Large-Scale Environmental DNA Metabarcoding Shows a Comprehensive Fish Community in the East China Sea: Do Water Layer and Habitat Matter?

Biodiversity serves as the foundation for human survival and development. Marine fishes play a crucial role in supporting both global biodiversity and food sources. The conventional methods for fish diversity and fishery resources survey are inadequate to meet the growing demand for large-scale and long-period surveys. The eDNA metabarcoding approach provides an effective and non-invasive monitoring revolution, and has been applied to identify fish diversities. This study conducted a comprehensive comparison of fish diversity in the East China Sea on a large scale both horizontally and vertically. The results showed a total of 81 fish species, which were classified into 20 orders, 44 families and 72 genera. Although no statistically significant difference in fish diversity was found amongst the horizontal groups (east-middle-west, south-middle-north, and shallow-middle-deep) and the various sampling layers (surface-middle-bottom), discernible trends were obtained in this study. Fish diversity results revealed the orders of east > middle > west, middle > north > south and deep > shallow > middle in horizontal groups. Additionally, surface water exhibited a higher level of fish diversity than other water layers. Some fish species were only detected at specific vertical depths. The diverse composition of fish species across different water layers can be attributed to their distinct ecological types. The overall findings suggest that an increase of sampling stations and mixed samples should be collected in deeper water bodies for comprehensive understanding of fish diversity. This study can also provide the fundamental data and experimental design reference for future studies and fishery management.