Abstract
Deep-sea hydrothermal vents represent some of the most physiologically demanding poly-extreme environments on Earth, characterized by superheated fluids, high hydrostatic pressures, steep redox gradients, and toxic concentrations of heavy metals. In this study, we performed a comprehensive comparative metagenomic analysis of microbial communities sampled from disparate vent provinces: the basalt-hosted Lucky Strike vent field on the Mid-Atlantic Ridge and the ultramafic-influenced Kilo Moana field in the Eastern Lau Spreading Center. High-throughput shotgun sequencing coupled with hybrid de novo assembly and differential binning yielded 142 high-quality metagenome-assembled genomes (MAGs) spanning 18 bacterial and 4 archaeal phyla. Functional metabolic reconstruction revealed profound niche differentiation governed by geochemical regimes. While Campylobacteria dominated diffuse flow regions utilizing the reductive tricarboxylic acid (rTCA) cycle coupled to sulfur and hydrogen oxidation, Gammaproteobacteria favored chimney walls through the Calvin-Benson-Bassham (CBB) cycle. Furthermore, we identified lineage-specific structural and enzymatic adaptations, including enriched gene clusters encoding heavy-metal efflux pumps (CzcCBA and CopA systems), extensive DNA repair machineries (RadA/RecA and UvrABC excinucleases), and universal molecular chaperones (GroEL-GroES and DnaK). Comparative pan-genomic evaluations demonstrated high frequencies of horizontal gene transfer mediated by transposases and viral auxiliary metabolic genes, driving dynamic niche adaptation. Our findings illuminate the evolutionary trajectories and genomic flexibility that enable uncultured vent microbiomes to sustain primary production and biogeochemical cycling under persistent thermodynamic disequilibria.
