title: Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach.
abstract: We have constructed a large fosmid library from a mesophilic anaerobic digester and explored its 16S rDNA diversity using a high-density filter DNA-DNA hybridization procedure. We identified a group of 16S rDNA sequences forming a new bacterial lineage named WWE3 (Waste Water of Evry 3). Only one sequence from the public databases shares a sequence identity above 80% with the WWE3 group which hence cannot be affiliated to any known or candidate prokaryotic division. Despite representing a non-negligible fraction (5% of the 16S rDNA sequences) of the bacterial population of this digester, the WWE3 bacteria could not have been retrieved using the conventional 16S rDNA amplification procedure due to their unusual 16S rDNA gene sequence. WWE3 bacteria were detected by polymerase chain reaction (PCR) in various environments (anaerobic digesters, swine lagoon slurries and freshwater biofilms) using newly designed specific PCR primer sets. Fluorescence in situ hybridization (FISH) analysis of sludge samples showed that WWE3 microorganisms are oval-shaped and located deep inside sludge flocs. Detailed phylogenetic analysis showed that WWE3 bacteria form a distinct monophyletic group deeply branching apart from all known bacterial divisions. A new bacterial candidate division status is proposed for this group.
authors.affiliation: CEA/Genoscope, CNRS-UMR 8030 and Université d'Val d'Essonne, 91057 Evry, France.
authors.forename: Sonda
authors.initials: S
authors.lastname: Guermazi
authors.forename: Patrick
authors.initials: P
authors.lastname: Daegelen
authors.forename: Catherine
authors.initials: C
authors.lastname: Dauga
authors.forename: Delphine
authors.initials: D
authors.lastname: Rivière
authors.forename: Théodore
authors.initials: T
authors.lastname: Bouchez
authors.forename: Jean Jacques
authors.initials: JJ
authors.lastname: Godon
authors.forename: Gábor
authors.initials: G
authors.lastname: Gyapay
authors.forename: Abdelghani
authors.initials: A
authors.lastname: Sghir
authors.forename: Eric
authors.initials: E
authors.lastname: Pelletier
authors.forename: Jean
authors.initials: J
authors.lastname: Weissenbach
authors.forename: Denis
authors.initials: D
authors.lastname: Le Paslier
mesh_terms: D001421:Bacteria, Anaerobic / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D001673:Biodegradation, Environmental; D005602:France; D015723:Gene Library; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000145:classification / Q000302:isolation & purification*; D012722:Sewage / Q000382:microbiology*
chemical_list: D012336:RNA, Ribosomal, 16S; D012722:Sewage