Assessing benthic community structure and diversity in the Western Pacific polymetallic nodule area: insights from multi-primer eDNA metabarcoding

Introduction Deep-sea polymetallic nodules are considered a critical resource for meeting future global metal demands. However, current knowledge of benthic community composition and biodiversity patterns in these regions remains limited, impeding baseline studies. Methods In this study, we applied a multigene eDNA metabarcoding approach to analyze the community structure and diversity of prokaryotes (16S rRNA) and eukaryotes (18S rRNA and COI) in sediment layers (0–5 and 5–10 cm) from five sites within the Northwest Pacific polymetallic nodule province. Results The results revealed significant differences in eukaryotic community composition due to primer preferences: the V1V2 primer showed higher sensitivity for Foraminifera and Crustaceans, the V9 primer for Harpacticoida, whereas the COI primer demonstrated lower amplification efficiency compared with the two 18S rRNA primers. Furthermore, the alpha diversity of both bacterial and eukaryotic communities decreased significantly with increasing sediment depth, whereas no such clear trend was observed for archaeal communities. Discussion and conclusion Our study confirms the high efficiency of eDNA technology for biological monitoring in polymetallic nodule contract areas. It can overcome the limitations of traditional morphological methods and provide a scientific basis for biological baseline assessments prior to deep-sea mining.