Structure and function of the global topsoil microbiome

Mohammad Bahram^{1 2 3}, Falk Hildebrand⁴, Sofia K Forslund^{4 5 6}, Jennifer L Anderson⁷, Nadejda A Soudzilovskaia⁸, Peter M Bodegom⁸, Johan Bengtsson-Palme^{9 10 11}, Sten Anslan^{12 13}, Luis Pedro Coelho⁴, Helery Harend¹², Jaime Huerta-Cepas^{4 14}, Marnix H Medema¹⁵, Mia R Maltz¹⁶, Sunil Mundra¹⁷, Pål Axel Olsson¹⁸, Mari Pent¹², Sergei Põlme¹², Shinichi Sunagawa^{4 19}, Martin Ryberg⁷, Leho Tedersoo²⁰, Peer Bork^{21 22 23}

Affiliations

¹ Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia. bahram@ut.ee.
² Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. bahram@ut.ee.
³ Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden. bahram@ut.ee.
⁴ Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
⁵ Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin and the Max-Delbrück Center, Berlin, Germany.
⁶ Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
⁷ Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
⁸ Environmental Biology Department, Institute of Environmental Sciences, CML, Leiden University, Leiden, The Netherlands.
⁹ Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Göteborg, Göteborg, Sweden.
¹⁰ Centre for Antibiotic Resistance research (CARe), University of Göteborg, Göteborg, Sweden.
¹¹ Wisconsin Institute of Discovery, University of Wisconsin-Madison, Madison, WI, USA.
¹² Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.
¹³ Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany.
¹⁴ Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.
¹⁵ Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
¹⁶ Center for Conservation Biology, University of California, Riverside, Riverside, CA, USA.
¹⁷ Section for Genetics and Evolutionary Biology (Evogene), Department of Biosciences, University of Oslo, Oslo, Norway.
¹⁸ Biodiversity Unit, Department of Biology, Ecology building, Lund University, Lund, Sweden.
¹⁹ Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
²⁰ Natural History Museum, University of Tartu, Tartu, Estonia. leho.tedersoo@ut.ee.
²¹ Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. bork@embl.de.
²² Max Delbrück Centre for Molecular Medicine, Berlin, Germany. bork@embl.de.
²³ Department of Bioinformatics, University of Würzburg, Würzburg, Germany. bork@embl.de.

PMID:30069051
DOI: 10.1038/s41586-018-0386-6

Structure and function of the global topsoil microbiome

Mohammad Bahram et al. Nature.2018 Aug.

.2018 Aug;560(7717):233-237.

doi: 10.1038/s41586-018-0386-6. Epub 2018 Aug 1.

Authors

Affiliations

¹ Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia. bahram@ut.ee.
² Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. bahram@ut.ee.
³ Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden. bahram@ut.ee.
⁴ Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
⁵ Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin and the Max-Delbrück Center, Berlin, Germany.
⁶ Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
⁷ Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
⁸ Environmental Biology Department, Institute of Environmental Sciences, CML, Leiden University, Leiden, The Netherlands.
⁹ Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Göteborg, Göteborg, Sweden.
¹⁰ Centre for Antibiotic Resistance research (CARe), University of Göteborg, Göteborg, Sweden.
¹¹ Wisconsin Institute of Discovery, University of Wisconsin-Madison, Madison, WI, USA.
¹² Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.
¹³ Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany.
¹⁴ Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.
¹⁵ Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
¹⁶ Center for Conservation Biology, University of California, Riverside, Riverside, CA, USA.
¹⁷ Section for Genetics and Evolutionary Biology (Evogene), Department of Biosciences, University of Oslo, Oslo, Norway.
¹⁸ Biodiversity Unit, Department of Biology, Ecology building, Lund University, Lund, Sweden.
¹⁹ Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
²⁰ Natural History Museum, University of Tartu, Tartu, Estonia. leho.tedersoo@ut.ee.
²¹ Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. bork@embl.de.
²² Max Delbrück Centre for Molecular Medicine, Berlin, Germany. bork@embl.de.
²³ Department of Bioinformatics, University of Würzburg, Würzburg, Germany. bork@embl.de.

PMID:30069051
DOI: 10.1038/s41586-018-0386-6

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^1-4. 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.

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Structure and function of the global topsoil microbiome

Affiliations

Structure and function of the global topsoil microbiome

Authors

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Abstract

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LinkOut - more resources

Full Text Sources

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Medical