Active root-inhabiting microbes identified by rapid incorporation of plant-derived carbon into RNA

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 104; no. 43; pp. 16970 - 16975
• Main Authors: Vandenkoornhuyse, Philippe, Mahé, Stéphane, Ineson, Philip, Staddon, Phil, Ostle, Nick, Cliquet, Jean-Bernard, Francez, André-Jean, Fitter, Alastair H, Young, J. Peter W
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 23.10.2007; National Acad Sciences
• Subjects: Agrostis capillaris; Agrostis stolonifera; Bacteria; Bacteria - isolation & purification; biochemical pathways; Biological Sciences; biosynthesis; Burkholderia; Carbon; Carbon - metabolism; Carbon Isotopes; Continental interfaces, environment; DNA; Flowers & plants; Fungi; Fungi - genetics; Fungi - isolation & purification; Gene Expression Regulation, Fungal; Isotopes; legumes; microbial physiology; Microorganisms; Molecular Sequence Data; mycorrhizal fungi; Phylogenetics; Phylogeny; Plant roots; Plant Roots - microbiology; Plants; Product labeling; Reverse Transcriptase Polymerase Chain Reaction; Ribonucleic acid; RNA; RNA, Bacterial - genetics; RNA, Bacterial - metabolism; RNA, Fungal - genetics; RNA, Fungal - metabolism; RNA, Ribosomal - genetics; roots; Sciences of the Universe; species diversity; stable isotope probing RNA analysis; stable isotopes; symbionts; Symbiosis; Trifolium repens; vesicular arbuscular mycorrhizae; stable isotope probing; ribosomal RNA; arbuscular mycorrhiza; symbiosis; endophytes
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.0705902104

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 ¹³CO₂ 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 ¹³C. Eight were phylogenetically close to Burkholderiales, which encompass known symbionts; the others were potentially new bacterial root symbionts. By analyzing unlabeled and ¹³C-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.