Beyond methane

New research suggests methane production isn’t restricted to just one archaeal phylum, as previously thought and an evolution of methane metabolism for using bigger substrates.
Published in Microbiology
Beyond methane

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Methane is a well-known gas for scientists. The simplest of hydrocarbons has been studied by a wide diversity of scholars, from climate researchers (due to its big impact in climate change) to astrobiologists (who proposed a possible existence of life in worlds like Titan, which possesses methane lakes). On Earth, methane metabolism is incredibly interesting for microbiologist since it has been proposed to be one of the earliest one in Earth history.

Until recently, methane production (or methanogenesis) and anaerobic methane oxidation had been restricted to one group of archaea: the phylum Euryarchaeota. Methanogens are organisms able to produce methane, while anaerobic methane oxidizers (or methanotrophs) are organisms able to degrade methane anaerobically in a process called anaerobic oxidation of methane (AOM). Both performed these processes using the same enzyme, called methyl-coenzyme M reductase or MCR (see image below). MCR can work in both directions either producing methane (like in methanogens) or oxidizing it (like in methanotrophs).

MCR showed a high specificity for methane1. However, in the last years, several articles have raised more attention in the versatility of methane metabolism and in the MCR enzyme, as new findings suggest that this metabolic pathway could not be restricted to Euryarchaeota, and that the mcr genes could have evolved, in some organisms, to use bigger alkanes than methane.

These two recent articles have shown for the first time that mcr genes are found in organisms different than Euryarchaeota. Evans and colleagues were the first to show mcr genes in metagenomic genomes from the recently described phylum Bathyarchaeota2. Their mcr genes were highly divergent from any other mcr genes found so far. Another article published last year showed the presence of mcr genes in another metagenomics bin from a new phylum called Verstraetearchaeota3. In both of them, it was suggested that these organisms are performing methanogenesis.

Another article, published also last year by Laso-Pérez and colleagues, has shown for the first time the use of MCR to metabolize a substrate different than methane: butane4. The organisms responsible of that were named Candidatus Syntrophoarchaeum and belong to an unknown group within the Euryarchaeota. Butane has four atoms and therefore the MCR enzyme is presumably highly modified to accommodate a much larger substrate than methane with just one carbon. This hypothesis is supported by phylogenetic analysis, which showed that mcr genes of Ca. Syntrophoarchaeum were highly different than the traditional ones of methanogens and methanotrophs. Surprisingly, these genes fall closely to the Bathyarchaeota mcr genes. Since the Bathyarchaeota paper was based just on genome analyses, it could not be discarded that Bathyarchaeota is implicated in the metabolism of larger substrates than methane. Related sequences of both Candidatus Syntrophoarchaeum and Bathyarchaeota have been found in different deep-sea environment what could indicate an important environmental role of these microorganisms in the cycling of alkanes.

All these findings point towards the emergence of new directions in methane metabolism research and of other related substrates. Methane metabolism seems not to be restricted to just one phylum, arguing in favor of methanogenesis as one of the earliest metabolism in Earth’s history. Neither methane metabolism genes (like the MCR enzyme) seem to be as exclusive as thought before. Higher alkanes than methane, like propane and butane, could be degraded in the environment using modified MCRs which can be important for natural gas cycling and management and maybe the production of future biofuels5.


1) Scheller, S., Goenrich, M., Thauer, R. K., & Jaun, B. (2013). Methyl-coenzyme M reductase from methanogenic archaea: Isotope effects on the formation and anaerobic oxidation of methane. J. Am. Chem. Soc, 135(40), 14975-14984.

2) Evans, P. N., Parks, D. H., Chadwick, G. L., Robbins, S. J., Orphan, V. J., Golding, S. D., & Tyson, G. W. (2015). Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science, 350(6259), 434-438.

3) Vanwonterghem, I., Evans, P. N., Parks, D. H., Jensen, P. D., Woodcroft, B. J., Hugenholtz, P., & Tyson, G. W. (2016). Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nature Microbiology, 1, 16170.

4) Laso-Pérez, R., Wegener, G., Knittel, K., Widdel, F., Harding, K. J., Krukenberg, V., Meier, D.V., Richter, M., Tegetmeyer, H., Riedel, D., Richnow, H. H., Adrian, L., Reemtsma, T., Lechtenfeld, O.J. and Musat, F. (2016). Thermophilic archaea activate butane via alkyl-coenzyme M formation. Nature, 539(7629), 396-401.

5) Ragsdale, S. W. (2016). Microbiology: Deep-sea secrets of butane metabolism. Nature, 539(7629), 367-368.

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