Review article

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

Lionel Ranjard^1,2*, Samuel Dequiedt^1,2, Claudy Jolivet³, Nicolas P.A. Saby³, Jean Thioulouse⁴, Jérome Harmand^6,7, Patrice Loisel⁶, Alain Rapaport⁶, Saliou Fall⁵, Pascal Simonet⁵, Richard Joffre⁸, Nicolas Chemidlin-Prévost Bouré^1,2, Pierre-Alain Maron^1,2, Christophe Mougel^1,2, Manuel P. Martin³, Benoît Toutain³, Dominique Arrouays³ and Philippe Lemanceau^1,2

¹ INRA-Université de Bourgogne, UMR Microbiologie du Sol et de l’Environnement, CMSE, 17 rue Sully, B.V. 86510, 21065 Dijon Cedex, France
² Platform GenoSol, INRA-Université de Bourgogne, CMSE, 17 rue Sully, B.V. 86510, 21065 Dijon Cedex, France
³ INRA Orléans - US 1106, Unité INFOSOL, avenue de la Pomme de Pin, BP 20619, Adron, 45166 Olivet Cedex, France
⁴ Université de Lyon, 69000 Lyon, France ; Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, 69622 Villeurbanne, France
⁵ Équipe “Génomique Microbienne Environnementale” (Environmental Microbial Genomics Group), UMR CNRS 5005, Laboratoire Ampère, École Centrale de Lyon, 36 avenue Guy de Collongue, 69134 Ecully Cedex, France
⁶ INRA-INRIA MERE research project, UMR ASB, place Pierre Viala, 34060 Montpellier Cedex, France
⁷ LBE-INRA, UR050, avenue des étangs, 11100 Narbonne, France
⁸ UMR 5175 CNRS, Équipe DREAM - Centre d’Écologie Fonctionnelle et Évolutive, 1919 route de Mende, 34293 Montpellier Cedex 5, France

^* Corresponding author: ranjard@dijon.inra.fr

Accepted: 19 August 2009

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.