Reconstruction of metagenome-assembled genomes involved in methane cycling from ancient Siberian permafrost sediments

Abstract:

Considerable amount of ancient methane has been recorded in various strata of permafrost up to several hundred meters deep. However, the microorganisms responsible for past and present methane production and anaerobic methane oxidation (AOM) remain underexplored. The DNA preserved in the ancient permafrost records microbial lineages involved in methane cycling through geological time. By using metagenomic sequencing of DNA after repair, three metagenome-assembled genomes (MAGs) were reconstructed from marine permafrost sediment (>100 kyr old) located along the coast of East Siberian Sea. Phylogenetic analyses revealed that one MAG was identified as methanogen affiliated with Methanoregula whereas the other two were closely related to anaerobic methanotrophs belonging to ANME-1 and ANME-2. The methanogenic MAG showed high AAI (Average amino acid identity) with other known Methanoregula species (up to 90.2%). Much lower AAI values (69%-80%) were found between the two methanotrophic MAGs and other reported members of ANME-1 and ANME-2, highlighting the phylogenetic novelty of ANMEs in ancient marine permafrost. All MAGs contained genes encoding methyl-coenzyme M reductase, the crucial enzyme responsible for the last step in methanogenesis and the first step in AOM. The methanogenic MAG was found to be hydrogenotrophic whereas the two methanotrophic MAGs (ANME-1 and ANME-2) can potentially perform sulfate-dependent AOM via a syntrophic relationship with sulfate-reducing bacteria in the marine sediment. The highly damaged DNA from all three MAGs indicated that these archaeal lineages have died upon freezing in the cryogenic environments over time. Therefore, these methanogenic and methanotrophic lineages from the permafrost likely contributed to methane cycling in the marine sediment prior to freezing 100 kyr ago.