Lignite coal burning seam in the remote Altai Mountains harbors a hydrogen-driven thermophilic microbial community

Thermal ecosystems associated with underground coal combustion sites are rare and less studied than geothermal features. Here we analysed microbial communities of near-surface ground layer and bituminous substance in an open quarry heated by subsurface coal fire by metagenomic DNA sequencing. Taxonomic classification revealed dominance of only a few groups of Firmicutes. Near-complete genomes of three most abundant species, ‘Candidatus Carbobacillus altaicus’ AL32, Brockia lithotrophica AL31, and Hydrogenibacillus schlegelii AL33, were assembled. According to the genomic data, Ca. Carbobacillus altaicus AL32 is an aerobic heterotroph, while B. lithotrophica AL31 is a chemolithotrophic anaerobe assimilating CO2 via the Calvin cycle. H. schlegelii AL33 is an aerobe capable of both growth on organic compounds and carrying out CO2 fixation via the Calvin cycle. Phylogenetic analysis of the large subunit of RuBisCO of B. lithotrophica AL31 and H. schlegelii AL33 showed that it belongs to the type 1-E. All three Firmicutes species can gain energy from aerobic or anaerobic oxidation of molecular hydrogen, produced as a result of underground coal combustion along with other coal gases. We propose that thermophilic Firmicutes, whose spores can spread from their original geothermal habitats over long distances, are the first colonizers of this recently formed thermal ecosystem

Genome sequence of the copper resistant and acid-tolerant Desulfosporosinus sp. BG isolated from the tailings of a molybdenum-tungsten mine in the Transbaikal area

Here, we report on the draft genome of a copper-resistant and acidophilic Desulfosporosinus sp. BG, isolated from the tailings of a molybdenum-tungsten mine in Transbaikal area. The draft genome has a size of 4.52 Mb and encodes transporters of heavy metals. The phylogenetic analysis based on concatenated ribosomal proteins revealed that strain BG clusters together with the other acidophilic copper-resistant strains Desulfosporosinus sp. OT and Desulfosporosinus sp. I2. The K+-ATPase, Na+/H+ antiporter and amino acid decarboxylases may participate in enabling growth at low pH. The draft genome sequence and annotation have been deposited at GenBank under the accession number NZ_MASS00000000

Genome of the candidate phylum Aminicenantes bacterium from a deep subsurface thermal aquifer revealed its fermentative saccharolytic lifestyle

Bacteria of candidate phylum OP8 (Aminicenantes) have been identified in various terrestrial and marine ecosystems as a result of molecular analysis of microbial communities. So far, none of the representatives of Aminicenantes have been isolated in a pure culture. We assembled the near-complete genome of a member of Aminicenantes from the metagenome of the 2-km-deep subsurface thermal aquifer in Western Siberia and used genomic data to analyze the metabolic pathways of this bacterium and its ecological role. This bacterium, designated BY38, was predicted to be rod shaped, it lacks flagellar machinery but twitching motility is encoded. Analysis of the BY38 genome revealed a variety of glycosyl hydrolases that can enable utilization of carbohydrates, including chitin, cellulose, starch, mannose, galactose, fructose, fucose, rhamnose, maltose and arabinose. The reconstructed central metabolic pathways suggested that Aminicenantes bacterium BY38 is an anaerobic organotroph capable of fermenting carbohydrates and proteinaceous substrates and performing anaerobic respiration with nitrite. In the deep subsurface aquifer Aminicenantes probably act as destructors of buried organic matter and produce hydrogen and acetate. Based on phylogenetic and genomic analyses, the novel bacterium is proposed to be classified as Candidatus Saccharicenans subterraneum

Metagenome sequence of a microbial community from the gold mine tailings in the Kuzbass area, Russia

The metagenome of a microbial community of the sediments from a highly acidic iron-rich puddle at the tailings dump of the Komsomolskaya gold mine in the Kuzbass area, Siberia, Russia, was sequenced. Binning of contigs yielded a near-complete genome of the dominant bacterium, representing a novel deep lineage of Deltaproteobacteria

Metagenome sequence of a microbial community from the gold mine tailings in the Kuzbass area, Russia

The metagenome of a microbial community of the sediments from a highly acidic iron-rich puddle at the tailings dump of the Komsomolskaya gold mine in the Kuzbass area, Siberia, Russia, was sequenced. Binning of contigs yielded a near-complete genome of the dominant bacterium, representing a novel deep lineage of Deltaproteobacteria

A metagenomic window into the 2-km-deep terrestrial subsurface aquifer revealed multiple pathways of organic matter decomposition

We have sequenced metagenome of the microbial community of a deep subsurface thermal aquifer in the Tomsk Region of the Western Siberia, Russia. Our goal was the recovery of near-complete genomes of the community members to enable accurate reconstruction of metabolism and ecological roles of the microbial majority, including previously unstudied lineages. The water, obtained via a 2.6 km deep borehole 1-R, was anoxic, with a slightly alkaline pH, and a temperature around 45°C. Microbial community, as revealed by 16S rRNA gene profiling over 2 years, mostly consisted of sulfate-reducing Firmicutes and Deltaproteobacteria, and uncultured lineages of the phyla Chlorofexi, Ignavibacteriae and Aminicenantes (OP8). 25 composite genomes with more than 90% completeness were recovered from metagenome and used for metabolic reconstruction. Members of uncultured lineages of Chlorofexi and Ignavibacteriae are likely involved in degradation of carbohydrates by fermentation, and are also capable of aerobic and anaerobic respiration. The Chlorofexi bacterium has the Wood-Ljungdahl pathway of CO2 fixation. The recently identified candidate phylum Riflebacteria accounted for 5%–10% of microbial community. Metabolic reconstruction of a member of Riflebacteria predicted that it is an anaerobe capable to grow on carbohydrates by fermentation or dissimilatory Fe(III) reduction