Comparative genomics of three Methanocellales strains reveal novel taxonomic and metabolic features

Methanocellales represents a new order of methanogens, which is widespread in environments and plays specifically the important role in methane emissions from paddy fields. To gain more insights into Methanocellales, comparative genomic studies were performed among three Methanocellales strains through the same annotation pipeline. Genetic relationships among strains revealed by genome alignment, pan-genome reconstruction and comparison of amino average identity suggest that they should be classified in different genera. In addition, multiple copies of cell cycle regulator proteins were identified for the first time in Archaea. Core metabolisms were reconstructed, predicting certain unique and novel features for Methanocellales, including a set of methanogenesis genes potentially organized toward specialization in utilizing low concentrations of H2, a new route of disulfide reduction catalysed by a disulfide-reducing hydrogenase (Drh) complex phylogenetically related to sulfate-reducing prokaryotes, an oxidative tricarboxylic acid (TCA) cycle, a sophisticated nitrogen uptake and regulation system as well as a versatile sulfur utilization system. These core metabolisms are largely conserved among the three strains, but differences in gene copy number and metabolic diversity are evident. The present study thus adds new dimensions to the unique ecophysiology of Methanocellales and offers a road map for further experimental characterization of this methanogen lineage.