Bacteria-archaea metabolic complementarity as a driver of ecosystem functioning in Chinese coastal sediments

Introduction The East China Sea (ECS), a continental shelf sea influenced by Yangtze River discharge and human activities, hosts highly diverse and structurally heterogeneous microbial assemblages in shallow sediments, shaped by complex hydrological and biogeochemical gradients. Methods Here, 16S rRNA gene high-throughput sequencing and environmental parameter analysis across three depth intervals (50 m, 50–100 m, 100–200 m) were used to systematically characterize the vertical distribution of bacterial and archaeal communities. Results and discussion Multivariate statistics identified organic carbon, oxygen, and sulfur availability as key drivers of microbial community structure. Co-occurrence network and functional profiling uncovered distinct ecological divergence: bacteria dominate oxidative processes including nitrogen and sulfur cycling as well as organic matter degradation, while archaea, predominantly Bathyarchaeia , occupy modular anaerobic niches specialized in methanogenesis and reductive pathways. This functional complementarity sustains integrated biogeochemical cycling in dynamic marine sediments. Our study advances understanding of prokaryotic community responses to vertical environmental gradients and their ecological roles in coastal sediment biogeochemical cycling.