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

Abstract

Information on diversity indices and abundance of individual species is crucial for the assessment of ecosystem health, especially for endangered ecosystems 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 scleractinian corals from 14 families were detected. In addition, a log-linear correlation was found between the abundance of eDNA reads and visually determined relative coral cover at the genus level, suggesting a predictive relationship between eDNA reads and coral cover. Results also showed diurnal variation between day and night samples in the number of eDNA reads, purported to relate to the activity phases of corals. The use of uniquely labeled fusion primers, gave comparable results to a commercially available library preparation kit. Especially with frequent use, fusion primers can be very cost-effective, and therefore a consideration for large-scale studies. Using a custom reference database of 89 sequences from coral tissue samples of 23 different coral genera produced better results than querying against NCBI GenBank, highlighting the importance of locally optimized databases. We consider these results important for establishing eDNA as a complementary tool to visual surveys to track changes in coral diversity and cover.