Comparative Genomics Reveal Functional Diversification of the Methanogen Methanosarcina mazei
Methanogenic archaea play a major role in global carbon cycle processes, participating in the conversion of organic carbon to the greenhouse gas methane in oxygen-limited environments such as waterlogged soils and wetland sediments. Different types of methanogens are capable of converting either hydrogen and carbon dioxide or intermediate fermentation products (e.g., acetate and methanol) into methane; both processes are key components of carbon decomposition food webs. In a new study, researchers at the University of Illinois have completed a comparative genomics study on 56 different isolates of the metabolically versatile methanogen Methanosarcina mazei cultivated from sediments of the Columbia River in Oregon. While all isolates are members of the same species, they showed a surprising degree of genomic diversity and formed a distinct pattern of subgroups (i.e., clades) based on their site of isolation. The investigators were able to identify a core genome shared by all isolates, but other genetic elements were variable in distribution and showed evidence of transfer between different clades of M. mazei. Several of the variable genes encoding proteins involved the methanogenic metabolism, cofactor utilization, and (most intriguingly) uptake of organic substrates. These observations led the researchers to hypothesize that M. mazei has evolved into strains optimized for specific ecological niches in the sedimentary environments, a phenomenon that has been observed in environmental populations of bacteria. This hypothesis was supported by physiological experiments showing that isolates from different M. mazei clades varied in their ability to use the organic compound trimethylamine for methanogensis. These results advance our mechanistic understanding of a key step in the global carbon cycle and highlight the importance of analyzing metabolically significant differences that occur in microbes at the subspecies level.
Youngblut, N. D., J. S. Wirth, J. R. Henriksen, M. Smith, H. Simon, W. W. Metcalf, and R. J. Whitaker. 2015. “Genomic and Phenotypic Differentiation Among Methanosarcina mazei Populations from Columbia River Sediment,” The ISME Journal, DOI: 10.1038/ismej.2015.31.