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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...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Association for the Advancement of Science 2018
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.
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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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