Mini-Metagenomics Approach Helps Identify Novel Archaeal Methane Metabolism.
Obsidian Pool hot spring at Yellowstone National Park. (Bob Lindstrom, NPS)
Methane-producing archaea are estimated to produce 500 million tons of methane a year, which is over half the total global methane production. They are thought to use billions of tons of the carbon dioxide trapped in biomass each year to do so. As such, they are considered to have a substantial influence on the global carbon cycle. All methanogenic archaea use one of three pathways for methanogenesis: hydrogen-dependent and CO2-reducing, or hydrogenotrophic (most common); methylotrophic; and, acetoclastic. All three pathways require the gene cluster for methane production known as Mcr. Until recently, the Mcr gene cluster was found only in the archaeal lineage Euryarchaeota; recent studies now suggest the gene cluster predates this microbial group.
Recently published in the Proceedings of the National Academy of Sciences, researchers at Stanford University, the Chan Zuckerberg Biohub, and the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science user facility, report the discovery of a novel archaeum from a hot spring that has the genetic machinery to perform hydrogenotrophic methanogenesis and is not a member of the Euryarchaeota. The archaeum is a member of the Verstraetearchaeota, and the finding lends credence to the idea that the hydrogenotrophic pathway predates the Euryarchaeota lineage and was present in the last common ancestor of the Euryarchaeota and Verstraetearchaeota lineages.
The archaeal genome was detected in samples collected by Stephen Quake’s team at Yellowstone National Park’s Obsidian Pool hot spring. The researchers applied mini-metagenomics to these samples by sorting the microbes into small pools of cells that were then sequenced separately. From these samples, 111 metagenome-assembled genomes (MAGs) were recovered, most of them archaea. The Quake lab had previously collaborated with the JGI on a proposal using this approach through the Emerging Technologies Opportunity Program (ETOP). Following that work, they partnered once more with JGI Microbial Program head Tanja Woyke and her Single Cells team member Frederik Schulz to screen the microbial communities collected.
The team noticed some of the genomes diverged evolutionarily from other previously discovered genomes. When they analyzed the reconstructed metabolisms, they found that one of the MAGs contained the complete set of genes needed for hydrogen-dependent and CO2-reducing methanogenesis. These two things combined led us to conclude that our new methanogen did not belong to the Euryarchaeota, the archaeal “superphylum” where this type of methanogenesis is typically observed, but to the “TACK” superphylum,” said study first author Bojk Berghuis. “This provided us with genetic evidence to tie together the evolutionary history of the different types of methanogenesis occurring in the entire archaeal domain of life.”
References:
- Berghuis BA et al. Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens. Proc Nat Acad Sci. 2019 February 27. doi: 1073/pnas.1815631116
- JGI Science Highlight: New Technology to Access Microbial Dark Matter