Integrated eDNA and conventional surveys of coral reef fishes at submerged banks, shoals, and offshore Islands in Southern Vietnam

Abstract

The integrating environmental DNA (eDNA) metabarcoding with traditional methods, such as underwater visual census (UVC) and piscicide-based specimen collection (SPC), offers enhanced opportunities for biodiversity assessment, particularly in logistically challenging deep-water coral reef environments. This study combined all three methods across 15 reef sites in Southern Vietnam, including eight submerged banks and shoals and two Con Dao offshore islands. A total of 70 UVC transects were completed, along with SPC using natural ichthyocide, and eDNA analysis of 98 filter-feeder samples (50 sponges, 48 bivalves). A total of 248 reef fish species were recorded, spanning 131 genera, 53 families, 27 orders, and 2 classes. Of these, 230 species were found at the submerged banks and shoals, and 99 species were recorded at the offshore islands, with higher diversity observed in southern locations. Species detection varied significantly by method: UVC recorded the most with 167 species (67.3%), followed by SPC with 70 species (28.2%), and eDNA with 58 species (23.4%). Minimal overlap was observed, with only three species (1.2%) detected by all three methods. Pairwise overlaps were also low: 14 species (6.6%) between eDNA and UVC, six species (4.9%) between eDNA and SPC, and 30 species (14.5%) between UVC and SPC. These findings demonstrate that each method provides a unique perspective on the community composition, confirming that the integration of all three is essential for a comprehensive and accurate assessment of reef fish diversity.