The First Genomic and Proteomic Characterization of a Deep-Sea Sulfate Reducer: Insights into the Piezophilic Lifestyle of Desulfovibrio piezophilus

Abstract

Desulfovibrio piezophilus strain C1TLV30T is a piezophilic anaerobe that was isolated from wood falls in the Mediterranean deep-sea. D. piezophilus represents a unique model for studying the adaptation of sulfate-reducing bacteria to hydrostatic pressure. Here, we report the 3.6 Mbp genome sequence of this piezophilic bacterium. An analysis of the genome revealed the presence of seven genomic islands as well as gene clusters that are most likely linked to life at a high hydrostatic pressure. Comparative genomics and differential proteomics identified the transport of solutes and amino acids as well as amino acid metabolism as major cellular processes for the adaptation of this bacterium to hydrostatic pressure. In addition, the proteome profiles showed that the abundance of key enzymes that are involved in sulfate reduction was dependent on hydrostatic pressure. A comparative analysis of orthologs from the non-piezophilic marine bacterium D. salexigens and D. piezophilus identified aspartic acid, glutamic acid, lysine, asparagine, serine and tyrosine as the amino acids preferentially replaced by arginine, histidine, alanine and threonine in the piezophilic strain. This work reveals the adaptation strategies developed by a sulfate reducer to a deep-sea lifestyle.

Temporal and spatial constraints on community assembly during microbial colonization of wood in seawater

“…The presence of abundant sequences of D. piezophilus in our aquarium woods also indicates that our experiments in cold water in the dark were able to attract such emblematic species. It also demonstrates that D. piezophilus, thought to be a typical piezophile (Khelaifia et al, 2011;Pradel et al, 2013), may also thrive under atmospheric pressure conditions. The clear differences in term of community composition between oak and pine in both the aquarium and the canyon could be due to different wood chemical composition.…”

Ecological succession leads to chemosynthesis in mats colonizing wood in sea water

“…Deltaproteobacteria were dominated by sequences related to the Desulfovibrio genera (Otu3) previously found associated to wood falls (Khelaifia et al, 2011;Kalenitchenko et al, 2015). This genera of sulfatereducing bacteria is strictly anaerobic, uses fermentation end products as a carbon source, respires sulfate and thus produces hydrogen sulfide (Pradel et al, 2013). The mat thickness increase with time may be linked to the displacement of the oxygensulfide interface from the wood surface toward the seawater as observed on other Epsilonproteobacteria mats (Wirsen et al, 2002;Sievert et al, 2007).…”

“…The proportion of dsr and apr genes increased at the end of the experiment supporting the hypothesis of the presence of sulfate-reducing Desulfovibrio-related bacteria (Otu3), which quickly dominated the wood mat community. The common presence of Desulfovibrio in wood falls (Bienhold et al, 2013;Fagervold et al, 2013;Pradel et al, 2013;Kalenitchenko et al, 2015) and measures of hydrogen sulfide pulses on wood surfaces after 1 month (Yücel et al, 2013;Kalenitchenko et al, 2015) suggests the importance of this genera for the production of hydrogen sulfide from wood falls. In addition, the bacterial community's potential to use hydrogen sulfide as electron donor was confirmed by the detection of the sulfur oxidation protein coding gene soxB.…”

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

“…30 MPa) (Khelaifia et al, 2011). Comparative analysis of the 3.6 Mb genome of D. piezophilus indicated the presence of several genomic regions and amino acid substitutions that could be involved in adaptation to high pressure (Pradel et al, 2013). In the likewise piezophilic and genome-sequenced D. hydrothermalis AM13, transcriptomic analysis indicated the energy metabolism to be optimized for growth at high pressure and accumulated glutamate as a possible piezolyte (Amrani et al, 2014).…”