A novel tail: One story from the rare taxa of the coal seam microbiome

Abstract

A substantial portion of global coal seam methane reserves are biogenically produced. To enhance methane production, recent research has focussed on genetic surveying of the microbial life inhabiting these coal seams. These surveys have revealed that the most abundant organisms in these microbial communities are taxa specialised in metabolism of various simple substrates, and are typically methanogens, their (presumably) syntrophic acetate-oxidising bacterial partners, and other bacterial taxa associated with biomass recycling. Although abundant, these microbes are incapable of directly accessing the vast majority of recalcitrant carbon contained within the coal geopolymer. Instead, these more abundant taxa likely rely on the low abundance but diverse taxa, known as the ‘rare taxa’, to transform the carbon within coal into simpler, more labile substrates. Since these rare taxa typically have low taxonomic resolution, their probable activities within the coal seam environment are difficult to infer using the standard 16S rDNA community surveys. Therefore, the present study aimed to develop a method for identifying and characterising these rare taxa using a metagenomic approach. Using this method, a near-complete genome from a Deltaproteobacteria sp. (CSMB_808; designation taken from the Coal Seam Microbiome reference set) was recovered from a metagenome sampling the Surat Basin, Australia, and comprised only 0.5% of the total 16S rDNA sequences recovered from this metagenome. Genetically, CSMB_808 appears to be a motile fatty acid and possibly alkane-degrader within the coal seam environment, and may play an important role in the coal-to-methane degradative pathways. Despite the near-completeness of the recovered genome, the taxonomic resolution of this deltaproteobacterium was unable to be clarified due to insufficient described close relatives. Together, the low taxonomic resolution, relatively low 16S rDNA abundance, and ability to degrade putative upstream metabolites that may facilitate methanogenesis in the coal seam environment, indicates that this method of analysis can assist in understanding other important but uncharacterised rare taxa of the coal seam microbiome. A clearer understanding of the function of these taxa would allow targeted strategies to enhance methane production, as well as contributing valuable knowledge of carbon cycling in the terrestrial subsurface.