Microbial succession, community assembly and adaptation over five years in a newly discovered deep-sea cold seep

Deep-sea cold seeps, characterized by the release of hydrocarbon-rich fluids such as methane from the seafloor, create unique ecosystems. Microorganisms serve as pioneers, initially colonizing early-stage cold seeps and providing matter and energy for subsequent colonizers. However, microbial succession, community assembly, and adaptation in these environments remain largely unexplored. Here, we collected sediment samples from a newly discovered early-stage cold seep site, QDN-W07, in the South China Sea at varying depths over five years, and two previously reported cold seep sites, QDN-S18 and HM-ROV01, for comparative analysis. Amplicon sequencing revealed a high relative abundance of ANME-3 and Methylomonadaceae in surface sediments, and indicated changes in microbial community structures over time. Dispersal limitation and homogeneous selection dominated community assembly, while decreased intensity of microbial association influencing assembly mechanism over time. Metagenomic analysis of core microbiome, comprising 172 metagenomic-assembled genomes at QDN-W07, revealed tolerance to low temperatures and oxygen. Core microbiome genomes were enriched with genes related to the oxidation of multiple inorganic compounds, especially aerobic methane oxidation. Overall, this study enhances our understanding of deep biosphere life, biogeochemical cycling, and the ecological management of cold seep environments.