The patterns of microbial community distribution and co-occurrence in water columns and sediments of Haima cold seep

Deep-sea cold seeps are essential components of global biodiversity and biogeochemical cycles, whereas the community distribution and co-occurrence patterns of cold seep microorganisms remain poorly understood. Here, we investigated the microeukaryotic and prokaryotic communities across different water layers and benthic habitats in the Haima cold seep of the South China Sea and revealed distinct vertical and horizontal patterns in microbial distribution and co-occurrence between the water columns and sediments. Prokaryotic intra-domain interactions predominated over inter-species correlations in networks, and bacteria-microeukaryote interactions were more abundant in the network of water columns than in sediments, indicating that environmental preferences of microorganisms differed between these environments. The environmental factors and deterministic processes appeared to exert a more pronounced influence on the distribution patterns of microeukaryotes than on prokaryotes in the water columns, whereas the opposite was observed in the sediments. Additionally, microbial co-occurrence patterns were segregated and primarily shaped by deterministic processes. The species interactions were more complex in the euphotic zone and clam (one of the most dominant megabenthos) habitats than those in other water layers and benthic habitats, and the microbial co-occurrence patterns in the euphotic zone and mussel beds were likely influenced by strong selection factors such as light, organic carbon, mussel activities, and high methane concentrations. Our study provides new perspectives on how microorganisms adapt to the different environmental conditions in deep-sea cold seeps, deepening our understanding of microbial ecology in deep-sea extreme environments.IMPORTANCEOur study revealed the vertical and horizontal patterns of microbial community distribution and co-occurrence, highlighting how different ecological processes shape microbial communities in the water column and sediments, as well as between microeukaryotes and prokaryotes. This indicated that the balance of deterministic and stochastic processes was influenced by the environment and taxonomic classification in deep-sea cold seeps. The species interactions in the euphotic zone and clam habitat were more complex than those in other water layers and benthic habitats, and the euphotic zone and mussel beds served as hotspots of intense environmental selection. Our findings revealed that microorganisms responded to these challenging environments in deep-sea cold seeps through various strategies, including different environmental preferences. By elucidating the mechanisms driving the microbial community diversity and species coexistence, this work provides new perspectives on how microorganisms adapt to the environments in deep-sea cold seeps.