Dynamics and identification of soil microbial populations actively assimilating carbon from 13C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques

Autor: Lionel Ranjard, Christophe Mougel, Odile Berge, Feth el Zahar Haichar, Christine Marol, Frédéric Gibiat, Virginie Nowak, Jérôme Balesdent, Jean Lévêque, Philippe Lemanceau, Catherine Hénault, Laetitia Bernard, Pierre-Alain Maron
Přispěvatelé: Microbiologie du Sol et de l'Environnement (MSE), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMIRE), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Groupe de Recherches Appliquées en Phytotechnologie (GRAP), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Microbiologie du Sol et de l'Environnement ( MSE ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes ( LEMIRE ), Université de la Méditerranée - Aix-Marseille 2-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ), Groupe de Recherches Appliquées en Phytotechnologie ( GRAP ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA )
Jazyk: angličtina
Rok vydání: 2007
Předmět:
MESH: Sequence Analysis
DNA
MESH: Biodegradation
Environmental
MESH : Carbon Radioisotopes
[SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry
MESH : Ecosystem
RNA
Ribosomal
16S
MESH : DNA
Bacterial
MESH: Ecosystem
Carbon Radioisotopes
MESH: Carbon Radioisotopes
Triticum
Soil Microbiology
2. Zero hunger
0303 health sciences
Carbon Isotopes
biology
Planctomycetes
Bacterial
04 agricultural and veterinary sciences
MESH: RNA
Ribosomal
16S
[ SDE.MCG ] Environmental Sciences/Global Changes
RNA
Bacterial
Biodegradation
Environmental
Biodegradation
MESH : Carbon Isotopes
Proteobacteria
MESH: RNA
Bacterial
Soil microbiology
Sequence Analysis
DNA
Bacterial
16S
Ribosomal Intergenic Spacer analysis
[SDE.MCG]Environmental Sciences/Global Changes
MESH : Biodegradation
Environmental
MESH : Soil Microbiology
[ SDV.SA.SDS ] Life Sciences [q-bio]/Agricultural sciences/Soil study
MESH: Triticum
[SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study
Microbiology
Actinobacteria
Environmental
03 medical and health sciences
MESH : Triticum
[SDV.EE.ECO]Life Sciences [q-bio]/Ecology
environment/Ecosystems
Botany
MESH : Bacteria
Gemmatimonadetes
Ecology
Evolution
Behavior and Systematics
Ecosystem
Ribosomal
[SDV.GEN]Life Sciences [q-bio]/Genetics
Bacteria
030306 microbiology
Soil organic matter
MESH: Carbon Isotopes
Sequence Analysis
DNA
DNA
MESH : RNA
Bacterial
Ribosomal RNA
[ SDU.STU.GC ] Sciences of the Universe [physics]/Earth Sciences/Geochemistry
biology.organism_classification
MESH: DNA
Bacterial
[ SDV.EE.ECO ] Life Sciences [q-bio]/Ecology
environment/Ecosystems
MESH : RNA
Ribosomal
16S
MESH: Bacteria
MESH: Soil Microbiology
040103 agronomy & agriculture
0401 agriculture
forestry
and fisheries
RNA
[ SDV.GEN ] Life Sciences [q-bio]/Genetics
MESH : Sequence Analysis
DNA
Zdroj: Environmental Microbiology
Environmental Microbiology, 2007, 9 (3), pp.752-764. ⟨10.1111/j.1462-2920.2006.01197.x⟩
Environmental Microbiology, Wiley-Blackwell, 2007, 9 (3), pp.752-764. ⟨10.1111/j.1462-2920.2006.01197.x⟩
Environmental Microbiology, Society for Applied Microbiology and Wiley-Blackwell, 2007, 9 (3), pp.752-764. ⟨10.1111/j.1462-2920.2006.01197.x⟩
Environmental Microbiology, Wiley-Blackwell, 2007, 9 (3), pp.752-764. 〈10.1111/j.1462-2920.2006.01197.x〉
ISSN: 1462-2912
1462-2920
DOI: 10.1111/j.1462-2920.2006.01197.x⟩
Popis: International audience; This work is the first report on the use of DNA-, RNA-SIP approaches to elucidate the dynamics and the diversity of bacterial populations actively assimilating C derived from plant residues labelled at more than 90% (13)C. Wheat-residues, were incorporated and incubated into soil microcosms for 28 days. At the end of the incubation time, no more than 55% of the total CO(2) released was (13)C-labelled, suggesting the occurrence of an important priming effect process. After 7 days, more than 30% of the whole DNA extracted were labelled, allowing an efficient separation of labelled from unlabelled DNA using density gradient centrifugation. The genetic structure of bacterial community, assessed by Automated Ribosomal Intergenic Spacer Analysis technique, was deduced from the (13)C- and (12)C-fractions of control and enriched conditions, over the time course of the experiment. Dynamics showed that wheat residues directly induced a rapid and durable stimulation of fresh organic matter (FOM) degrading populations ((13)C), while specific soil organic matter (SOM) degrading populations ((12)C) seemed to be indirectly stimulated only at the early time point (t7d). After 14 days of incubations, 16S rRNA clone libraries were elaborated on (12)C- and (13)C-RNA extracted from enriched microcosms, as well as (12)C-RNA extracted from control condition. Stimulation of the beta- and gamma-subgroups of proteobacteria, where numerous populations were previously described as r-strategists or copiotrophic organisms, was recorded in the (13)C-fraction. In the mean time, several phyla like Actinobacteria, Cyanobacteria, Candidate, Gemmatimonadetes and Planctomycetes were only present in (12)C fractions. Surprisingly, several sequences affiliated to species characterized as oligotrophic organisms were retrieved in both types of fraction. Trophic relationships between soil bacteria involved in FOM and SOM degradation were discussed on the basis of different hypotheses of Fontaine and colleagues (2003) concerning the mechanisms of the priming effect induction.
Databáze: OpenAIRE
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