title: Active root-inhabiting microbes identified by rapid incorporation of plant-derived carbon into RNA.
abstract: Plant roots harbor a large diversity of microorganisms that have an essential role in ecosystem functioning. To better understand the level of intimacy of root-inhabiting microbes such as arbuscular mycorrhizal fungi and bacteria, we provided (13)CO(2) to plants at atmospheric concentration during a 5-h pulse. We expected microbes dependent on a carbon flux from their host plant to become rapidly labeled. We showed that a wide variety of microbes occurred in roots, mostly previously unknown. Strikingly, the greatest part of this unsuspected diversity corresponded to active primary consumers. We found 17 bacterial phylotypes co-occurring within roots of a single plant, including five potentially new phylotypes. Fourteen phylotypes were heavily labeled with the (13)C. Eight were phylogenetically close to Burkholderiales, which encompass known symbionts; the others were potentially new bacterial root symbionts. By analyzing unlabeled and (13)C-enriched RNAs, we demonstrated differential activity in C consumption among these root-inhabiting microbes. Arbuscular mycorrhizal fungal RNAs were heavily labeled, confirming the high carbon flux from the plant to the fungal compartment, but some of the fungi present appeared to be much more active than others. The results presented here reveal the possibility of uncharacterized root symbioses.
authors.affiliation: Centre National de la Recherche Scientifique, Unité Mixte de Recherche (UMR) 6553 EcoBio, IFR90/FR2116, Centre Armoricain de Recherche sur l'Environnement, Université de Rennes I, Campus de Beaulieu, 35042 Rennes Cedex, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Vandenkoornhuyse
authors.forename: Stéphane
authors.initials: S
authors.lastname: Mahé
authors.forename: Philip
authors.initials: P
authors.lastname: Ineson
authors.forename: Phil
authors.initials: P
authors.lastname: Staddon
authors.forename: Nick
authors.initials: N
authors.lastname: Ostle
authors.forename: Jean-Bernard
authors.initials: JB
authors.lastname: Cliquet
authors.forename: André-Jean
authors.initials: AJ
authors.lastname: Francez
authors.forename: Alastair H
authors.initials: AH
authors.lastname: Fitter
authors.forename: J Peter W
authors.initials: JP
authors.lastname: Young
mesh_terms: D001419:Bacteria / Q000302:isolation & purification*; D002244:Carbon / Q000378:metabolism*; D002247:Carbon Isotopes; D005658:Fungi / Q000235:genetics / Q000302:isolation & purification*; D015966:Gene Expression Regulation, Fungal; D008969:Molecular Sequence Data; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology*; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D012331:RNA, Fungal / Q000235:genetics / Q000378:metabolism*; D012335:RNA, Ribosomal / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D002247:Carbon Isotopes; D012329:RNA, Bacterial; D012331:RNA, Fungal; D012335:RNA, Ribosomal; D002244:Carbon