Isolation of a methyl-reducing methanogen outside the Euryarchaeota

Methanogenic archaea are main contributors to methane emissions, and thus play a crucial role in carbon cycling and global warming. Until recently, methanogens were confined to the phylum Euryarchaeota, but metagenomic studies revealed the presence of genes encoding the methyl coenzyme M reductase complex in other archaeal clades, thereby opening up the premise that methanogenesis is taxonomically more widespread. Nevertheless, laboratory cultivation of these non-Euryarchaeal methanogens was missing to allow the study of their physiology and to corroborate their potential methanogenic capability. Here we describe a thermophilic co-culture from an oil field, containing a single archaeon (strain LWZ-6) belonging to the proposed order Candidatus Verstraetearchaeia, together with a H2-producing Acetomicrobium sp. CY-2. Strain LWZ-6, for which we propose the name Verstraetearchaeum methanopetracarbonis, is a H2-dependent methylotrophic methanogen. Although previous metagenomic studies speculated on the fermentative potential of Verstraetearchaeial methanogens, strain LWZ-6 does not ferment sugars, peptides, and amino acids. Its energy metabolism is linked to methanogenesis, with methanol and monomethylamine as electron acceptors and H2 as electron donor. Comparative (meta)genome analysis revealed that H2-dependent methylotrophic methanogenesis is a shared trait among Verstraetearchaeia. Our findings corroborate that the diversity of methanogens expands beyond the classical Euryarchaeota and change our current conception of the global carbon cycle.