Distribution of dehalococcoidia in the anaerobic deep water of a remote meromictic crater lake and detection of dehalococcoidia-derived reductive dehalogenase homologous genes

Corinne Biderre-Petit (1, 2) , Eric Dugat-Bony (3) , Mickaël Mege (1, 2) , Nicolas Parisot (1, 2) , Lorenz Adrian (4) , Anne Moné (1, 2) , Jérémie Denonfoux (5) , Eric Peyretaillade (5) , Didier Debroas (1, 2) , Delphine Boucher (5) , Pierre Peyret (5)

1 LMGE - Laboratoire Microorganismes : Génome et Environnement
2 LMGE - Laboratoire Microorganismes : Génome et Environnement
3 GMPA - Génie et Microbiologie des Procédés Alimentaires
4 UFZ - Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research
5 CIDAM - Conception, Ingénierie et Développement de l'Aliment et du Médicament

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.

Mots clés: strain cbdb1; genome sequence; vertical-distribution; tetrachloroethene; sediments; france; lac pavin; single-cell; microbial communities; polychlorinated-biphenyls

Domaines: Sciences du Vivant [q-bio]

Corinne Biderre-Petit, Eric Dugat-Bony, Mickaël Mege, Nicolas Parisot, Lorenz Adrian, et al.. Distribution of dehalococcoidia in the anaerobic deep water of a remote meromictic crater lake and detection of dehalococcoidia-derived reductive dehalogenase homologous genes. PLoS ONE, 2016, 11 (1), ⟨10.1371/journal.pone.0145558⟩. ⟨hal-01599389v2⟩