Fish diversity assessment in the Yuanshui River during the ten-year fishing ban using environmental DNA metabarcoding

To understand the status of fish diversity in the middle reaches of the Yangtze River’s Yuanshui River basin during the ten-year fishing ban, this study employed environmental DNA (eDNA) metabarcoding technology. Fish resources were surveyed and diversity analyzed across 38 sampling points within seven river sections of the Yuanshui River basin in September 2023. The results were compared with data obtained using conventional fishing gear methods from four identical sections (Changde, Yuanling, Chenxi, Hongjiang) to explore the application of eDNA technology for fish resource monitoring in the Yangtze River basin and to investigate the similarities and differences in monitoring outcomes between the two methods. The eDNA metabarcoding approach identified a total of 94 fish species, belonging to 10 orders, 17 families, and 57 genera. Cypriniformes was the most abundant order (65 species, 69.15%), and Cyprinidae dominated (54 species, 57.45%) within families. Among the 94 species, 12 were endemic to the Yangtze River basin, 11were key protected wildlife species in Hunan Province, and 3 were non-native species. The predominant ecological traits of the fish assemblage were characterized by lentic-resident habits (56.38%), omnivorous feeding (63.83%), and demersal habitat utilization (45.74%). Diadromous migrants, herbivorous feeders, and lower water column species were relatively scarce. A comparative study in four identical sections of the Yuanshui River utilized environmental DNA (eDNA) metabarcoding and conventional fishing gear to assess fish diversity. Across all sections, eDNA detected a total of 89 fish species while conventional methods detected 93 species, with 62 species co-detected by both approaches. Site-specific comparisons revealed that within the Changde section, eDNA identified 70 species compared to 55 species captured by conventional gear, resulting in 40 shared species. In the Yuanling section, eDNA detected 71 species against 53 species from conventional sampling, yielding 35 co-detected species. The Chenxi section showed eDNA detection of 44 species and conventional gear detection of 38 species, with 20 species found by both methods. Similarly, in the Hongjiang section, eDNA recorded 49 species and conventional methods 47 species, also sharing 20 species. Both the total number of fish species and the number of shared species detected in the Changde and Yuanling sections were significantly higher than those in the Chenxi and Hongjiang sections. Within the same river section, the Shannon diversity index and Pielou evenness index calculated based on the conventional fishing gear data were consistently greater than those derived from the eDNA analysis. This study demonstrates the high credibility of environmental DNA (eDNA) technology for monitoring fish stocks within the Yangtze River Basin. Combining eDNA methods with conventional fishing gear surveys provides a more comprehensive assessment of fish diversity throughout the basin. These findings offer valuable references for evaluating the effectiveness of fishing bans, protecting fish resources, and informing fisheries management strategies in the Yuanshui River and broader Yangtze Basin.