Single-Cell Genome and Group-Specific
dsrAB
Sequencing Implicate Marine Members of the Class
Dehalococcoidia
(Phylum
Chloroflexi
) in Sulfur Cycling
Authors: Wasmund Kenneth , Cooper Myriel , Schreiber Lars , Lloyd Karen G. , Baker Brett J. , Petersen Dorthe G. , Jørgensen Bo Barker , Stepanauskas Ramunas , Reinhardt Richard , Schramm Andreas , Loy Alexander , Adrian Lorenz 
Published: May 2016

ABSTRACT

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.

IMPORTANCE
Sediments underlying our oceans are inhabited by microorganisms in cell numbers similar to those estimated to inhabit the oceans. Microorganisms in sediments consist of various diverse and uncharacterized groups that contribute substantially to global biogeochemical cycles. Since most subsurface microorganisms continue to evade cultivation, possibly due to very slow growth, we obtained and analyzed genomic information from a representative of one of the most widespread and abundant, yet uncharacterized bacterial groups of the marine subsurface. We describe several key features that may contribute to their widespread distribution, such as respiratory flexibility and the potential to use oxidized sulfur compounds, which are abundant in marine environments, as electron acceptors. Together, these data provide important information that can be used to assist in designing enrichment strategies or other postgenomic studies, while also improving our understanding of the diversity and distribution of
dsrAB
genes, which are widely used functional marker genes for sulfur-cycling microbes.