Environmental DNA (eDNA) metabarcoding is a method that extracts species information from environmental samples, thereby aiding in the establishment or enhancement of biodiversity assessments. This study employed eDNA and Underwater Visual Census (UVC) to obtain baseline data on the biodiversity of Mischief Reef, explore the efficacy of eDNA in detecting functional organisms, and shed light on alterations in community structure and their contributing factors. Initially, we detected organisms at nine stations with eDNA and UVC in spring, detected 178 fish and macroinvertebrates (crustacean and mollusca) species by eDNA, 151 species by UVC, respectively. The One-way analysis of variance results showed that eDNA method was superior to UVC method in detecting phylum, class, order, family, genus, and species (p < 0.01). The functional space of eDNA organisms encompassed that of UVC organisms. Significant positive correlations were found between eDNA and attributes such as activity period, diet, mean trophic level (TL), maximum body length range, and fishing vulnerability. No correlations were observed between UVC and functional attributes of organisms. The taxonomic diversity, phylogenetic diversity, and functional diversity monitored by eDNA were all significantly higher than those monitored by UVC. The interaction between the biodiversity monitored by eDNA and the environment was more significant than that monitored by UVC. Our study underscores the effectiveness of eDNA in identifying functional organisms in coral reefs and in reflecting differences in ecosystem community structure.
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