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Structure and function of the global topsoil microbiome

Bahram, Mohammad; Hildebrand, Falk; Forslund, Sofia K.; Anderson, Jennifer L.; Soudzilovskaia, Nadejda A.; Bodegom, Peter M.; Bengtsson-Palme, Johan; Anslan, Sten; Coelho, Luis Pedro and Harend, Helery, et al. (2018) In Nature 560(7717). p.233-237
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... (More)

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.

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Nature
volume
560
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7717
pages
5 pages
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Nature Publishing Group
external identifiers
  • scopus:85051166064
ISSN
0028-0836
DOI
10.1038/s41586-018-0386-6
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English
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be55d74e-9729-41d3-bad4-ffeb17608c16
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2018-09-10 11:59:54
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2019-05-26 04:54:20
@article{be55d74e-9729-41d3-bad4-ffeb17608c16,
  abstract     = {<p>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<sup>1–4</sup>. 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.</p>},
  author       = {Bahram, Mohammad and Hildebrand, Falk and Forslund, Sofia K. and Anderson, Jennifer L. and Soudzilovskaia, Nadejda A. and Bodegom, Peter M. and Bengtsson-Palme, Johan and Anslan, Sten and Coelho, Luis Pedro and Harend, Helery and Huerta-Cepas, Jaime and Medema, Marnix H. and Maltz, Mia R. and Mundra, Sunil and Olsson, Pål Axel and Pent, Mari and Põlme, Sergei and Sunagawa, Shinichi and Ryberg, Martin and Tedersoo, Leho and Bork, Peer},
  issn         = {0028-0836},
  language     = {eng},
  month        = {08},
  number       = {7717},
  pages        = {233--237},
  publisher    = {Nature Publishing Group},
  series       = {Nature},
  title        = {Structure and function of the global topsoil microbiome},
  url          = {http://dx.doi.org/10.1038/s41586-018-0386-6},
  volume       = {560},
  year         = {2018},
}