Environmental DNA detects higher fish diversity than traditional methods in one of the world's largest rivers

Biomonitoring is challenging in the world's largest rivers, especially in those with intensive navigation and other in-water human activities. Environmental DNA (eDNA) has emerged as a promising tool for detecting organisms in these large rivers but large-scale and real-time quantitative comparison with traditional methods is lacking. In this study, we investigated fish diversity in the Yangtze River, one of the largest rivers in the world. The fish communities inhabiting 22 segments along 1900 km of the middle and lower reaches of the river were investigated using both eDNA metabarcoding and traditional gillnetting. eDNA outperformed gillnetting as it detected over two times more fish species (119 vs. 55), including better detection of rare and non-native species. Moreover, eDNA abundance was significantly correlated with fish abundance and biomass calculated using traditional gillnetting. Although eDNA carries sequencing-related biases, it offers a quantitative approach comparable to gillnetting, which suffers from its own methodological limitations. Our large-scale and real-time comparison study demonstrates that eDNA detects higher fish diversity than traditional methods in the main channel of the Yangtze River. eDNA is as an efficient tool to monitor fishes, thus offering potential for the monitoring of biodiversity in the largest rivers of the globe. • Real-time eDNA and traditional gillnetting for fishes were compared in the Yangtze River. • eDNA detected more fish species than gillnetting (119 vs. 55). • eDNA was better at detecting rare and non-native species. • eDNA-based fish abundance and gillnet-based fish abundance and biomass were correlated. • eDNA has a great application potential in monitoring biodiversity in large rivers.