Structure and function of the global topsoil microbiome

Mohammad Bahram (), Falk Hildebrand, Sofia K. Forslund, Jennifer L. Anderson, Nadejda A. Soudzilovskaia, Peter M. Bodegom, Johan Bengtsson-Palme, Sten Anslan, Luis Pedro Coelho, Helery Harend, Jaime Huerta-Cepas, Marnix H. Medema, Mia R. Maltz, Sunil Mundra, Pål Axel Olsson, Mari Pent, Sergei Põlme, Shinichi Sunagawa, Martin Ryberg, Leho Tedersoo () and Peer Bork ()
Additional contact information
Mohammad Bahram: University of Tartu
Falk Hildebrand: European Molecular Biology Laboratory
Sofia K. Forslund: European Molecular Biology Laboratory
Jennifer L. Anderson: Uppsala University
Nadejda A. Soudzilovskaia: CML, Leiden University
Peter M. Bodegom: CML, Leiden University
Johan Bengtsson-Palme: The Sahlgrenska Academy, University of Göteborg
Sten Anslan: University of Tartu
Luis Pedro Coelho: European Molecular Biology Laboratory
Helery Harend: University of Tartu
Jaime Huerta-Cepas: European Molecular Biology Laboratory
Marnix H. Medema: Bioinformatics Group, Wageningen University
Mia R. Maltz: University of California, Riverside
Sunil Mundra: University of Oslo
Pål Axel Olsson: Ecology building, Lund University
Mari Pent: University of Tartu
Sergei Põlme: University of Tartu
Shinichi Sunagawa: European Molecular Biology Laboratory
Martin Ryberg: Uppsala University
Leho Tedersoo: Natural History Museum, University of Tartu
Peer Bork: European Molecular Biology Laboratory

Nature, 2018, vol. 560, issue 7717, 233-237

Abstract: 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 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.

Date: 2018
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DOI: 10.1038/s41586-018-0386-6

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