Mechanistic Multitrophic Insight on Seasonal Hypoxia Impacts in Urbanized Estuarine Ecosystems

Seasonal hypoxia is intensifying in urbanized estuaries worldwide, posing escalating threats to biodiversity and ecosystem functioning across food webs. Despite growing concern, how oxygen depletion alters ecological dynamics across trophic levels remains poorly understood, highlighting the urgent need for integrated and multitrophic assessments. Here, we conducted a comprehensive analysis in the Pearl River Estuary, a globally representative urbanized estuary, by integrating multidimensional data sets including environmental DNA (eDNA) and traditional plankton monitoring, species functional traits, biomass and water quality. Our findings reveal pronounced community reassembly under hypoxic conditions, characterized by increases in pollution-tolerant and invasive taxa, and concurrent declines of sensitive taxa. While α-diversity increased significantly across all taxonomic groups (median increased 35%–65%), β-diversity declined, indicating community homogenization to some extent under hypoxia stress. The complexity of organismal networks declined under hypoxia, with decreases of 12%–30% in node number, average degree, and clustering coefficient, and a >70% loss of fish nodes; microbial taxa increasingly occupied central network positions. Structural equation modeling identified that hypoxia disrupted internal regulatory pathways, shifting the system from biodiversity-driven top-down control to bottom-up dominance, effectively decoupling biodiversity from ecosystem functions. Overall, this study provides one of the few multitrophic frameworks to mechanistically elucidate how seasonal hypoxia restructures biodiversity, weakens trophic regulation, and compromises ecosystem resilience in urbanized estuarine systems.