Complementary ecological indicators of fish communities in a barraged estuary: eDNA metabarcoding versus conventional surveys

Estuaries, where freshwater and seawater converge, are characterized by dynamic habitats and high biodiversity. However, intensive anthropogenic modifications have profoundly disrupted their ecological structure and functions. Fish communities are particularly susceptible to such alterations, requiring careful attention through effective monitoring and sustained management efforts. In this study, we used environmental DNA (eDNA) metabarcoding and conventional fishing surveys as complementary ecological indicators of fish communities in the Nakdong River Estuary, an estuarine continuum fragmented by an estuarine barrage. Two sampling campaigns were conducted at seven sampling points representing the estuarine salinity gradient. Fish were surveyed using multiple fishing gears, and DNA extracted from filtered water samples was amplified using the fish-specific MiFish-U primer. Our comparative analysis revealed distinct functional roles for each method: fishing surveys were more effective for detecting locally established freshwater fish, whereas eDNA metabarcoding served as a highly sensitive indicator for marine-origin and transient species. Along the estuarine gradient, fishing surveys reflected abrupt community changes near the barrage, while eDNA metabarcoding captured more gradual ecological transitions. Multivariate analyses further demonstrated that fishing surveys are sensitive to fine-scale spatial differences, whereas eDNA metabarcoding reflects broader spatial connectivity. These results suggest that eDNA metabarcoding detects mobile or transient species through DNA signals and effectively captures broad-scale habitat connectivity, while fishing surveys provide direct evidence of species presence and emphasize resident community structures. Integrating these dual-indicator approaches could provide a more comprehensive monitoring framework for the management and ecological restoration of human-impacted estuarine ecosystems worldwide.