Abstract
Methanogenic archaea are genotypically and phenotypically diverse organisms that are integral to carbon cycling in anaerobic environments. Owing to their genetic tractability and ability to be readily cultivated, Methanosarcina spp. have become a powerful model system for understanding methanogen biology at the cellular systems level. However, relatively little is known of how genotypic and phenotypic variation is partitioned in Methanosarcina populations inhabiting natural environments and the possible ecological and evolutionary implications of such variation. Here, we have identified how genomic and phenotypic diversity is partitioned within and between Methanosarcina mazei populations obtained from two different sediment environments in the Columbia River Estuary (Oregon, USA). Population genomic analysis of 56 M. mazei isolates averaging <1% nucleotide divergence revealed two distinct clades, which we refer to as ‘mazei-T’ and ‘mazei-WC’. Genomic analyses showed that these clades differed in gene content and fixation of allelic variants, which point to potential differences in primary metabolism and also interactions with foreign genetic elements. This hypothesis of niche partitioning was supported by laboratory growth experiments that revealed significant differences in trimethylamine utilization. These findings improve our understanding of the ecologically relevant scales of genomic variation in natural systems and demonstrate interactions between genetic and ecological diversity in these easily cultivable and genetically tractable model methanogens.
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Acknowledgements
We thank Maya Errabolu for helping collect gas chromatography measurements, Gargi Kulkarni for isolating M. mazei WWM610 and everyone involved in the Genomes to Life: Biological Systems Research on the Role of Microbial Communities in Carbon Cycling project, especially Matt Benedict, Judy Luke and Sarah Reinhart. We also thank Mary Elizabeth Metcalf, Nicolai Müller, Petra Kohler, Madeline López-Muñoz, Thom Mand, Andrew He Fu and Jeremy Ellermeier for providing assistance with anaerobic cultivation and gas chromatography analysis. This material is based on work supported in part by the Department of Energy under grant no. DE-SC0005348.
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Youngblut, N., Wirth, J., Henriksen, J. et al. Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment. ISME J 9, 2191–2205 (2015). https://doi.org/10.1038/ismej.2015.31
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DOI: https://doi.org/10.1038/ismej.2015.31
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