Seawater eDNA and Underwater Visual Surveys Reveal Genus-Level Reef-Building Coral Communities in the Wanshan Archipelago, South China Sea

Environmental DNA (eDNA) metabarcoding is increasingly used as a complementary tool for coral biodiversity assessment, but its performance in subtropical, estuary-influenced reef systems remains insufficiently tested. This study combined seawater eDNA metabarcoding with concurrent underwater visual surveys and historical records to assess reef-building scleractinian corals in the Wanshan Archipelago, Pearl River Estuary. In June 2022, surface and bottom seawater samples were collected from seven sites, yielding 14 eDNA samples, and dive-based photographic surveys were conducted concurrently. A universal 18S rRNA assay was used for high-throughput sequencing, and eDNA detections were compared with visual and historical survey data at the genus level. eDNA detected 13 families and 21 genera, with Porites and Echinopora as dominant genera. eDNA recovered more genera than concurrent visual surveys in all five regional comparisons, although the two methods yielded overlapping but partly distinct genus inventories. Surface-water eDNA showed a slight, site-dependent advantage in genus recovery and overlap with concurrent visual surveys, whereas correspondence with historical records varied among regions; surface and bottom samples shared most genera but also contributed complementary layer-specific detections. Community composition showed spatial clustering broadly consistent with geographic proximity. These findings indicate that seawater eDNA provides complementary genus-level information and support paired surface- and bottom-water sampling for a more complete exploratory characterization of coral diversity in complex subtropical coastal reef systems.