Comparison of fish fauna evaluated using aqueous eDNA, sedimentary eDNA, and catch surveys in Tokyo Bay, Central Japan

This study evaluated fish fauna using aqueous environmental DNA (eDNA), sedimentary eDNA, and bottom-trawl catch survey data, based on 2-year field samplings in Tokyo Bay, central Japan. Aqueous eDNA detected the highest number of fish species, followed by sedimentary eDNA and then catch surveys. Due to the prevalence of hypoxia in the inner and central areas during summer and the influence of open ocean water in the mouth area during autumn, the number and composition of fish species detected by each data type by area (inner, central, and mouth areas) significantly differed depending on the season. Among the dominant species in Tokyo Bay, pelagic and inshore fishes were more frequently detected by eDNA (both in water and sediment) than by catch surveys. In contrast, cartilaginous and benthic fishes inhabiting sandy or muddy bottoms tended to be recorded by catch surveys rather than by eDNA. For non-dominant species, eDNA was more sensitive than catch surveys; occasional migratory fishes were more likely to be detected by aqueous eDNA, while small, rare fish species inhabiting rocky reef areas tended to be detected by sedimentary eDNA. Thus, information from aqueous eDNA, sedimentary eDNA, and catch survey samples could complement each other to improve the accuracy and representativeness of fish fauna monitoring.