Identification of cellulolytic bacteria in soil by stable isotope probing.
Plant residues, mainly made up of cellulose, are the largest fraction of organic carbon material in terrestrial ecosystems. Soil microorganisms are mainly responsible for the transfer of this carbon to the atmosphere, but their contribution is not accurately known. The aim of the present study was to identify bacterial populations that are actively involved in cellulose degradation, using the DNA-stable isotope probing (DNA-SIP) technique. (13)C-cellulose was produced by Acetobacter xylinus and incubated in soil for 7, 14, 30 and 90 days. Total DNA was extracted from the soil, the (13)C-labelled (heavy) and unlabelled (light) DNA fractions were separated by ultracentrifugation, and the structure of active bacterial communities was analysed by bacterial-automated ribosomal intergenic spacer analysis (B-ARISA) and characterized with denaturing gradient gel electrophoresis (DGGE). Cellulose degradation was associated with significant changes in bacterial community structure issued from heavy DNA, leading to the appearance of new bands and increase in relative intensities of other bands until day 30. The majority of bands decreased in relative intensity at day 90. Sequencing and phylogenetic analysis of 10 of these bands in DGGE profiles indicated that most sequences were closely related to sequences from organisms known for their ability to degrade cellulose or to uncultured soil bacteria.
Haichar
Feth El Zahar
FZ
CEA, DSV, DEVM, Laboratoire d'Ecologie Microbienne de la Rhizosphère et des Environnements extrêmes (LEMiRE), UMR 6191 CNRS, CEA, Aix Marseille-Univ, IFR-E 112, Saint-Paul-Lez-Durance F-13108, France.
Achouak
Wafa
W
Christen
Richard
R
Heulin
Thierry
T
Marol
Christine
C
Marais
Marie-France
MF
Mougel
Christophe
C
Ranjard
Lionel
L
Balesdent
Jérôme
J
Berge
Odile
O
D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D002247:Carbon Isotopes / Q000378:metabolism*; D002482:Cellulose / Q000378:metabolism*; D002499:Centrifugation, Density Gradient; D004269:DNA, Bacterial / Q000032:analysis*; D021903:DNA, Ribosomal Spacer / Q000032:analysis; D017753:Ecosystem; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology
D002247:Carbon Isotopes; D004269:DNA, Bacterial; D021903:DNA, Ribosomal Spacer; D012336:RNA, Ribosomal, 16S; D002482:Cellulose