Multi-marker eDNA metabarcoding reveals more abundant coral biodiversity in a subtropical coastal reef ecosystem

Environmental DNA (eDNA) metabarcoding has emerged as a powerful tool for monitoring biodiversity, particularly for taxa that are difficult to survey visually. Our study applied a multi-marker environmental DNA (eDNA) metabarcoding approach targeting the nuclear (ITS2) and mitochondrial (12S) genes to assess scleractinian coral diversity in the coastal waters of eastern Shenzhen, China. Compared to traditional diver-based surveys, the eDNA method detected more genera (42 versus 23) and species (77 versus 63), with 55 % of the genera detected by eDNA overlapping with those recorded during visual surveys, thus demonstrating the reliability and advantages of the eDNA approach. Spatial analyses identified offshore biodiversity as "hot-spots" with higher coral diversity and minimal anthropogenic disturbance, whereas urbanized nearshore areas formed "cold-spots". Seasonal sampling revealed the highest detection rates in autumn, likely reflecting environmental conditions that enhance eDNA persistence. Water temperature, salinity, and nutrient concentrations strongly influence coral eDNA abundance and shape detection patterns. Although methodological challenges such as incomplete reference databases and primer biases remain, our findings demonstrate that multi-marker eDNA metabarcoding provides a sensitive, scalable, and complementary tool for coral biodiversity monitoring. Expanding reference databases and refining assay methods will enhance the accuracy and conservation relevance of eDNA-based assessments, particularly in managing coral ecosystems in rapidly urbanizing coastal regions.