Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling

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  • Kenneth Wasmund
    Kenneth WasmundDivision of Microbial Ecology, Department of Microbiology and Ecosystem Science, Faculty of Life Sciences, University of Vienna, Vienna, Austria.Helmholtz Centre for Environmental Research – UFZ, Leipzig, GermanyAustria
  • Myriel Cooper
    Myriel CooperHelmholtz Centre for Environmental Research – UFZ, Leipzig, GermanyGermany
  • Lars Schreiber
    Lars Schreiber
  • Karen G. Lloyd
    Karen G. Lloyd
  • Brett J. Baker
    Brett J. BakerMarine Science Institute, University of Texas at AustinUnited States
  • Dorthe Groth Petersen
    Dorthe Groth Petersen
  • Bo Barker Jørgensen
  • Ramunas Stepanauskas
    Ramunas StepanauskasBigelow Laboratory for Ocean SciencesUnited States
  • Richard Reinhardt
    Richard ReinhardtMax Planck Genome Ctr Cologne, Max Planck SocietyGermany
  • Andreas Schramm
  • Alexander Loy
    Alexander LoyDivision of Microbial Ecology, Department of Microbiology and Ecosystem Science, Faculty of Life Sciences, University of Vienna, Vienna, Austria.Austria
  • Lorenz Adrian
    Lorenz AdrianHelmholtz Centre for Environmental Research – UFZ, Leipzig, GermanyGermany
The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, and yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (DEH-C11) with a 16S rRNA gene that was affiliated with a diverse cluster of 16S rRNA gene sequences prevalent in marine sediments was obtained from sediments of Aarhus Bay, Denmark. The distinctive gene content of this cell suggests metabolic characteristics that differ from those of known DEH and Chloroflexi. The presence of genes encoding dissimilatory sulfite reductase (Dsr) suggests that DEH could respire oxidized sulfur compounds, although Chloroflexi have never been implicated in this mode of sulfur cycling. Using long-range PCR assays targeting DEH dsr loci, dsrAB genes were amplified and sequenced from various marine sediments. Many of the amplified dsrAB sequences were affiliated with the DEH Dsr clade, which we propose equates to a family-level clade. This provides supporting evidence for the potential for sulfite reduction by diverse DEH species. DEH-C11 also harbored genes encoding reductases for arsenate, dimethyl sulfoxide, and halogenated organics. The reductive dehalogenase homolog (RdhA) forms a monophyletic clade along with RdhA sequences from various DEH-derived contigs retrieved from available metagenomes. Multiple facts indicate that this RdhA may not be a terminal reductase. The presence of other genes indicated that nutrients and energy may be derived from the oxidation of substituted homocyclic and heterocyclic aromatic compounds. Together, these results suggest that marine DEH play a previously unrecognized role in sulfur cycling and reveal the potential for expanded catabolic and respiratory functions among subsurface DEH.
Original languageEnglish
Article numbere00266-16
JournalmBio (Online)
Volume7
Issue number3
ISSN2150-7511
DOIs
StatePublished - 3 May 2016

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