Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments

Abstract

Metagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated the methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiments. Detection of gene amplicons of methyl-coenzyme M reductase subunit A (mcrA) indicated a wide diversity of Mcr-encoding archaea across geothermal features with differing physicochemical regimes. From three selected hot springs we recovered twelve Mcr-encoding metagenome assembled genomes (MAGs) affiliated with lineages of cultured methanogens as well as Candidatus (Ca.) Methanomethylicia, Ca. Hadesarchaeia, and Archaeoglobi. These MAGs encoded the potential for hydrogenotrophic, aceticlastic, or hydrogen-dependent methylotrophic methanogenesis, or anaerobic short-chain alkane oxidation. While Mcr-encoding archaea represented a minor fraction of the microbial community of hot springs, mesocosm experiments with methanogenic precursors resulted in stimulation of methanogenic activity and the enrichment of lineages affiliated with Methanosaeta and Methanothermobacter as well as with uncultured Mcr-encoding archaea including Ca. Korarchaeia, Ca. Nezhaarchaeia, and Archaeoglobi. Altogether, we revealed that diverse Mcr-encoding populations with the metabolic potential to produce methane from different precursors persist in the geothermal environments of YNP. This study highlights the importance of combining environmental metagenomics with laboratory-based experiments to expand our understanding of uncultured Mcr-encoding archaea and their potential impact on microbial carbon transformations in geothermal environments and beyond.

Cultivation and visualization of a methanogen of the phylum Thermoproteota

“…In a recent survey of 100 geothermal features in Yellowstone National Park (YNP), we identified the Lower Culex Basin (LCB) as an area with strong potential for anaerobic methane cycling 16 . From sediments of one of these hot springs, designated feature LCB070, we obtained a metagenome from which we reconstructed several MCR-encoding MAGs.…”

“…Locality. Sediment from a hot spring, identified as feature LCB070 in a recent survey 16 of Yellowstone National Park (WY, USA) geothermal features.…”

“…yellowstonensis, from Yellowstone National Park. This archaeon was cultured from an unnamed hot spring in Yellowstone National Park that we identified as feature LCB070 in a recent survey 16 . The archaeon is a thermophilic methylreducing hydrogenotrophic methanogen growing as coccoid cells with a diameter of 845 ± 163 nm.…”

“…However, so far, no methanogen from outside the Euryarchaeota has been cultured or even visualized by microscopy, and there is no experimental evidence to support metagenome-based predictions of their metabolism. Geothermal features, such as hot springs, have recently been shown to harbor a wide diversity of MCR-encoding archaea 3,4,[14][15][16][17] . The extreme nature of hot springs reduces their community complexity relative to temperate environments, which makes them promising sources for targeted cultivation of these microorganisms.…”

Methylotrophic methanogenesis in the Archaeoglobi revealed by cultivation ofCa.Methanoglobus hypatiae from a Yellowstone hot spring

“…16S rRNA and mcrA gene amplicon sequence data generated in a recent microbial diversity survey of 100 geothermal features in YNP (33) were used to analyze the distribution of Archaeoglobi related to Ca. M. hypatiae (SI Appendix, Fig.…”