Multi-Year eDNA Metabarcoding Reveals Fish Community Dynamics in the Jiangsu Section of the Yangtze River Mainstem Under the Fishing Ban

Abstract

Environmental DNA (eDNA) metabarcoding is an efficient, non-invasive approach for surveying fish diversity in complex habitats such as large rivers. This study conducted continuous eDNA monitoring along the Jiangsu section of the Yangtze River mainstem from 2022 to 2024 to characterize spatiotemporal variations in fish community composition and diversity during the fishing ban period. To improve species identification accuracy, a regional 12S rRNA barcode database was constructed, containing 141 fish species and 1204 sequences. Genetic distance analysis revealed a clear barcode gap, with inter-specific and intra-specific distances of 0.232 and 0.007, respectively, and 65.96% of species formed well-supported monophyletic clades in the phylogenetic tree, indicating useful taxonomic resolution for many of the included taxa. Using this regional reference database, eDNA-based monitoring detected 131 fish species over three years, 72.52% of which occurred in all three years. Cypriniformes consistently dominated (54.92–67.16%), showing a relative abundance trend that first increased and then declined, with dominant species changing annually. Alpha diversity analysis showed a significant decline in Chao1 richness from 83.33 to 36.75, while the Shannon index decreased slightly from 2.69 to 2.43. In contrast, Pielou_J evenness increased from 0.62 to 0.68, suggesting a shift toward lower richness but more even abundance distribution. These patterns may reflect the combined influences of multiple environmental and anthropogenic factors during the study period. Spatially, alpha diversity in the Tai–Tong reach was significantly lower than in the Ning–Zhen and Zhen–Tai reaches (p < 0.05), and community composition in 2022 and 2024 was clearly separated from upstream reaches. However, differences among reaches disappeared in 2023, suggesting interannual variation in spatial differentiation, likely associated with flow-driven mixing and transport. Overall, this study reveals multi-year fish community dynamics in the Jiangsu section of the Yangtze River mainstem and demonstrates that a regional barcode database combined with eDNA metabarcoding provides an effective approach for large-river fish monitoring and biodiversity assessment.