Exploring microbial function in the generation of biogenic methane from organic matter in coal seams

Biogenic methane from subsurface coal seams is an important resource for global energy security, providing a useful intermediate fuel in the transition to renewable energy. Although genetic surveys of the coal seam microbiome have revealed communities of bacteria and archaea, the degradation pathways are not yet known for conversion of the coal to methane. Not only this, but the key microbes responsible for degradation of the complex organic matter within the coal are also unknown. This thesis contains a series of studies aimed at understanding these key microbes and degradation pathways. The first of these studies examines the biogeographic distribution of methanogenic archaea in coal seams of Australia and North America, finding that methanogen populations are distinct between coal-bearing basins and providing insights to the likely methanogenic substrates provided from the coal biodegradation in each basin. The second study presented here identifies and examines an unusual microbe (Deltaproteobacteria “CSMB_808”) which was found in a metagenome from the Surat Basin, Australia. Although CSMB_808 is commonly detected in 16S rRNA surveys of Australian coal seams, its taxonomy and genome are characterised here for the first time. The third and fourth experiments described in this work seek to identify the aromatic degrading taxa in coal seams using two different approaches: one culture-dependant and one culture-independent approach. The culture-dependant study created enrichment cultures using aromatic compounds as sole sources of carbon to attempt to identify “first-biters” within the coal to methane degradation pathway. Conversely, the culture-independent approach used metagenomic and bioinformatic methods to identify genes for aromatic compound degradation within coal seam metagenomes. The remainder of the genomes of these aromatic degrading organisms were assembled using information on the contiguous sequences of the identified aromatic- degrading genes. From these latter two studies, a number of candidate aromatic degraders were identified. Of these, a novel taxon from the Fibrobacteres-Chlorobi-Bacteroidetes superphylum appears to be capable of utilising a wide range of aromatic compounds in coal seams, and may be an important rate-limiting microbe for coal degradation in the Powder River Basin, USA. Overall, this thesis identifies important variations in global methanogen communities, describes the genome and probable function of a novel taxon within the coal seam and finally, identifies putative catabolists of organic matter in coal. These findings have important implications for biostimulation, bioaugmentation and exploration of biogenic methane in coal seams. Not only this, but these findings also provide insights into bacterial bioremediation options from the coal seam microbiome for the treatment of toxic aromatic pollutants, and reveal carbon cycling and atmospheric emissions pathways from subsurface environments.