Comparative Metagenomic Analysis of Marine eDNA Investigating the Production Crisis of Aquacultured Saccharina japonica

Aquaculture farms cultivating Saccharina japonica are highly active in Wando, Korea, and Rongcheng, China. However, the yield of S. japonica significantly declined in the Rongcheng region in 2022 compared to previous records, whereas that in Wando remained at a normal level, presumably due to the presence of a pathogenic microbiome. We used environmental DNA (eDNA) metagenomic analysis to compare the microbial compositions of seawater from aquaculture farms in Wando and Rongcheng. Seawater samples were collected from one Korean site in Wando (WA) and two Chinese sites in Ailian Bay (AB) and Lidao Bay (LB). Metagenomic analysis focusing on the microbial 16S rRNA identified 38 phyla and 58 families of microbiomes in all regions. Potentially pathogenic bacterial groups associated with S. japonica in AB and LB were more abundant than in WA, suggesting their potential influence on mortality and the decline in the harvest yield of S. japonica. The microbial composition of WA was distinguished from those of the other two sites, which clustered together with higher similarity. Since the S. japonica aquaculture industry is important for both countries, this comparative eDNA monitoring is a valuable initiation towards the next step of problem-solving practices in coastal management in these two aquaculture systems.