Distribution, diversity, and physiology of uncultured MCR-encoding microbial populations in Yellowstone Hot Springs

Abstract

Methane, a climate active gas, is an integral component to the global carbon cycle. Microbial activity mediates the transformations of carbon, with methanogenic archaea driving the conversion of organic matter to methane in anoxic environments. Understanding the distribution and activity of methanogenic archaea is essential for estimating their contribution to the carbon cycle and global methane emissions. In the last decade, metagenomic sequencing has expedited the formulation of hypotheses regarding archaea classified outside of established methanogenic lineages, which possess genes responsible for methane production. However, the verification of these hypotheses is often hindered by the difficulties encountered in culturing these organisms. Additionally, these organisms often encode other energy conserving pathways, thus underscoring the necessity for experimental validation of their metabolism. This dissertation is dedicated to exploring the diversity and physiology of methanogenic populations in hot springs of Yellowstone National Park beginning with the collection of primary data from previously uncharacterized geothermal features. To date, this has resulted in the most extensive geochemical and microbiological survey conducted within the Yellowstone geothermal complex. This dataset served as a foundational basis for investigating uncultured methanogenic lineages and their activities in geothermal environments. Through the integration of amplicon sequencing, metagenomics, and mesocosm experiments, the presence and diversity of methanogenic communities in hot springs was revealed and novel lineages were stimulated under methanogenic conditions, resulting in their enrichment. This study emphasizes the impact able to be achieved by combining environmental metagenomics with laboratory-based experiments. To further explore the methanogenic potential revealed by these experiments, our focus shifted towards enriching a novel methanogenic lineage. Through our efforts, we were successful in cultivating the first methanogenic member of the family Archaeoglobaceae, providing genomic and transcriptomic evidence to validate its ability to live as a methyl-reducing methanogen, reducing methylamines to methane. Comprehensively, the work presented here broadens our understanding of methanogenic communities in Yellowstone National Park and contributes to the broader understanding of methanogenesis in geothermal environments.