title: Distribution of Dehalococcoidia in the Anaerobic Deep Water of a Remote Meromictic Crater Lake and Detection of Dehalococcoidia-Derived Reductive Dehalogenase Homologous Genes.
abstract: Here we describe the natural occurrence of bacteria of the class Dehalococcoidia (DEH) and their diversity at different depths in anoxic waters of a remote meromictic lake (Lake Pavin) using 16S rRNA gene amplicon sequencing and quantitative PCR. Detected DEH are phylogenetically diverse and the majority of 16S rRNA sequences have less than 91% similarity to previously isolated DEH 16S rRNA sequences. To predict the metabolic potential of detected DEH subgroups and to assess if they encode genes to transform halogenated compounds, we enriched DEH-affiliated genomic DNA by using a specific-gene capture method and probes against DEH-derived 16S rRNA genes, reductive dehalogenase genes and known insertion sequences. Two reductive dehalogenase homologous sequences were identified from DEH-enriched genomic DNA, and marker genes in the direct vicinity confirm that gene fragments were derived from DEH. The low sequence similarity with known reductive dehalogenase genes suggests yet-unknown catabolic potential in the anoxic zone of Lake Pavin.
authors.affiliation: Laboratoire "Microorganismes: Génome et Environnement," Clermont Université, Université Blaise Pascal, F-63000, Clermont-Ferrand, France.|Laboratoire Microorganismes, Génome et Environnement, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 6023, F-63171, Aubière, France.
authors.forename: Corinne
authors.initials: C
authors.lastname: Biderre-Petit
authors.affiliation: UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850, Thiverval-Grignon, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Dugat-Bony
authors.affiliation: Laboratoire "Microorganismes: Génome et Environnement," Clermont Université, Université Blaise Pascal, F-63000, Clermont-Ferrand, France.|Laboratoire Microorganismes, Génome et Environnement, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 6023, F-63171, Aubière, France.
authors.forename: Mickaël
authors.initials: M
authors.lastname: Mege
authors.affiliation: Laboratoire "Microorganismes: Génome et Environnement," Clermont Université, Université Blaise Pascal, F-63000, Clermont-Ferrand, France.|Laboratoire Microorganismes, Génome et Environnement, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 6023, F-63171, Aubière, France.|Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001, Clermont-Ferrand, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Parisot
authors.affiliation: Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, D-04318, Leipzig, Germany.
authors.forename: Lorenz
authors.initials: L
authors.lastname: Adrian
authors.affiliation: Laboratoire "Microorganismes: Génome et Environnement," Clermont Université, Université Blaise Pascal, F-63000, Clermont-Ferrand, France.|Laboratoire Microorganismes, Génome et Environnement, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 6023, F-63171, Aubière, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Moné
authors.affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001, Clermont-Ferrand, France.
authors.forename: Jérémie
authors.initials: J
authors.lastname: Denonfoux
authors.affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001, Clermont-Ferrand, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Peyretaillade
authors.affiliation: Laboratoire "Microorganismes: Génome et Environnement," Clermont Université, Université Blaise Pascal, F-63000, Clermont-Ferrand, France.|Laboratoire Microorganismes, Génome et Environnement, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 6023, F-63171, Aubière, France.
authors.forename: Didier
authors.initials: D
authors.lastname: Debroas
authors.affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001, Clermont-Ferrand, France.
authors.forename: Delphine
authors.initials: D
authors.lastname: Boucher
authors.affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001, Clermont-Ferrand, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Peyret
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D041862:Chloroflexi / Q000145:classification / Q000201:enzymology / Q000235:genetics*; D016680:Genome, Bacterial; D060106:Lakes / Q000382:microbiology*; D010088:Oxidoreductases / Q000235:genetics* / Q000378:metabolism; D010100:Oxygen / Q000378:metabolism; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000145:classification / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013696:Temperature
chemical_list: D001426:Bacterial Proteins; D012336:RNA, Ribosomal, 16S; D010088:Oxidoreductases; D010100:Oxygen