Research on the changes in fish composition in the Chongqing section of the Fujiang River based on eDNA technology

Abstract

To accurately assess riverine fish diversity, which is crucial for aquatic ecosystem conservation, this study utilized environmental DNA (eDNA) metabarcoding as a non-invasive and efficient alternative to traditional survey methods that have limitations, such as being damaging and inefficient. We collected water samples from 14 sites in the Chongqing section of the Fujiang River during the fish spawning (June), feeding (August), and wintering (November) periods of 2023, analyzed fish community composition through high-throughput sequencing of the 12S rRNA and COI genes and compared these results with data from traditional net fishing. The eDNA technique detected 72, 53, and 63 fish species in the three respective periods, which were significantly higher than the number of species captured by traditional fishing methods (40 in August and 37 in October). The results showed that the Cyprinidae family was the dominant family in terms of species number across all seasons, accounting for 65.08% to 71.70% of the detected species. Importantly, eDNA successfully detected nationally protected species such as Leptobotia elongata and Procyris rabaudi, as well as multiple endemic and invasive species, with overall species richness peaking during the June spawning period. This study confirms that eDNA metabarcoding offers higher sensitivity and comprehensiveness for monitoring riverine fish diversity, especially for rare and endangered species, and provides critical scientific data on seasonal community dynamics for the conservation and management of the Fujiang River basin.