Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments

ISME J. 2018 Feb;12(2):411-423. doi: 10.1038/ismej.2017.173. Epub 2017 Nov 14.


Methanogens have long been considered strictly anaerobic and oxygen-sensitive microorganisms, but their ability to survive oxygen stress has also been documented. Indeed, methanogens have been found in oxidative environments, and antioxidant genes have been detected in their genomes. How methanogens adapt to oxidative environments, however, remain poorly understood. Here, we systematically predicted and annotated antioxidant features from representative genomes across six well-established methanogen orders. Based on functional gene content involved in production of reactive oxygen species, Hierarchical Clustering analyses grouped methanogens into two distinct clusters, corresponding to the Class I and II methanogens, respectively. Comparative genomics suggested a systematic shift in metabolisms across the two classes, resulting in an enrichment of antioxidant features in the Class II. Moreover, meta-analysis of 16 S rRNA gene sequences obtained from EnvDB indicated that members of Class II were more frequently recovered from microaerophilic and even oxic environments than the Class I members. Phylogenomic analysis suggested that the Class I and II methanogens might have evolved before and around the Great Oxygenation Event, respectively. The enrichment of antioxidant features in the Class II methanogens may have played a key role in the adaption of this group to oxidative environments today and historically.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antioxidants / chemistry
  • Bayes Theorem
  • Cluster Analysis
  • DNA Repair
  • Euryarchaeota / genetics*
  • Euryarchaeota / metabolism
  • Genome, Bacterial
  • Genomics*
  • Methane / metabolism*
  • Oxidative Stress*
  • Phylogeny
  • RNA, Bacterial / genetics
  • RNA, Ribosomal, 16S / genetics
  • Reactive Oxygen Species / metabolism


  • Antioxidants
  • RNA, Bacterial
  • RNA, Ribosomal, 16S
  • Reactive Oxygen Species
  • Methane