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PMID: 16011748 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester.

Environmental microbiology ·Vol. 7 ·No. 8 ·2005-08-00 ·Pages 1104-15

Chouari R, Le Paslier D, Daegelen P, Ginestet P, Weissenbach J, Sghir A

Abstract

A culture-independent molecular phylogenetic approach was used to study prokaryotic diversity in an anaerobic sludge digester. Two 16S rRNA gene libraries were constructed using total genomic DNA, and amplified by polymerase chain reaction (PCR) using primers specific for archaeal or bacterial domains. Phylogenetic analysis of 246 and 579 almost full-length 16S rRNA genes for Archaea and Bacteria, respectively, was performed using the ARB software package. Phylogenetic groups affiliated with the Archaea belong to Euryarchaeota and Crenarchaeota. Interestingly, we detected a novel monophyletic group of 164 clones representing 66.6% of the archaeal library. Culture enrichment and probe hybridization show that this group grows better under formate or H2-CO2. Within the bacterial library 95.6% of the operational taxonomic units (OTUs) represent novel putative phylotypes never described before, and affiliated with eight divisions. The Bacteroidetes phylum is the most abundant and diversified phylogenetic group representing 38.8% of the OTUs, followed by the gram-positives (27.7%) and the Proteobacteria (21.3%). Sequences affiliated with phylogenetic divisions represented by few cultivated representatives such as the Chloroflexi, Synergistes, Thermotogales or candidate divisions such as OP9 and OP8 are represented by <5% of the total OTUs. A comprehensive set of 15 16S and 23S rRNA-targeted oligonucleotide hybridization probes was used to quantify these major groups by dot blot hybridization within 12 digester samples. In contrast to the clone library, Firmicutes and Actinobacteria together accounted for 21.8 +/- 14.9% representing the most abundant phyla. They were surprisingly followed by the Chloroflexi representing 20.2 +/- 4.6% of the total 16S rRNA. The Proteobacteria and the Bacteroidetes group accounted for 14.4 +/- 4.9% and 14.5 +/- 4.3%, respectively, WWE1, a novel lineage, accounted for 11.9 +/- 3.1% while Planctomycetes and Synergistes represented <2% each. Using the novel set of probes we extended the coverage of bacterial populations from 52% to 85.3% of the total rRNA within the digester samples.

MeSH Terms

Anaerobiosis Archaea/classification,genetics,growth & development Bacteria/classification,genetics,growth & development DNA, Archaeal/analysis DNA, Bacterial/analysis DNA, Ribosomal/analysis Gene Library Genes, rRNA Molecular Sequence Data Phylogeny Polymerase Chain Reaction RNA, Ribosomal, 16S/genetics RNA, Ribosomal, 23S/genetics Sequence Analysis, DNA Sewage/microbiology

Chemicals

DNA, Archaeal DNA, Bacterial DNA, Ribosomal RNA, Ribosomal, 16S RNA, Ribosomal, 23S Sewage

Authors & Affiliations

6 authors, click to expand affiliations / ORCID

Chouari Rakia

CNRS-UMR 8030, Genoscope and Université d'Evry Val d'Essonne, 2, rue Gaston Crémieux, 91057 Evry, France.

Le Paslier Denis

Daegelen Patrick

Ginestet Philippe

Weissenbach Jean

Sghir Abdelghani

Article Info

Journal

Environmental microbiology

Abbr.

Environ Microbiol

ISSN

1462-2912

DOI

10.1111/j.1462-2920.2005.00795.x

Published

2005-08-00

Pages

1104-15

Language

English

Region

England

NLM ID

100883692

Subset

Databases

GENBANK

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PubMed source DOI: 10.1111/j.1462-2920.2005.00795.x View journal details

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Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester.

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