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Biogeography of soil bacteria and archaea across France
Over the last two decades, a considerable effort has been made to decipher the biogeography of soil microbial communities as a whole, from small to broad scales. In contrast, few studies have focused on the taxonomic groups constituting these communities; thus, our knowledge of their ecological attr...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Association for the Advancement of Science
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031370/ https://www.ncbi.nlm.nih.gov/pubmed/29978046 http://dx.doi.org/10.1126/sciadv.aat1808 |
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author | Karimi, Battle Terrat, Sébastien Dequiedt, Samuel Saby, Nicolas P. A. Horrigue, Walid Lelièvre, Mélanie Nowak, Virginie Jolivet, Claudy Arrouays, Dominique Wincker, Patrick Cruaud, Corinne Bispo, Antonio Maron, Pierre-Alain Bouré, Nicolas Chemidlin Prévost Ranjard, Lionel |
author_facet | Karimi, Battle Terrat, Sébastien Dequiedt, Samuel Saby, Nicolas P. A. Horrigue, Walid Lelièvre, Mélanie Nowak, Virginie Jolivet, Claudy Arrouays, Dominique Wincker, Patrick Cruaud, Corinne Bispo, Antonio Maron, Pierre-Alain Bouré, Nicolas Chemidlin Prévost Ranjard, Lionel |
author_sort | Karimi, Battle |
collection | PubMed |
description | Over the last two decades, a considerable effort has been made to decipher the biogeography of soil microbial communities as a whole, from small to broad scales. In contrast, few studies have focused on the taxonomic groups constituting these communities; thus, our knowledge of their ecological attributes and the drivers determining their composition and distribution is limited. We applied a pyrosequencing approach targeting 16S ribosomal RNA (rRNA) genes in soil DNA to a set of 2173 soil samples from France to reach a comprehensive understanding of the spatial distribution of bacteria and archaea and to identify the ecological processes and environmental drivers involved. Taxonomic assignment of the soil 16S rRNA sequences indicated the presence of 32 bacterial phyla or subphyla and 3 archaeal phyla. Twenty of these 35 phyla were cosmopolitan and abundant, with heterogeneous spatial distributions structured in patches ranging from a 43- to 260-km radius. The hierarchy of the main environmental drivers of phyla distribution was soil pH > land management > soil texture > soil nutrients > climate. At a lower taxonomic level, 47 dominant genera belonging to 12 phyla aggregated 62.1% of the sequences. We also showed that the phylum-level distribution can be determined largely by the distribution of the dominant genus or, alternatively, reflect the combined distribution of all of the phylum members. Together, our study demonstrated that soil bacteria and archaea present highly diverse biogeographical patterns on a nationwide scale and that studies based on intensive and systematic sampling on a wide spatial scale provide a promising contribution for elucidating soil biodiversity determinism. |
format | Online Article Text |
id | pubmed-6031370 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | American Association for the Advancement of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-60313702018-07-05 Biogeography of soil bacteria and archaea across France Karimi, Battle Terrat, Sébastien Dequiedt, Samuel Saby, Nicolas P. A. Horrigue, Walid Lelièvre, Mélanie Nowak, Virginie Jolivet, Claudy Arrouays, Dominique Wincker, Patrick Cruaud, Corinne Bispo, Antonio Maron, Pierre-Alain Bouré, Nicolas Chemidlin Prévost Ranjard, Lionel Sci Adv Research Articles Over the last two decades, a considerable effort has been made to decipher the biogeography of soil microbial communities as a whole, from small to broad scales. In contrast, few studies have focused on the taxonomic groups constituting these communities; thus, our knowledge of their ecological attributes and the drivers determining their composition and distribution is limited. We applied a pyrosequencing approach targeting 16S ribosomal RNA (rRNA) genes in soil DNA to a set of 2173 soil samples from France to reach a comprehensive understanding of the spatial distribution of bacteria and archaea and to identify the ecological processes and environmental drivers involved. Taxonomic assignment of the soil 16S rRNA sequences indicated the presence of 32 bacterial phyla or subphyla and 3 archaeal phyla. Twenty of these 35 phyla were cosmopolitan and abundant, with heterogeneous spatial distributions structured in patches ranging from a 43- to 260-km radius. The hierarchy of the main environmental drivers of phyla distribution was soil pH > land management > soil texture > soil nutrients > climate. At a lower taxonomic level, 47 dominant genera belonging to 12 phyla aggregated 62.1% of the sequences. We also showed that the phylum-level distribution can be determined largely by the distribution of the dominant genus or, alternatively, reflect the combined distribution of all of the phylum members. Together, our study demonstrated that soil bacteria and archaea present highly diverse biogeographical patterns on a nationwide scale and that studies based on intensive and systematic sampling on a wide spatial scale provide a promising contribution for elucidating soil biodiversity determinism. American Association for the Advancement of Science 2018-07-04 /pmc/articles/PMC6031370/ /pubmed/29978046 http://dx.doi.org/10.1126/sciadv.aat1808 Text en Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC). http://creativecommons.org/licenses/by-nc/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license (http://creativecommons.org/licenses/by-nc/4.0/) , which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited. |
spellingShingle | Research Articles Karimi, Battle Terrat, Sébastien Dequiedt, Samuel Saby, Nicolas P. A. Horrigue, Walid Lelièvre, Mélanie Nowak, Virginie Jolivet, Claudy Arrouays, Dominique Wincker, Patrick Cruaud, Corinne Bispo, Antonio Maron, Pierre-Alain Bouré, Nicolas Chemidlin Prévost Ranjard, Lionel Biogeography of soil bacteria and archaea across France |
title | Biogeography of soil bacteria and archaea across France |
title_full | Biogeography of soil bacteria and archaea across France |
title_fullStr | Biogeography of soil bacteria and archaea across France |
title_full_unstemmed | Biogeography of soil bacteria and archaea across France |
title_short | Biogeography of soil bacteria and archaea across France |
title_sort | biogeography of soil bacteria and archaea across france |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031370/ https://www.ncbi.nlm.nih.gov/pubmed/29978046 http://dx.doi.org/10.1126/sciadv.aat1808 |
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