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; Eric Dugat-Bony; Mickaël Mege; Nicolas Parisot; Lorenz Adrian; Anne Moné; Jérémie Denonfoux; Eric Peyretaillade; Didier Debroas; Delphine Boucher; Pierre Peyret

doi:10.1371/journal.pone.0145558

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 Jan 6;11(1):e0145558. doi: 10.1371/journal.pone.0145558. eCollection 2016.

Authors

Corinne Biderre-Petit^{1

2}, Eric Dugat-Bony³, Mickaël Mege^{1

2}, Nicolas Parisot^{1

2

4}, Lorenz Adrian⁵, Anne Moné^{1

2}, Jérémie Denonfoux⁴, Eric Peyretaillade⁴, Didier Debroas^{1

2}, Delphine Boucher⁴, Pierre Peyret⁴

Affiliations

¹ Laboratoire "Microorganismes: Génome et Environnement," Clermont Université, Université Blaise Pascal, F-63000, Clermont-Ferrand, France.
² Laboratoire Microorganismes, Génome et Environnement, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 6023, F-63171, Aubière, France.
³ UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850, Thiverval-Grignon, France.
⁴ Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001, Clermont-Ferrand, France.
⁵ Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, D-04318, Leipzig, Germany.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacterial Proteins / genetics*
Bacterial Proteins / metabolism
Chloroflexi / classification
Chloroflexi / enzymology
Chloroflexi / genetics*
Genome, Bacterial
Lakes / microbiology*
Oxidoreductases / genetics*
Oxidoreductases / metabolism
Oxygen / metabolism
Phylogeny
RNA, Ribosomal, 16S / chemistry
RNA, Ribosomal, 16S / classification
RNA, Ribosomal, 16S / genetics
Real-Time Polymerase Chain Reaction
Sequence Analysis, DNA
Temperature

Substances

Bacterial Proteins
RNA, Ribosomal, 16S
Oxidoreductases
Oxygen

Grants and funding

This work was funded by the following: Deutsche Forschungsgemeinschaft FOR1530 (to LA), Direction Générale de l’Armement (DGA) (to NP), CNRS and Région Auvergne (to JD), Agence De l'Environnement et de la Maitrise de l'Energie (ADEME) (to EDB), French National Programme INSU-EC2CO (EChlore Project) (to CBP and PP), ANR Programme PRECODD (EVASOL Project) (to EDB, PP and CBP), Université Blaise Pascal and Ministère de la Recherche et de la Technologie. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.