A taxonomic and physiologic characterization was carried out on Thioclavastrain ElOx9T, which was isolated from a bacterial consortium enriched on electrodes poised at electron donating potentials. The isolate is Gram-negative, catalase-positive and oxidase-positive; the cells are motile short rods. The bacterium is facultatively anaerobic with the ability to utilize nitrate as an electron acceptor. Autotrophic growth with H2 and S0 (oxidized to sulfate) was observed. The isolate also grows heterotrophically with organic acids and sugars. Growth was observed at salinities from 0 to 10% NaCl and at temperatures from 15 to 41 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs in the genus Thioclava; it had the highest sequence similarity of 98.8 % to Thioclava atlantica13D2W-2T, followed by Thioclava dalianensis DLFJ1-1T with 98.5 % similarity, Thioclava pacificaTL 2T with 97.7 % similarity, and then Thioclava indicaDT23-4T with 96.9 %. All other sequence similarities were below 97 % to characterized strains. The digital DNA–DNA hybridization estimated when compared to T. atlantica 13D2W-2T, T. dalianensisDLFJ1-1T, T. pacificaTL 2T and T. indicaDT23-4T were 15.8±2.1, 16.7+2.1, 14.3±1.9 and 18.3±2.1 %. The corresponding average nucleotide identity values between these strains were determined to be 65.1, 67.8, 68.4 and 64.4 %, respectively. The G+C content of the chromosomal DNA is 63.4 mol%. Based on these results, a novel species Thioclavaelectrotropha sp. nov. is proposed, with the type strain ElOx9T (=DSM 103712T=ATCC TSD-100T).
The deep subsurface is an enormous repository of microbial life. However, the metabolic capabilities of these microorganisms and the degree to which they are dependent on surface processes are largely unknown. Due to the logistical difficulty of sampling and inherent heterogeneity, the microbial populations of the terrestrial subsurface are poorly characterized. In an effort to better understand the biogeochemistry of deep terrestrial habitats, we evaluate the energetic yield of chemolithotrophic metabolisms and microbial diversity in the Sanford Underground Research Facility (SURF) in the former Homestake Gold Mine, SD, USA. Geochemical data, energetic modeling, and DNA sequencing were combined with principle component analysis to describe this deep (down to 8100 ft below surface), terrestrial environment. SURF provides access into an iron-rich Paleoproterozoic metasedimentary deposit that contains deeply circulating groundwater. Geochemical analyses of subsurface fluids reveal enormous geochemical diversity ranging widely in salinity, oxidation state (ORP 330 to −328 mV), and concentrations of redox sensitive species (e.g., Fe2+ from near 0 to 6.2 mg/L and Σ S2- from 7 to 2778μg/L). As a direct result of this compositional buffet, Gibbs energy calculations reveal an abundance of energy for microorganisms from the oxidation of sulfur, iron, nitrogen, methane, and manganese. Pyrotag DNA sequencing reveals diverse communities of chemolithoautotrophs, thermophiles, aerobic and anaerobic heterotrophs, and numerous uncultivated clades. Extrapolated across the mine footprint, these data suggest a complex spatial mosaic of subsurface primary productivity that is in good agreement with predicted energy yields. Notably, we report Gibbs energy normalized both per mole of reaction and per kg fluid (energy density) and find the later to be more consistent with observed physiologies and environmental conditions. Further application of this approach will significantly expand our understanding of the deep terrestrial biosphere.
The shallow submarine hydrothermal systems of Tutum Bay, Papua New Guinea, are an ideal opportunity to study the influence of arsenic on a marine ecosystem. Previous reports have demonstrated that the hydrothermal vents in Tutum Bay release arsenic in reduced hydrothermal fluids into the marine environment at the rate of 1.5 kg of arsenic/day. Aqueous arsenite is oxidized and adsorbed onto hydrous ferric oxides [HFOs] surrounding the venting area. We demonstrate here that microorganisms are key in both the oxidation of FeII and AsIII in the areas immediately surrounding the vent source. Surveys of community diversity in biofilms and in vent fluid indicate the presence of zeta-Proteobacteria, alpha-Proteobacteria, Persephonella, and close relatives of the archaeon Nitrosocaldus. The iron oxidizing zeta-Proteobacteria are among the first colonizers of solid substrates near the vents, where they appear to be involved in the precipitation of the hydrous ferric oxides (HFOs). Further, the biofilm communities possess the genetic capacity for the oxidation of arsenite. The resulting arsenate is adsorbed onto the HFOs, potentially removing the arsenic from the immediate marine system. No evidence was found for dissimilatory arsenate reduction, but the arsenate may be remobilized by detoxification mechanisms. This is the first demonstration of the genetic capacity for arsenic cycling in high temperature, shallow-sea vent communities, supporting recent culture-based findings in similar systems in Greece (Handley et al., 2010). These reports extend the deep-sea habitat of the zeta-Proteobacteria to shallow submarine hydrothermal systems, and together implicate biological oxidation of both iron and arsenite as primary biogeochemical processes in these systems, providing a mechanism for the partial removal of aqueous arsenic from the marine environment surrounding the vents.