restored peatland forests while explicitly considering an uncertain future and diverse outcomes. This includes their continuous monitoring and the adoption of a precautionary approach to prevent further damage both to these ecosystems and to surrounding intact peatlands.

Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies.

Despite increasing knowledge on host-associated microbiomes, little is known about mechanisms underlying fungus-microbiome interactions. This study aimed to examine the relative importance of host genetic, geographic and environmental variations in structuring fungus-associated microbiomes. We analyzed the taxonomic composition and function of microbiomes inhabiting fungal fruiting-bodies in relation to host genetic variation, soil pH and geographic distance between samples. For this, we sequenced the metagenomes of 40 fruiting-bodies collected from six fairy rings (i.e., genets) of a saprotrophic fungus Marasmius oreades. Our analyses revealed that fine genetic variations between host fungi could strongly affect their associated microbiome, explaining, respectively, 25% and 37% of the variation in microbiome structure and function, whereas geographic distance and soil pH remained of secondary importance. These results, together with the smaller genome size of fungi compared to other eukaryotes, suggest that fruiting-bodies are suitable for further genome-centric studies on host-microbiome interactions.

A trait-based ecological perspective on the soil microbial antibiotic-related genetic machinery.

Antibiotic resistance crisis dictates the need for resistance monitoring and the search for new antibiotics. The development of monitoring protocols is hindered by the great diversity of resistance factors, while the "streetlight effect" denies the possibility of discovering novel drugs based on existing databases. In this study, we address these challenges using high-throughput environmental screening viewed from a trait-based ecological perspective. Through an in-depth analysis of the metagenomes of 658 topsoil samples spanning Europe, we explored the distribution of 241 prokaryotic and fungal genes responsible for producing metabolites with antibiotic properties and 485 antibiotic resistance genes. We analyzed the diversity of these gene collections at different levels and modeled the distribution of each gene across environmental gradients. Our analyses revealed several nonparallel distribution patterns of the genes encoding sequential steps of enzymatic pathways synthesizing large antibiotic groups, pointing to gaps in existing databases and suggesting potential for discovering new analogues of known antibiotics. We show that agricultural activity caused a continental-scale homogenization of microbial antibiotic-related machinery, emphasizing the importance of maintaining indigenous ecosystems within the landscape mosaic. Based on the relationships between the proportion of the genes in the metagenomes with the main predictors (soil pH, land cover type, climate temperature and humidity), we illustrate how the properties of chemical structures dictate the distribution of the genes responsible for their synthesis across environments. With this understanding, we propose general principles to facilitate the discovery of antibiotics, including principally new ones, establish abundance baselines for antibiotic resistance genes, and predict their dissemination.

Bacterial community dynamics across developmental stages of fungal fruiting bodies.

Increasing evidence suggest that bacteria form diverse communities in various eukaryotic hosts, including fungi. However, little is known about their succession and the functional potential at different host development stages. Here we examined the effect of fruiting body parts and developmental stages on the structure and potential function of fungus-associated bacterial communities. Using high-throughput sequencing, we characterized bacterial communities and their associated potential functions in fruiting bodies from ten genera belonging to four major mushroom-forming orders and three different developmental stages of a model host species Cantharellus cibarius. Our results demonstrate that bacterial community structure differs between internal and external parts of the fruiting body but not between inner tissues. The structure of the bacterial communities showed significant variation across fruiting body developmental stages. We provide evidence that certain functional groups, such as those related to nitrogen fixation, persist in fruiting bodies during the maturation, but are replaced by putative parasites/pathogens afterwards. These data suggest that bacterial communities inhabiting fungal fruiting bodies may play important roles in their growth and development.

Fruitbody chemistry underlies the structure of endofungal bacterial communities across fungal guilds and phylogenetic groups.

Eukaryote-associated microbiomes vary across host taxa and environments but the key factors underlying their diversity and structure in fungi are still poorly understood. Here we determined the structure of bacterial communities in fungal fruitbodies in relation to the main chemical characteristics in ectomycorrhizal (EcM) and saprotrophic (SAP) mushrooms as well as in the surrounding soil. Our analyses revealed significant differences in the structure of endofungal bacterial communities across fungal phylogenetic groups and to a lesser extent across fungal guilds. These variations could be partly ascribed to differences in fruitbody chemistry, particularly the carbon-to-nitrogen ratio and pH. Fungal fruitbodies appear to represent nutrient-rich islands that derive their microbiome largely from the underlying continuous soil environment, with a larger overlap of operational taxonomic units observed between SAP fruitbodies and the surrounding soil, compared with EcM fungi. In addition, bacterial taxa involved in the decomposition of organic material were relatively more abundant in SAP fruitbodies, whereas those involved in release of minerals were relatively more enriched in EcM fruitbodies. Such contrasts in patterns and underlying processes of the microbiome structure between SAP and EcM fungi provide further evidence that bacteria can support the functional roles of these fungi in terrestrial ecosystems.

The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics.

Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr.) Kuyper, to classify fungal and bacterial genomic sequences, and obtained a nearly complete fungal genome containing 93% of core eukaryotic genes. Comparative genomics reveals that I. terrigena is more similar to ectomycorrhizal and brown rot fungi than to white rot fungi. The reduction in lignin degradation capacity has been independent from and significantly faster than in closely related ectomycorrhizal clades supporting that ectomycorrhizal symbiosis evolved independently in Inocybe. The microbiome of I. terrigena fruiting-bodies includes bacteria with known symbiotic functions in other fungal and non-fungal host environments, suggesting potential symbiotic functions of these bacteria in fungal tissues regardless of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues for characterizing fungal genomes and microbiome.

Bacterial Communities in Boreal Forest Mushrooms Are Shaped Both by Soil Parameters and Host Identity.

Despite recent advances in understanding the microbiome of eukaryotes, little is known about microbial communities in fungi. Here we investigate the structure of bacterial communities in mushrooms, including common edible ones, with respect to biotic and abiotic factors in the boreal forest. Using a combination of culture-based and Illumina high-throughput sequencing, we characterized the bacterial communities in fruitbodies of fungi from eight genera spanning four orders of the class Agaricomycetes (Basidiomycota). Our results revealed that soil pH followed by fungal identity are the main determinants of the structure of bacterial communities in mushrooms. While almost half of fruitbody bacteria were also detected from soil, the abundance of several bacterial taxa differed considerably between the two environments. The effect of host identity was significant at the fungal genus and order level and could to some extent be ascribed to the distinct bacterial community of the chanterelle, representing Cantharellales-the earliest diverged group of mushroom-forming basidiomycetes. These data suggest that besides the substantial contribution of soil as a major taxa source of bacterial communities in mushrooms, the structure of these communities is also affected by the identity of the host. Thus, bacteria inhabiting fungal fruitbodies may be non-randomly selected from environment based on their symbiotic functions and/or habitat requirements.