Biodiversity exploration of Formosa Ridge cold seep in the South China Sea using an eDNA metabarcoding approach

The Formosa Ridge, also named Site F, is an active cold seep marine ecosystem site that has been studied since it was discovered on the continental slope of the northeast South China Sea (SCS). However, few studies have focused on the eukaryotic diversity at Site F. Environmental DNA (eDNA) technology is a non-invasive method applied in biodiversity surveys with a high species detection probability. In the present study, we identified multi-trophic biodiversity using eDNA metabarcoding combined with multiple ribosomal RNA gene (rDNA) markers. We detected 142 phytoplankton, 90 invertebrates, and 64 fish species by amplifying the 18S rRNA gene V4 region, the 18S rRNA gene V9 region, and the 12S rRNA gene. The results elucidated dissimilar trends of different assemblages with depth. The diversity of phytoplankton and invertebrate assemblages markedly decreased with depth, whereas little change was observed within the fish assemblage. We comprehensively assessed the relationship between the three assemblages and environmental factors (temperature, salinity, depth, dissolved oxygen, and chlorophyll a). These factors strongly impacted on phytoplankton and invertebrates, but only slightly on fish. We inferred the finding might be due to fish having a strong migration capacity and wide distribution. This study indicates that eDNA metabarcoding with multiple markers is a powerful tool for marine biodiversity research that is able to provide technical support and knowledge for resource management and biodiversity protection efforts.