Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota

Abstract

Methanogenesis is the primary biogenic source of methane in the atmosphere and a key contributor to climate change. The long-standing dogma that methanogenesis originated within the Euryarchaeota was recently challenged by the discovery of putative methane-metabolizing genes in members of the Bathyarchaeota, suggesting that methanogenesis may be more phylogenetically widespread than currently appreciated. Here, we present the discovery of divergent methylcoenzyme M reductase genes in population genomes recovered from anoxic environments with high methane flux that belong to a new archaeal phylum, the Verstraetearchaeota. These archaea encode the genes required for methylotrophic methanogenesis, and may conserve energy using a mechanism similar to that proposed for the obligate H 2 -dependent methylotrophic Methanomassiliicoccales and recently described Candidatus 'Methanofastidiosa'. Our findings indicate that we are only beginning to understand methanogen diversity and support an ancient origin for methane metabolism in the Archaea, which is changing our understanding of the global carbon cycle.

Effects of alternative electron acceptors on the activity and community structure of methane-producing and consuming microbes in the sediments of two shallow boreal lakes

“…Yet, to the best of our knowledge, this is the first report showing active mcrA expression (albeit low) by the very recently described phyla Verstraetearchaeota (Vanwonterghem et al 2016) in any environment, as well as the second report after a study from Lake Pavin , to show the active mcrA expression of Methanomassiliicoccales in lake sediments.…”

“…Framebot (FunGene website, http://fungene.cme.msu.edu/FunGenePipeline; Wang et al 2013) was used to correct frameshift errors in the mcrA reads. The 16S rRNA gene sequences were assigned to taxonomies with a naïve Bayesian classifier (bootstrap value cut off = 75%) (Wang et al 2007) using the Greengenes database, which was amended by sequences of the recently described archaeal phyla Verstraetearchaeota presented in Vanwonterghem et al (2016). Unclassified sequences as well as the sequences classified as chloroplasts, mitochondria, and eukaryota were removed.…”

“…Each sample was subsampled to the size of the smallest The bacterial and archaeal OTUs were classified into functional groups. For the archaea, these were: (1) acetate, (2) H 2 + CO 2 , (3) methyl compound (Nazaries et al 2013), (4) H 2 + methyl compound consuming methanogens (Borrel et al 2013;Vanwonterghem et al 2016),…”

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

“…These include elucidation of several phyla previously lacking genomic representatives [27][28][29] , including the Patescibacteria superphylum 4 , which has subsequently been referred to as the 'Candidate Phyla Radiation' (CPR) as it may consist of upwards of 35 candidate phyla 10,30 . Notable evolutionary and metabolic insights include the discovery of eukaryotic-like cytoskeleton genes in the archaeon Lokiarchaeota 31,32 and the identification of putative methane-metabolizing genes in the Bathyarchaeota and Verstraetearchaeota phyla 33,34 . These initial studies demonstrate the need for additional genomic representatives across the tree of life in order to more fully appreciate microbial evolution and metabolism.…”

Reverse Methanogenesis and Respiration in Methanotrophic Archaea

“…More ANME phylotypes in different environments and possibly new archaeal clades involved in AOM may yet have to be discovered. For example, methyl coenzyme M reductase A genes ( mcrA ) from Bathyarchaeota (formerly known as Miscellaneous Crenarchaeota Group) and from the new archaeal phylum Verstraetearchaeota were recently found, indicating their involvement in methane metabolism [37, 38]. …”