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Recent discoveries have shown that the marker gene for anaerobic methane cycling ( mcrA ) is more widespread in the  Archaea  than previously thought. However, it remains unclear whether novel  mcrA  genes associated with the Bathyarchaeota and Verstraetearchaeota are distributed across diverse environments. We examined two geochemically divergent but putatively methanogenic regions of Yellowstone National Park to investigate whether deeply-rooted archaea possess and express novel  mcrA  genes  in situ . Small-subunit (SSU) rRNA gene analyses indicated that Bathyarchaeota were predominant in seven of ten sediment layers, while the Verstraetearchaeota and Euryarchaeota occurred in lower relative abundance. Targeted amplification of novel  mcrA  genes suggested that diverse taxa contribute to alkane cycling in geothermal environments. Two deeply-branching  mcrA  clades related to Bathyarchaeota were identified, while highly abundant verstraetearchaeotal  mcrA  sequences were also recovered. In addition, detection of SSU rRNA and  mcrA  transcripts from one hot spring suggested that predominant Bathyarchaeota were also active, and that methane cycling genes are expressed by the Euryarchaeota, Verstraetearchaeota, and an unknown lineage basal to the Bathyarchaeota. These findings greatly expand the diversity of the key marker gene for anaerobic alkane cycling and outline the need for greater understanding of the functional capacity and phylogenetic affiliation of novel  mcrA  variants.

Occurrence and expression of novel methyl-coenzyme M reductase gene (mcrA) variants in hot spring sediments