Multidimensional Drivers of Fish Community Assembly Across Seasonal and Hydrographic Gradients in the Yangtze River Estuary and Adjacent East China Sea: Insights from eDNA Analyses

Marine fish communities in the Yangtze River Estuary and Adjacent East China Sea (YRE-ECS) are subject to complex environmental gradients; however, their multidimensional assembly mechanisms remain insufficiently resolved. Here, we integrated environmental DNA (eDNA) metabarcoding, co-occurrence network analysis, and environmental profiling to examine fish community structure across vertical layers, hydrographic zones, and seasons. Vertically, surface communities dominated by pelagic-associated Perciformes and Clupeiformes showed more variable assembly patterns, whereas bottom communities enriched in Gobiiformes and Pleuronectiformes were more strongly associated with temperature and dissolved oxygen. Horizontally, among three zones delineated by salinity and hydrographic characteristics, the Mixed Transitional Water (MTW) supported the most diverse and interactive assemblages and functioned as an ecological connector between estuarine (EHSW) and offshore (OWSW) waters. Seasonally, community structure shifted markedly: spring communities exhibited higher diversity and denser trophic networks supported by zooplankton-rich, phototrophic plankton (e.g., Arthropoda, Bacillariophyta), whereas autumn communities were simpler, dominated by Chlorophyta and microbial taxa, with fish assemblages showing increased modularity and reliance on fewer planktonic groups. This seasonal pattern suggests a transition from diversified energy pathways to more constrained trophic coupling. βNTI and Mantel analyses jointly revealed a stratified environment-response-feedback framework driving community differentiation through combined stochastic and deterministic mechanisms. These findings highlight the importance of integrated spatial-temporal monitoring and suggest that protecting transitional zones and spring food-web integrity is critical for ecosystem resilience in the YRE-ECS.