# 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

## TL;DR

This study uses environmental DNA to explore how seasonal and environmental factors shape fish communities in the Yangtze River Estuary and East China Sea.

## Contribution

The study reveals how multidimensional environmental and seasonal gradients jointly influence fish community assembly patterns in a dynamic estuarine-coastal system.

## Key findings

- Surface and bottom fish communities differ in species composition and assembly patterns.
- The Mixed Transitional Water zone supports the most diverse and interactive fish assemblages.
- Spring communities show higher diversity and complex trophic networks compared to autumn.

## Abstract

Fish communities in estuaries and adjacent coastal seas are shaped by strong environmental gradients and seasonal variability, yet how these factors jointly influence community organization remains incompletely understood. In this study, we investigated fish communities in the Yangtze River Estuary and Adjacent East China Sea using environmental DNA, a non-invasive approach that allows species to be detected from water samples without direct capture. Fish communities were compared across water depths, hydrographic zones, and seasons. We found that surface and bottom communities differed not only in species composition but also in their assembly patterns. In addition, pronounced spatial variation was observed across estuarine-offshore transition areas, which supported higher diversity and more complex species associations. Seasonal changes were also evident, with spring communities showing greater complexity than those observed in autumn. Together, these results indicate that water depth, hydrological setting, and seasonal dynamics interact to structure fish communities in estuarine-coastal systems. This study demonstrates the value of environmental DNA for studying fish community patterns across multiple spatial and temporal scales and provides ecological insights that are relevant for understanding biodiversity organization in highly dynamic coastal environments.

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.