The Coal Seam Microbiome (CSMB) reference set, a lingua franca for the microbial coal-to-methane community

Abstract

Microbial generation of methane from organic matter in coal represents an opportunity to improve environmental and economic outcomes of coal seam gas production. This has prompted research interest in microbial communities responsible for its generation. While advances have been made in understanding the overall structure of these communities and in methods to stimulate methane generation through nutrient additions, many questions still remain as to the metabolic roles played by the majority of the taxa in coal seams. One confounding issue faced by the coal seam microbiology community is an inability to compare OTUs (Operational Taxonomic Units) from 16S rDNA community surveys between studies. The aim of this study is to provide a common language for researchers studying coal seam microbes so that any given OTU from a coal seam community can be readily referenced to OTUs from other studies. To meet this aim a new Coal Seam MicroBiome (CSMB) reference set of OTU sequences was constructed from both new data obtained through community surveys of 28 coal seam formation water samples across three eastern Australian coal basins, along with all compatible, publicly available community surveys. To illustrate the power of the CSMB set for enabling comparisons the set was used to compare the co-occurrence of OTUs from publicly available compatible coal seam community surveys. Additionally, 16S rDNA sequence data from all compatible coal seam isolates and/or reconstructed genomes from published studies were mapped to the CSMB set. Resultant analysis revealed that a large number of published surveys have shared CSMB OTUs and a number of isolate and reconstructed genomes matched CSMB OTUs observed in surveys of the coal seam formation waters across the USA, Canada, China, India, Japan and Australia. This report details these observations of co-occurrence, as well as providing information on downloading, mapping and adding new sequences to the CSMB set.