Evolutionary diversification and metabolic adaptations of ANME-1 archaea

Abstract Anaerobic methanotrophic archaea (ANME) of the ANME-1 clade are pivotal regulators of the global carbon cycle, yet the genomic basis underlying their ecological diversification and broad environmental distribution remains poorly understood. Here, we conducted a comparative phylogenomic and genomic analysis of 132 ANME-1 metagenome-assembled genomes (MAGs) spanning hydrothermal vents, cold seeps, and other marine and terrestrial habitats. Our analysis substantially expands the genomic representation of ANME-1 diversity, resolving 14 distinct genus-level phylogenetic clusters organized into three monophyletic subclades (ANME-1a, 1b, and 1c) with distinct biogeographic patterns and habitat preferences. Notably, we identify a conserved Fae-Hps gene configuration that provides a candidate route for formaldehyde processing in the near-universal absence of the canonical mer gene across ANME-1 genomes. Furthermore, we observed lineage-associated distributions of ADP-forming acetyl-CoA synthetase ( acs ), with genes detected in ANME-1a and ANME-1b, suggesting lineage-associated differences in acetate activation potential. Available ANME-1c genomes are associated with hydrothermal environments and show the highest predicted optimum growth temperatures (median 71.6 °C), whereas ANME-1a and ANME-1b display broader predicted pH and salinity ranges consistent with their wider representation across marine and non-marine habitats. Our findings reveal a highly modular metabolic architecture integrating a conserved core pathway for anaerobic oxidation of methane with lineage-variable electron transport systems (e.g., Rnf, Ehb, and MHCs), which may contribute to the niche differentiation and the broad ecological distribution of ANME-1 across Earth’s diverse anoxic habitats.