An environmental DNA metabarcoding approach versus a visual survey for reefs of Koh Pha‐ngan in Thailand

Information on diversity indices and abundance of individual species is crucial for the assessment of ecosystem health, especially for endangered ecosystems such as coral reefs. The application of environmental DNA (eDNA) to monitor coral biodiversity is, however, just beginning to come into focus for marine biologists. In this study, an eDNA metabarcoding approach of seawater samples in three different reefs on Koh Pha-ngan, Thailand, was compared with simultaneously collected visual census data. In addition, differences in read abundance and number of genera detected between daytime and nighttime eDNA samples were examined, and a local coral barcode reference database (n=23 genera; COI gene) was constructed to improve assignment of eDNA reads to the genus level. As a technical extension of existing assays, two methods for library construction were compared: a commercial kit and in-house developed fusion primers.
Combining eDNA metabarcoding and visual data, 29 different genera of scle..., Visual surveys, coral tissue collection and seawater sampling for eDNA metabarcoding were conducted from July to September 2019 at the three sampling sites, Haad Khom, Haad Salad and Haad Yao, along the northwestern shore of Koh Pha-ngan, in the Gulf of Thailand. For visual surveys at each of the three sites, six 30-m transects were aligned perpendicularly to the shore at 5–10 m intervals. Photos of a frame (0.25 m²) were taken every 2 m on alternating sides along a transect. Thus, 16 quadrats per transect were photographed. Scleractinia were visually identified from the photographs to genus level using the Indo Pacific Coral Finder (Kelley, 2016) and analyzed using 50 random points per quadrat (for a total of 800 points per transect) in CPCe (Kohler & Gill, 2006) for an estimate of coral cover and biodiversity. Statistical analyses were computed in RStudio (RStudio Team, 2020).
To build a genetic reference database, tissues and photos were taken of 138 different coral colonies (34 ...,