Ecological distribution and metabolic potential of Marine Group II archaea in the Eastern Indian Ocean: Evidence for heterotrophic carbon fixation

Marine Group II (MGII) archaea are globally distributed in oceanic waters, yet their ecological functions and metabolic potentials remain elusive due to the lack of pure culture. Here, we investigate the diversity, distribution, and metabolic potential of MGII archaea in the Eastern Indian Ocean using high-throughput sequencing and metagenomic analyses. We identified 37 MGII operational taxonomic units(OTUs), with surface and deep chlorophyll maximum (DCM) layers dominated by clade O1, O3, and P, and deeper waters by O4 and H, reflecting depth-specific ecological niches shaped by environmental gradients. Metagenomic reconstruction yielded 29 archaeal metagenome-assembled genomes (MAGs), including two novel MGII genomes within the Poseidoniaceae and Thalassarchaeaceae families. Metagenomic analysis further revealed previously uncharacterized pathways in MGII, including heterotrophic inorganic carbon fixation via anaplerotic pathways. Notably, the clade N1, prevalent in the DCM, shows strong potential for inorganic carbon assimilation, implicating MGII archaea in the microbial carbon pump and CO₂ sequestration. Our results underscore the critical, yet underappreciated, role of MGII archaea in marine biogeochemical cycles and global carbon sink, emphasizing their contribution to CO₂ sequestration in oligotrophic marine environments.