Protocols for Investigating the Microbiology of Coal-Bed-Produced Waters

Abstract

Coal-bed methane (CBM) has emerged as a globally important source of natural gas, and recent studies have revealed that microbial production of methane in CBM formations plays a significant role. Coal-bed formations are complex ecosystems with large reservoirs of organic substrates comprised of aliphatic, aromatic, and heterocyclic compounds. The biotransformation of this organic matter to methane by microbial communities, however, is not well elucidated. The latter has important implications with regard to energy recovery from subsurface environments. Although coal beds and other deep subsurface systems pose significant challenges with respect to field sampling and analysis, recent methodological advances have provided novel insights into the ecology and metabolism of coal-bed microbial communities. Specifically, the availability of affordable sequencing technologies and advances in mass spectrometry have allowed an unprecedented ability to study in situ processes governing microbial metabolism in subsurface environments. The following protocols include methodologies for the collection of coal-bed-produced water for traditional cultivation and most probable number (MPN) techniques, community DNA extraction and sequence-based molecular analyses, and metabolite profiling. The described techniques are intended as primers for several cultivation, molecular, and mass spectrometry applications and are adaptable to a range of field and experimental conditions.