Ecological impacts of deep-sea cage culture on fish communities in the South China Sea based on environmental DNA

Considering the environmental pollution of land-based and marine nearshore aquaculture, deep-sea cage culture has gradually become a more popular model for mariculture. Fish, an important biological group in marine ecosystems, are one of the main biological indicators of the quality of the ecological environment. West Island, in Sanya Bay, South China Sea, China, is situated in a national coral reef nature reserve, and its surrounding water is the location of the deep-sea cage culture. In this study, α and β species diversity in deep-sea cage and non-cage culture areas surrounding West Island in the South China Sea were studied based on environmental DNA (eDNA) metabarcoding to analyze the impacts of deep-sea cages on the fish community. According to the results, cage culture did not cause a change in fish species richness, but the Shannon-Wiener index and Simpson’s index of fish decreased. The major fish farming species Trachinotus ovatus had absolute dominance in the cage culture area (eDNA abundance exceeded 60%) and might be the main reason for the low level of species diversity in this area. In addition, the results of fish β-diversity indicated that there were significant differences in the composition of the fish community between deep-sea cage and non-cage culture areas; the dominant species in the cage area were omnivorous, while the dominant species in the non-cage area were carnivorous. Therefore, we speculated that cage culture may have caused changes in the feeding structure of the fish community.