Structure and function of the global topsoil microbiome

Abstract

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 communities. 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.

Spatial and temporal turnover of soil microbial communities is not linked to function in a primary tropical forest

“…The species richness of both bacteria and fungi was higher in our study than many other ecosystems (Fierer and Jackson ). Higher diversity may increase resource competition among bacteria and fungi, which can structure communities at both local (e.g., current study) and global scales (Bahram et al ). Finally, variation in bacterial and fungal communities can be related to deterministic niche‐related factors discussed above or to neutral ecological drift occurring because of stochastic birth, death, and growth that often dominates at small spatial scales (Martiny et al ).…”

“…Different aspects of C cycling have been correlated with microbial biomass, presence of specific taxa, or ratios between microbial phyla (Fierer et al , , Waring et al , Clemmensen et al ). These correlations mean that the spatial distributions of microorganisms can be used to describe the spatial array of soil C and nutrient stocks (Averill et al ), which is greatly facilitated by increasingly available data on spatial patterns of microbial abundance (Xu et al ), composition (Kivlin et al , Delgado‐Baquerizo et al ), and function (Margalef et al , Bahram et al ) at global and regional scales (Talbot et al , Wang et al ). However, microbial data are typically based on single time point snapshots and do not consider temporal stability.…”

Long‐read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

“…Although the curating pipeline discarded the majority of CCS reads, many of which might still be of high quality, the 650 OTUs that passed all filtering steps comprised a large and broad diversity of eukaryotes. Almost all major microbial lineages were sampled, from known abundant taxa in soils such as Ciliophora, Cercozoa, Apicomplexa and fungi, to rarer lineages in soil such as the mainly aquatic Bacillariophyceae (diatoms) and Chlorophyta (green algae) (Bahram et al, ; Foissner, ; Geisen, Cornelia, Jörg, & Michael, ; Geisen et al, , ; Mahé et al, ). A few main protist groups lacked new OTUs altogether, including Cryptista, Retaria, Rhodophyceae and Glaucophyta, but these are almost exclusively aquatic and thus less likely to be recovered among soil sequences even if present in the environment at very low abundance (Geisen et al, ; Lallias et al, ; de Vargas et al, ).…”

Relationships between plant diversity and soil microbial diversity vary across taxonomic groups and spatial scales

“…However, studies have revealed inconsistent results. In contrast, with a few exceptions (Bahram et al 2018), most studies find no increase in soil microbial diversity from polar to equatorial regions (Fenchel and Finlay 2004, Fuhrman 2009, Fierer et al 2011, Hendershot et al 2017. In contrast, with a few exceptions (Bahram et al 2018), most studies find no increase in soil microbial diversity from polar to equatorial regions (Fenchel and Finlay 2004, Fuhrman 2009, Fierer et al 2011, Hendershot et al 2017.…”