Agronomy for Sustainable Development

, Volume 30, Issue 2, pp 359–365

Biogeography of soil microbial communities: a review and a description of the ongoing french national initiative

Authors

    • UMR Microbiologie du Sol et de l’Environnement, CMSEINRA-Université de Bourgogne
    • Platform GenoSolINRA-Université de Bourgogne, CMSE
  • Samuel Dequiedt
    • UMR Microbiologie du Sol et de l’Environnement, CMSEINRA-Université de Bourgogne
    • Platform GenoSolINRA-Université de Bourgogne, CMSE
  • Claudy Jolivet
    • Unité INFOSOLINRA Orléans — US 1106
  • Nicolas P. A. Saby
    • Unité INFOSOLINRA Orléans — US 1106
  • Jean Thioulouse
    • Université de Lyon
    • Laboratoire de Biométrie et Biologie ÉvolutiveUniversité Lyon 1, CNRS, UMR 5558
  • Jérome Harmand
    • INRA-INRIA MERE research project, UMR ASB
    • LBE-INRAUR050
  • Patrice Loisel
    • INRA-INRIA MERE research project, UMR ASB
  • Alain Rapaport
    • INRA-INRIA MERE research project, UMR ASB
  • Saliou Fall
    • Équipe „Génomique Microbienne Environnementale” (Environmental Microbial Genomics Group), UMR CNRS 5005Laboratoire Ampère, École Centrale de Lyon
  • Pascal Simonet
    • Équipe „Génomique Microbienne Environnementale” (Environmental Microbial Genomics Group), UMR CNRS 5005Laboratoire Ampère, École Centrale de Lyon
  • Richard Joffre
    • Équipe DREAM — Centre d’Écologie Fonctionnelle et ÉvolutiveUMR 5175 CNRS
  • Nicolas Chemidlin-Prévost Bouré
    • UMR Microbiologie du Sol et de l’Environnement, CMSEINRA-Université de Bourgogne
    • Platform GenoSolINRA-Université de Bourgogne, CMSE
  • Pierre-Alain Maron
    • UMR Microbiologie du Sol et de l’Environnement, CMSEINRA-Université de Bourgogne
    • Platform GenoSolINRA-Université de Bourgogne, CMSE
  • Christophe Mougel
    • UMR Microbiologie du Sol et de l’Environnement, CMSEINRA-Université de Bourgogne
    • Platform GenoSolINRA-Université de Bourgogne, CMSE
  • Manuel P. Martin
    • Unité INFOSOLINRA Orléans — US 1106
  • Benoît Toutain
    • Unité INFOSOLINRA Orléans — US 1106
  • Dominique Arrouays
    • Unité INFOSOLINRA Orléans — US 1106
  • Philippe Lemanceau
    • UMR Microbiologie du Sol et de l’Environnement, CMSEINRA-Université de Bourgogne
    • Platform GenoSolINRA-Université de Bourgogne, CMSE
Review article

DOI: 10.1051/agro/2009033

Cite this article as:
Ranjard, L., Dequiedt, S., Jolivet, C. et al. Agronomy for Sustainable Development (2010) 30: 359. doi:10.1051/agro/2009033

Abstract

Microbial biogeography is the study of the distribution of microbial diversity on large scales of space and time. This science aims at understanding biodiversity regulation and its link with ecosystem biological functioning, goods and services such as maintenance of productivity, of soil and atmospheric quality, and of soil health. Although the initial concept dates from the early 20th century (Beijerinck (1913) De infusies en de ontdekking der backterien, in: Jaarboek van de Knoniklijke Akademie van Wetenschappen, Muller, Amsterdam), only recently have an increasing number of studies have investigated the biogeographical patterns of soil microbial diversity. A such delay is due to the constraints of the microbial models, the need to develop relevant molecular and bioinformatic tools to assess microbial diversity, and the non-availability of an adequate sampling strategy. Consequently, the conclusions from microbial ecology studies have rarely been generally applicable and even the fundamental power-laws differ because the taxa-area relationship and the influence of global and distal parameters on the spatial distribution of microbial communities have not been examined. In this article we define and discuss the scientific, technical and operational limits and outcomes resulting from soil microbial biogeography together with the technical and logistical feasibility. The main results are that microbial communities are not stochastically distributed on a wide scale and that biogeographical patterns are more influenced by local parameters such as soil type and land use than by distal ones, e.g. climate and geomorphology, contrary to plants and animals. We then present the European soil biological survey network, focusing on the French national initiative and the „ECOMIC-RMQS” project. The objective of the ECOMIC-RMQS project is to characterise the density and diversity of bacterial communities in all soils in the RMQS library in order to assess, for the first time, not only microbial biogeography across the whole of France but also the impact of land use on soil biodiversity (Réseau de Mesures de la Qualité des Sols = French Soil Quality Monitoring Network, 2200 soils covering all the French territory with a systematic grid of sampling). The scientific, technical and logistical outputs are examined with a view to the future prospects needed to develop this scientific domain and its applications in sustainable land use.

soil biogeographymicrobial communitiessoil surveymicrobial ecologydiversity

Copyright information

© INRA, EDP Sciences 2009