Environmental DNA metabarcoding enriches the conventional survey of a high diverse fish community in the Dongsha atoll

To effectively conserve coral reef ecosystems, it is essential to monitor changes in fish fauna using minimally invasive methods. In this study, we conducted a fish survey in the Dongsha Atoll using eDNA metabarcoding. Analyzing 37 sequencing units from 26 water samples collected across 12 sites from May 2017 to September 2018, we identified 421 species from 79 families. Among these, 192 species had not been recorded in previous conventional surveys. Some of these newly recorded species are fast-swimmers, while others may be larvae or eggs, which are challenging to observe visually. However, 68% of species documented in previous records were not detected in our study. This limitation is likely due to insufficient samplings, primer specificity, fish characteristics, and rapid DNA degradation in the dynamic physical and chemical conditions (e.g., temperature, pH) of the coastal environment. Despite that eDNA metabarcoding cannot capture the full range of species within the atoll, it effectively complements visual census surveys by enriching our understanding of the diverse fish community in marine habitats.