Prokaryotic Life Associated with Coal-Fire Gas Vents Revealed by Metagenomics

SIMPLE SUMMARY: The natural combustion of underground coal deposits leads to the release of large quantities of gases which contain molecular hydrogen and carbon monoxide. In places where hot coal gases are released to the surface, specific communities of thermophilic microorganisms develop. Unlike well-characterized geothermal ecosystems, the thermophiles associated with coal-fire gas vents are largely unexplored. In this work, using molecular genetic methods, we studied the composition and functional potential of bacterial and archaeal communities in the near-surface ground layer of an open quarry in Eastern Siberia, heated by an underground coal fire that began a few decades ago. The communities were dominated by only a few groups of bacteria of the phylum Firmicutes. Genome analysis predicted that they might obtain energy from the oxidation of hydrogen and carbon monoxide in coal gases. All these species were predicted to be spore-forming. Interestingly, closely related bacteria were found in various thermal environments, including burning coal seams, at distances of thousands of kilometers from the studied site. Spores of thermophilic Firmicutes can probably spread over long distances, which allows these microorganisms to colonize these thermal ecological niches. ABSTRACT: The natural combustion of underground coal seams leads to the formation of gas, which contains molecular hydrogen and carbon monoxide. In places where hot coal gases are released to the surface, specific thermal ecosystems are formed. Here, 16S rRNA gene profiling and shotgun metagenome sequencing were employed to characterize the taxonomic diversity and genetic potential of prokaryotic communities of the near-surface ground layer near hot gas vents in an open quarry heated by a subsurface coal fire. The communities were dominated by only a few groups of spore-forming Firmicutes, namely the aerobic heterotroph Candidatus Carbobacillus altaicus, the aerobic chemolitoautotrophs Kyrpidia tusciae and Hydrogenibacillus schlegelii, and the anaerobic chemolithoautotroph Brockia lithotrophica. Genome analysis predicted that these species can obtain energy from the oxidation of hydrogen and/or carbon monoxide in coal gases. We assembled the first complete closed genome of a member of uncultured class-level division DTU015 in the phylum Firmicutes. This bacterium, ‘Candidatus Fermentithermobacillus carboniphilus’ Bu02, was predicted to be rod-shaped and capable of flagellar motility and sporulation. Genome analysis showed the absence of aerobic and anaerobic respiration and suggested chemoheterotrophic lifestyle with the ability to ferment peptides, amino acids, N-acetylglucosamine, and tricarboxylic acid cycle intermediates. Bu02 bacterium probably plays the role of a scavenger, performing the fermentation of organics formed by autotrophic Firmicutes supported by coal gases. A comparative genome analysis of the DTU015 division revealed that most of its members have a similar lifestyle.