In the steaming hot springs of Tengchong, in China’s southwestern Yunnan Province, a team of researchers has uncovered a hidden world of methane-cycling microbes that is forcing scientists to rethink where methanogenesis—the biological production of methane—belongs on the tree of life. Methane is a potent greenhouse gas with profound implications for Earth’s climate, and for decades the process responsible for most of its global biological emissions was believed to be the exclusive domain of a single archaeal superphylum, the Euryarchaeota. The new study, published in BMC Biology, demonstrates that a second great branch of the archaea, Thermoproteota (formerly known as the TACK superphylum), not only carries the genetic machinery for methane metabolism but in these geothermal habitats appears to dominate it.
The research, led by Xiao-Xi Chen, Yan-Ni Qu, Yu-Xian Li, Zheng-Shuang Hua and colleagues, with contributions from Paul N. Evans at the University of Queensland, is built on an ambitious sampling campaign across 157 terrestrial geothermal springs in the Tengchong volcanic field. Using metagenomic sequencing—direct sequencing of the pooled DNA of entire microbial communities, without the need to culture anything in a laboratory—the team reconstructed 104 metagenome-assembled genomes, or MAGs, that contained genes for methyl-coenzyme M reductase, or Mcr. This enzyme complex sits at the heart of all known biological methane metabolism, catalyzing the final step of methanogenesis and, when run in reverse, the first step of anaerobic methane oxidation. Ninety of the recovered MAGs encoded what the researchers classify as Group II Mcr proteins, a lineage of the enzyme associated with Thermoproteota rather than the classical euryarchaeotal Group I Mcr lineages. Strikingly, in most of the spring samples examined, these Group II Mcr-encoding organisms were more abundant than their euryarchaeotal counterparts, overturning the expectation that Euryarchaeota should be the dominant methane-cyclers in such environments.
The single most numerous lineage among the recovered genomes was Methanosuratincolia, a class of Thermoproteota that has been repeatedly implicated in methane cycling in recent years but remains poorly characterized. By carefully annotating the gene neighborhoods of the Mcr locus in these organisms, the team delineated a typical operon structure associated with methyl catabolism across the group—an arrangement of co-localized genes encoding the enzymatic machinery needed to break down methylated compounds. This genomic architecture suggests that these hot spring archaea are equipped for methylotrophic methanogenesis, the pathway that uses substrates such as monomethylamine, dimethylamine and trimethylamine as the building blocks for methane. In the wet chemistry of a geothermal spring, where organic methylated compounds can be generated by the surrounding microbial community, such a metabolic strategy would allow these organisms to tap into a readily available carbon and energy source without requiring hydrogen or carbon dioxide.
The environmental context of the study proved to be as informative as the genomes themselves. Tengchong’s springs span an extraordinary range of physicochemical conditions, from near-neutral to strongly alkaline waters and from moderately warm pools to boiling, superheated vents. By correlating the composition of the Mcr-containing archaeal communities with measured environmental parameters, the researchers found that pH and temperature were the strongest predictors of where these organisms live. But the team went a step further than community profiling. Using metatranscriptomics—the sequencing of RNA extracted directly from the springs—they assessed which genes were actually being expressed by the resident microbes. The results were unambiguous: genes associated with methane metabolism showed high transcriptional activity in the hottest and most alkaline settings, specifically those springs exceeding 70 degrees Celsius and pH values above 9. In other words, these organisms are not merely present in extreme environments as dormant passengers; they are actively transcribing the machinery of methane cycling in conditions that would kill most known life.
A further surprise came from the reconstruction of three Bathyarchaeia MAGs carrying pathways potentially linked to hydrogenotrophic methanogenesis, the hydrogen-and-carbon-dioxide-based route to methane that is the classical pathway in Euryarchaeota. Bathyarchaeia is one of the most abundant and metabolically versatile groups of archaea in marine sediments and terrestrial subsurface environments, yet its members have long eluded cultivation. The finding that some Bathyarchaeia in Tengchong’s springs may combine hydrogenotrophic methanogenesis genes with heterotrophic metabolism—meaning they could both fix carbon via methane-related pathways and consume organic matter—adds a new layer of complexity to our understanding of the archaeal carbon cycle. It suggests that within a single lineage, the capacity to interconvert methylated compounds, hydrogen, carbon dioxide and methane may be woven together in ways that do not map neatly onto the textbook categories of methanogenic metabolism.
The evolutionary story that emerges from the study is equally provocative. Phylogenetic analyses of the methanogenesis-associated proteins, including the individual subunits of the Mcr complex and its associated cofactor-binding partners, are consistent with methylotrophic methanogenesis being the ancestral state among the currently sampled Mcr-containing Thermoproteota. From this ancestral core, the different lineages appear to have acquired, lost and modified hydrogenotrophic components independently over evolutionary time, producing the patchwork of metabolic capabilities observed today. The team also identified sequence-level signatures suggesting a possible horizontal gene transfer event between Mcr-containing Bathyarchaeia and Methanonezhaarchaeia—two deeply branching archaeal classes that both carry methane-cycling genes. Intriguingly, the direction of this transfer could not be resolved from the data, meaning that either group could have served as the donor of the methanogenesis genes to the other. Horizontal gene transfer, the movement of genetic material between organisms that are not parent and offspring, is increasingly recognized as a major force shaping the distribution of metabolic traits across the archaeal domain, and this finding adds methane cycling to the list of capacities that may have jumped between distantly related lineages.
The methodological rigor behind these conclusions deserves emphasis. Metagenomic assembly of environmental DNA into complete genomes is notoriously difficult in highly diverse communities, and the researchers took several steps to ensure that their Mcr-containing scaffolds were genuinely part of the genomes to which they were assigned. Assembly graph inspection, scaffold-level binning metrics, and assessments of sequence depth and genomic consistency were used to verify that the methane-cycling genes were embedded within the Bathyarchaeia and other Thermoproteota genomes rather than being contamination artifacts or unresolved chimeras. The study also examined gene expression profiles in samples where mcrABG genes were not detected, providing a comparative baseline that strengthened the interpretation of the transcriptomic signals from the methane-cycling populations. Such controls are critical in a field where the presence of a single gene in a metagenome has, in the past, been enough to trigger debates about whether the gene truly belongs to the organism whose genome it appears to inhabit.
The broader significance of the work lies in its implications for both climate science and evolutionary biology. Methane traps far more heat per molecule than carbon dioxide over short timescales, and global emissions are largely driven by biological methanogenesis carried out by archaea in wetlands, rice paddies, ruminant guts, landfills and marine sediments. If a second archaeal superphylum contributes meaningfully to methane cycling—particularly in extreme environments such as geothermal springs that were previously considered marginal players in the global methane budget—then existing models of methane flux may be incomplete. The Tengchong findings suggest that the diversity of methane-cycling archaea is substantially wider than currently represented in genomic databases, and that lineages such as Methanosuratincolia, Bathyarchaeia and Methanonezhaarchaeia may be carrying out methane metabolism at ecologically meaningful rates in hot, alkaline environments around the world.
The study also speaks to one of the deepest questions in biology: the origin of methanogenesis itself. Because methanogenesis is an ancient metabolism, plausibly dating back to some of the earliest forms of cellular life on Earth, the distribution of its enzymes across the tree of life carries information about the metabolic capabilities of our most distant ancestors. The evidence that methylotrophic methanogenesis is ancestral among sampled Mcr-containing Thermoproteota, with hydrogenotrophic capacities acquired later and in patchwork fashion, feeds into an ongoing debate about whether the last universal common ancestor of all life had methanogenic capabilities, and whether the pathway evolved once and spread by horizontal transfer, or arose independently in different lineages. While the new study cannot settle these questions definitively, its phylogenetic reconstructions of the Mcr, Cdh and MtaA protein families provide a substantially expanded dataset for future work.
What remains clear is that the archaeal domain still holds vast unexplored diversity with direct relevance to the planet’s carbon cycle. By expanding the known diversity of Mcr-containing archaea and offering new insights into their biogeography, ecological functions and evolutionary origins, the Tengchong study adds important pieces to a puzzle that connects molecular evolution, microbial ecology and global climate. As metagenomic surveys of extreme environments continue to multiply, it seems increasingly likely that the methane-cycling archaea we know today represent only a fraction of the lineages that have shaped, and continue to shape, the atmospheric chemistry of our planet. The steaming springs of Tengchong, it turns out, were not a niche curiosity but a window into one of biology’s oldest and most consequential inventions.
Subject of Research: Diversity, ecology and evolution of Group II Mcr-encoding archaea involved in methane cycling in terrestrial geothermal springs
Subject of Research: Biology
Article Title: Group II Mcr-encoding archaea exhibit methane-cycling potential in geothermal springs
Article References: Chen, X.-X., Qu, Y.-N., Li, Y.-X., Rao, Y.-Z., Li, Z.-W., Xie, Q.-J., Zhang, Y.-Q., Evans, P. N., Li, W.-J., & Hua, Z.-S. (2026). Group II Mcr-encoding archaea exhibit methane-cycling potential in geothermal springs. BMC Biology. https://doi.org/10.1186/s12915-026-02727-z
Image Credits: AI Generated
DOI: 10.1186/s12915-026-02727-z
Keywords: Terrestrial geothermal springs, Methanogenesis, Methyl-coenzyme M reductase (Mcr), Thermoproteota, Bathyarchaeia, Methanosuratincolia, Metagenome-assembled genomes, Horizontal gene transfer, Evolutionary history, Metatranscriptomics, Greenhouse gas, Methane cycling
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Morgan Morrow. (September 10, 2026). Methane-cycling archaea discovered in geothermal springs. Scienmag. https://scienmag.com/methane-cycling-archaea-discovered-in-geothermal-springs/
Morgan Morrow. “Methane-cycling archaea discovered in geothermal springs.” Scienmag, 10 September 2026, https://scienmag.com/methane-cycling-archaea-discovered-in-geothermal-springs/. Accessed 10 September 2026.
Morgan Morrow. “Methane-cycling archaea discovered in geothermal springs.” Scienmag. September 10, 2026. https://scienmag.com/methane-cycling-archaea-discovered-in-geothermal-springs/
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Tags: archaeal phylogeneticsarchaeal phylogeny and evolutionEarth’s greenhouse gas sourcesenvironmental DNA analysis of microbial communitiesgeothermal microbiome researchgeothermal spring microbiologygreenhouse gas emissions from geothermal habitatsimpact of geothermal microbes on climateimplications for global methane cyclemetagenomic sequencing of geothermal microbesmetagenomic sequencing of microbial communitiesmethane metabolism in archaeamethane-cycling archaeaMethane-cycling archaea in geothermal springsmicrobial diversity in hot springsmicrobial ecology of Tengchong hot springsmicrobial evolution of methane pathwaysmicrobial methane metabolismnovel methane-producing archaeanovel methanogenic archaeaTACK superphylum archaeaTACK superphylum methane production
