Evaluating the Use of eDNA Metabarcoding for Monitoring Macrofouling Communities in Net Cage Aquaculture in the Yellow Sea

Evaluating species composition and dynamic shifts within fouling communities is essential for developing effective strategies to manage biofouling in marine fish aquaculture. The coastal area in the Yellow Sea is a key area for cage aquaculture in China; however, this region faces significant challenges from biofouling organisms. Here, we employed an experimental approach in a filed mesocosm in a net cage aquaculture area in the Yellow Sea, with weekly monitoring of changes in macrofouling species on mesh nets and in the seawater, to assess the utility of water eDNA metabarcoding for identifying macrofoulers. We compared the temporal variation patterns in the composition and diversity of macrofouling communities identified through morphological method as well as COI and 18S rRNA metabarcoding. The results showed that metabarcoding detected the majority of macrofoulers identified through morphological method (64%), and revealed additional species that were overlooked by traditional monitoring approach. Furthermore, the changes in diversity and community composition over sampling dates in COI data were generally consistent with those in morphological identification, although a temporal lag existed between these two approaches. A notable shift in the fouling community occurred at the end of June with the appearance of Ectopleura crocea and Caprella sp., marking a pivotal change in its structure. Future research could focus on developing targeted primers for these key fouling species, which would enhance the efficiency of monitoring efforts.