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
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.