Exploration of anaerobic ethane degraders continues

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A year ago, our team uncovered the first archaeal lineage capable to oxidize the gaseous alkane ethane in the absence of oxygen. This archaeon, named ‘Candidatus Argoarchaeum ethanivorans’, was cultivated from a cold marine hydrocarbon seep in the Gulf of Mexico (Chen et al., 2019). Argoarchaeum uses a specific enzyme, alkyl-coenyzme M reductase, in short ACR, to initiate ethane oxidation, and sustains a syntrophic lifestyle with its bacteria partners at low temperatures (12 °C). These findings were well received, with our paper featured in press releases in German, English and Chinese, and mustering over 40 citations within one year since publication. After the release of our work, a great diversity of anaerobic microorganisms thriving on non-methane gaseous alkanes, in other words having physiological properties similar to those of Argoarchaeum, have been identified in nature. For example, the cultivation of a fast-growing, thermophilic archaeon Ca. Ethanoperedens exemplified an extended temperature niche that anaerobic ethane-oxidizers can occupy (Hahn et al., 2020). Moreover, environmental genomic surveys indicated that members of phylogenetically distinct archaeal lineages, including Helarchaeota, Bathyoarchaeota, Hadesarchaea, Archaeoglobi and Candidatus Methanoliparia, have the metabolic potential to activate and subsequently anaerobically oxidize non-methane gaseous hydrocarbons (Evans et al., 2015; Borrel et al., 2019; Laso-Pérez et al., 2019; Seitz et al., 2019; Wang et al., 2019a). Such phylogenetic diversity suggested that ACR-based alkane exploitation might have been an ancient characteristic evolving in the early history of archaea (Betts et al., 2018) and continues to play an essential role in hydrocarbon cycling across a wide range of modern ecosystems (Wang et al., 2019b). 

As the first author of this work, I had a joyful and successful PhD thesis defense last year in May 2019, shortly after our paper was published. The work was highlighted by the experts in my thesis evaluation committee, who nominated me as a candidate for the Presidential Scholarship of the Chinese Academy of Science (CAS), the highest Award for graduate students offered by CAS. My thesis was also selected as one of the top 100 excellent PhD dissertations in CAS. More importantly, by running through the whole research project that led to our Nature publication, I gained experimental techniques and bioinformatics skills necessary for cultivating as well as cracking the physiology and metabolism of novel microbial lineages in the environment. These skills served me well to secure a postdoctoral fellow position at the Helmholtz Centre for Environmental Research – UFZ in Leipzig, Germany, shortly after my defense. From this position I continue my research on hydrocarbon-oxidizing archaea, this time focusing on the metabolic peculiarities of Argoarchaeum and related archaea, and on the exchange of intermediates between the archaea and their bacterial partners. Still, the main challenge of this research lies in the extremely slow growth of these microbes. For example, any physiological experiments with Argoarchaeum take up to six months for an unambiguous result. Despite such drawbacks, it is always exciting when Argoarchaeum feeds back with expected results supporting our hypotheses, or puts us on unexpected lines of investigation. In all, patience and perseverance are key to catch a glimpse of the nature of these sluggish microbes.

The original publication can be found here, and the Behind the Paper blog post can be found here.

1. Betts, H.C., Puttick, M.N., Clark, J.W., Williams, T.A., Donoghue, P.C.J., and Pisani, D. (2018) Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin. Nature Ecology & Evolution 2: 1556-1562.

2. Borrel, G., Adam, P.S., McKay, L.J., Chen, L.-X., Sierra-García, I.N., Sieber, C.M.K. et al. (2019) Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nature Microbiology 4: 603-613.

3. Chen, S.-C., Musat, N., Lechtenfeld, O.J., Paschke, H., Schmidt, M., Said, N. et al. (2019) Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep. Nature 568: 108-111.

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

5. Hahn, C.J., Laso-Perez, R., Vulcano, F., Vaziourakis, K.M., Stokke, R., Steen, I.H. et al. (2020) "Candidatus Ethanoperedens," a thermophilic genus of archaea mediating the anaerobic oxidation of ethane. mBio 11.

6. Laso-Pérez, R., Hahn, C., van Vliet, D.M., Tegetmeyer, H.E., Schubotz, F., Smit, N.T. et al. (2019) Anaerobic Degradation of Non-methane alkanes by “Candidatus Methanoliparia” in hydrocarbon seeps of the Gulf of Mexico. mBio 10: e01814-01819.

7. Seitz, K.W., Dombrowski, N., Eme, L., Spang, A., Lombard, J., Sieber, J.R. et al. (2019) Asgard archaea capable of anaerobic hydrocarbon cycling. Nat Commun 10: 1822.

8. Wang, Y., Wegener, G., Hou, J., Wang, F., and Xiao, X. (2019a) Expanding anaerobic alkane metabolism in the domain of Archaea. Nature Microbiology 4: 595-602.

9. Wang, Y., Feng, X., Natarajan, V.P., Xiao, X., and Wang, F. (2019b) Diverse anaerobic methane- and multi-carbon alkane-metabolizing archaea coexist and show activity in Guaymas Basin hydrothermal sediment. Environmental Microbiology 21: 1344-1355.

 

Song-Can Chen

Postdoctoral researcher, Helmholtz-Centre for Environmental Research - UFZ