Environmental RNA mitigates fish ghosts associated with fish feeds for aquaculture in molecular ecological survey in a bay.

The use of environmental DNA (eDNA) for molecular ecological surveys has become widespread in ecological assessments of different water environments, including river, coastal, and marine areas. Considering potential contamination by environmental nucleic acids is crucial when interpreting these results. Research on fish ghosts, i.e., false positives generated by eDNA present in fish feed, remains limited, we examined the fish species present in the feed that may influence surveys near aquaculture facilities and fish processing plants using metabarcoding analysis of eDNA/RNA. Additionally, we simultaneously assessed whether the fish species present in the feed used for aquaculture in a heavily cultivated bay could be detected via metabarcoding analysis. Thus, we evaluated whether fish species present in the feed could be detected in ecological surveys in the marine environment. Overall, 51 fish species (DNA: 46, RNA: 31) were detected in 3 fish feed types. The detected species in DNA were more than those in RNA. Furthermore, the common species that were detected in feed and water samples in the bay were remarkably higher in eDNA than in eRNA. Moreover, the number of species detected in the eDNA tended to be maintained at a greater distance from the fishpond where they originated than those detected in the eRNA. Thus, eRNA is useful for fish ecosystem surveys in bays contaminated by fish feed owing to the lower RNA content in the samples than DNA and because it is not easily detected and diffused in the environment.