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

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.

Organohalide respiration in pristine environments: implications for the natural halogen cycle

“…This implies that predominant marine microorganisms related to known OHRB restricted to OHR may not rely on OHR for energy conservation, but rather on organotrophic and fermentative metabolic modes. Similar metabolic flexibility was proposed from two recently obtained single-amplified genomes from subseafloor sediments, DEH-C11 (Dehalococcoidia) (Wasmund et al, 2016) and An-B22 (Anaerolineales) (Fullerton et al, 2016), each harbouring a single rdhA gene. The predicted enzymes contain binding motifs for FeS clusters, one of the key features of known RdhA enzymes, suggesting functionality of the encoded enzyme.…”

“…Another metagenomic analysis of aquifer sediment contaminated with uranium but not organohalogens retrieved two Dehalococcoidia-related genomes that similarly lacked rdhA genes but contained genomic potential for versatile heterotrophic life styles including fermentation, CO 2 fixation and acetogenesis (Hug et al, 2013b). Combined with the reports from marine environments (Kaster et al, 2014;Wasmund et al, 2014;Fullerton et al, 2016;Wasmund et al, 2016), these findings reinforce that OHR is not the sole metabolic mode of Dehalococcoidia members.…”

“…The predicted enzymes contain binding motifs for FeS clusters, one of the key features of known RdhA enzymes, suggesting functionality of the encoded enzyme. However, no TAT signal was identified (Fullerton et al, 2016;Wasmund et al, 2016). Interestingly, the TAT motif was also absent from the Smkt1 cluster of rdhA genes obtained from (Kawai et al, 2014).…”

Comparative Study of Guaymas Basin Microbiomes: Cold Seeps vs. Hydrothermal Vents Sediments

“…Based on genomecentric metagenomic, members of these taxa have been proposed as potential degraders of organic matters in marine sediments, degrading aromatic compounds (Wasmund et al, 2016), scavenging dead cells (Lloyd et al, 2013;Robbins et al, 2016;Lazar et al, 2017) or fermenting various carbohydrates (Nobu et al, 2016). These heterotrophic microbial communities identified in both cold seep and hydrothermal sediments might be supported by the high sedimentary rates and the important microbial and meiofaunal biomass (Portail et al, 2015) likely generating the important organic carbon concentrations measured in the Guaymas Basin seafloor (Lin et al, 2017).…”

Genomic, transcriptomic and proteomic analyses of Dehalobacter UNSWDHB in response to chloroform

“…Membrane-integral chains B, C, D, I and non-membrane associated L showed higher abundance in post-induction cells, whereas chains membraneintegral H and K were exclusively expressed after TCM addition. In strain UNSWDHB, the nuoEFG genes encoding proteins involved in NADH binding and oxidation are absent in the complex I operon, as observed in D. restrictus genomes (Rupakula et al, 2013) and Dehalococcoides (Wasmund et al, 2016), suggesting that NADH is not the actual electron donor (Moparthi and Hagerhall, 2011). It is also possible that the 11-subunit version of the complex I contributes electrons to the menaquinone pool (potentially as a NADH:menaquinone-oxidoreductase), taking part in respiration and generation of proton motive force (PMF), as it contains a menaquinone binding subunit (Fig.…”