1. ¹CEA, DSV, iBEB, SBVME, Laboratoire d'Ecologie Microbienne de la Rhizosphère et des Environnements extrêmes (LEMiRE), UMR 6191 CNRS, CEA, Aix Marseille-Univ, FR ECCOREV Saint-Paul-Lez-Durance, France
2. ²CEA Cadarache, DSV/iBEB/SBVME/GRAP, F-13108 Saint Paul Lez, Durance, France
3. ³Institute of Biological and Environmental Sciences, University of Aberdeen, St Machar Drive Aberdeen, Aberdeen, Scotland, UK
4. ⁴INRA, Unite UR1119 Unite Geochimie des Sols et des Eaux, Aix en Provence, France

Correspondence: W Achouak, CEA, DSV, iBEB, SBVME, Laboratoire d'Ecologie Microbienne de la Rhizosphère et des Environnements extrêmes (LEMiRE), UMR 6191 CNRS, CEA, Aix Marseille-Univ, FR ECCOREV Saint-Paul-Lez-Durance F-13108, France. E-mail: wafa.achouak@cea.fr

Received 27 May 2008; Revised 10 July 2008; Accepted 10 July 2008; Published online 28 August 2008.

Abstract

The rhizosphere is active and dynamic in which newly generated carbon, derived from root exudates, and ancient carbon, in soil organic matter (SOM), are available for microbial growth. Stable isotope probing (SIP) was used to determine bacterial communities assimilating each carbon source in the rhizosphere of four plant species. Wheat, maize, rape and barrel clover (Medicago truncatula) were grown separately in the same soil under ¹³CO₂ (99% of atom ¹³C) and DNA extracted from rhizosphere soil was fractionated by isopycnic centrifugation. Bacteria-assimilating root exudates were characterized by denaturing gradient gel electrophoresis (DGGE) analysis of ¹³C-DNA and root DNA, whereas those assimilating SOM were identified from ¹²C-DNA. Plant species root exudates significantly shaped rhizosphere bacterial community structure. Bacteria related to Sphingobacteriales and Myxococcus assimilated root exudates in colonizing roots of all four plants, whwereas bacteria related to Sphingomonadales utilized both carbon sources, and were identified in light, heavy and root compartment DNA. Sphingomonadales were specific to monocotyledons, whereas bacteria related to Enterobacter and Rhizobiales colonized all compartments of all four plants, used both fresh and ancient carbon and were considered as generalists. There was also evidence for an indirect important impact of root exudates, through stimulation of SOM assimilation by a diverse bacterial community.