Environmental DNA metabarcoding reveals spatial patterns of benthic molluscan diversity across island reefs in the South China Sea.

Coral reef ecosystems in the South China Sea (SCS) represent globally significant biodiversity hotspots but are increasingly threatened by environmental change and anthropogenic pressures. In this study, we applied environmental DNA (eDNA) metabarcoding to assess the diversity and spatial distribution of benthic mollusks by with a focus on the subset of sequences annotated as Mollusca across 19 sampling sites spanning the Xisha, Zhongsha, and Nansha archipelagos. A total of 3338 amplicon sequence variants (ASVs) were quantification of annotation success to Mollusca, of which a fraction could be confidently assigned to 95 molluscan species. ASV richness was highest in the Nansha region, followed by Zhongsha and Xisha, while only six ASVs were shared among all regions, indicating pronounced spatial heterogeneity. Despite high beta diversity among sites (Bray-Curtis dissimilarity: 0.69-1.00), no significant differences in alpha diversity were detected among regions. Among the environmental variables examined, depth emerged as the primary factor influencing community structure. Comparison with traditional morphological surveys demonstrated that eDNA metabarcoding substantially enhances the detection of cryptic and rare taxa. These findings highlight the effectiveness of eDNA-based approaches for marine biodiversity assessment and provide a valuable baseline for conservation and ecosystem management in the SCS.