title: Stable isotope probing of carbon flow in the plant holobiont.
abstract: Microbial communities associated with a plant host, constituting a holobiont, affect the physiology and growth of the plant via metabolites that are mainly derived from their photosynthates. The structure and function of active microbial communities that assimilate root exudates can be tracked by using stable isotope probing (SIP) approaches. This article reviews results from ongoing SIP research in plant-microbe interactions, with a specific focus on investigating the fate of fresh and recalcitrant carbon in the rhizosphere with13C enriched-root exudates, in addition to identifying key players in carbon cycling. Finally, we discuss new SIP applications that have the potential to identify novel enzymes implicated in rhizoremediation or plant genes dedicated to root exudation by combining SIP approaches and genome wide associations studies.
authors.affiliation: Université Lyon1, CNRS, UMR5557, INRA, USC1364, Ecologie Microbienne, 69622 Villeurbanne, France. Electronic address: zahar.haichar@univ-lyon1.fr.
authors.forename: Feth El Zahar
authors.initials: FEZ
authors.lastname: Haichar
authors.affiliation: Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA/Cadarache, St-Paul-lez-Durance, France.
authors.forename: Thierry
authors.initials: T
authors.lastname: Heulin
authors.affiliation: Université Lyon1, CNRS, UMR5557, INRA, USC1364, Ecologie Microbienne, 69622 Villeurbanne, France.
authors.forename: Julien P
authors.initials: JP
authors.lastname: Guyonnet
authors.affiliation: Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA/Cadarache, St-Paul-lez-Durance, France.
authors.forename: Wafa
authors.initials: W
authors.lastname: Achouak
mesh_terms: D002247:Carbon Isotopes / Q000032:analysis*; D007553:Isotope Labeling / Q000379:methods*; D018517:Plant Roots / Q000378:metabolism* / Q000382:microbiology; D010944:Plants / Q000378:metabolism* / Q000382:microbiology; D012988:Soil Microbiology
chemical_list: D002247:Carbon Isotopes