Integrating environmental DNA and trawl surveys to assess seasonal dynamics of fish communities in the Oujiang River Estuary

Introduction Monitoring of estuarine fish biodiversity is often constrained by the inherent limitations of traditional survey methods and the complex, dynamic environmental conditions of estuarine habitats. Environmental DNA (eDNA) metabarcoding has emerged as a robust molecular tool for aquatic biodiversity assessment. Nevertheless, its complementary potential to conventional bottom trawling remains understudied in estuarine ecosystems. In this study, we integrated eDNA metabarcoding and bottom trawling to investigate the spatiotemporal dynamics of fish diversity in the Oujiang River Estuary (ORE). Methods Fish assemblage data were collected seasonally across four sampling periods at five fixed sites within the ORE. MiFish-U primers targeting the 12S rRNA gene were utilized for eDNA amplification. And twelve aquatic environmental variables were quantified to disentangle correlations between fish community structure and ambient environmental conditions. Multiple statistical approaches, including alpha diversity analysis, Principal Coordinate Analysis (PCoA) and PERMANOVA, were applied to quantify spatiotemporal shifts in fish assemblages, identify fish-environment correlations, and compare community discrepancies between the two survey methods. Results and discussion The combined approach detected a total of 100 fish species across 84 genera and 45 families. Specifically, eDNA metabarcoding identified 72 fish species, while bottom trawling captured 48 species, with only 20 species shared between the two methods. Fish assemblages exhibited distinct seasonal variations, with both survey methods revealing higher species richness during wet seasons. Temporal fluctuations in water temperature, dissolved oxygen, salinity and nutrient concentrations constituted the primary environmental drivers structuring estuarine fish assemblages, whereas spatial heterogeneity across sampling sites exerted no statistically significant influence on community composition. eDNA metabarcoding showed unique advantages in detecting pelagic, migratory, cryptic and endangered fish species, supporting effective biodiversity monitoring in topographically intricate estuarine waters. In contrast, bottom trawling provided reliable morphological identification and quantitative abundance data for demersal fish taxa, which helped resolve ambiguous species annotations derived from eDNA sequencing. In addition, seven IUCN-listed threatened fish species were documented during the field investigation. Collectively, our findings demonstrate that eDNA metabarcoding and bottom trawling serve as highly complementary, rather than mutually exclusive, tools for fish biodiversity assessment. The integration of the two methods enables a more comprehensive and accurate evaluation of estuarine fish diversity. This study validates the feasibility and efficacy of the combined monitoring framework for macrotidal estuaries and provides valuable scientific references for the ecological conservation and management of the Oujiang River Estuary as well as other similar coastal ecosystems.