Current research on microbial ecology in cold seep ecosystems primarily focuses on prokaryotic microorganisms involved in methane metabolism and sulfate reduction, while the community structure and regulatory mechanisms of microeukaryotes in cold seeps remain poorly understood. In this study, we conduct high-throughput sequencing of the 18S rRNA gene of eukaryotes in sediment samples from the new-born cold seep in the South China Sea, the Formosa cold seep, and the Haima cold seep. The results indicate that the microeukaryotic community in cold seeps is predominantly composed of Apicomplexa, Dinoflagellata, and Rhizaria. Significant variations in the microeukaryotic community structure were observed as the cold seep ecosystem evolved. Notably, the distribution pattern of Radiolaria transitioned from deep enrichment in newly formed cold seeps to surface enrichment in mature cold seeps. Additionally, the α diversity of the microeukaryotic community significantly increased with ecosystem succession. Interaction network analysis revealed that, compared to the new-born cold seeps, multiple metrics of network cohesion, connectivity, and stability in mature cold seeps were significantly enhanced. This change in network structure may be attributed to the formation of more complex and robust interspecies interactions (such as symbiosis, competition, and predation) in mature cold seeps, thereby enhancing the community’s resistance to disturbance and functional stability. Phylogenetic bin-based null model analysis revealed that stochastic processes (e.g., dispersal limitation) dominated the community assembly in both mature and new-born cold seeps from the 2022 samples, leading to increased community dissimilarity. In contrast, deterministic processes (e.g., homogeneous selection) were predominant in the 2023 sample from the new-born cold seep. Collectively, this study provides novel insights into the community structure and regulatory mechanisms of microeukaryotes during cold seep development.
 

cold seep,microeukaryotic diversity,ecological assembly processes