Environmental biomonitoring of reef fish community structure with eDNA metabarcoding in the Coral Triangle

Coral reef fishes perform a range of vital ecosystem functions, and can serve as indicators of ecological stress and resilience. However, many species are not observed when using Underwater Visual Census (UVC) during biomonitoring, and therefore overall biodiversity is often underestimated. Environmental DNA (eDNA) is proposed as an advanced and non-invasive next-generation biomonitoring method for determining the presence of aquatic organisms such as fish. Therefore, this study aimed to assess the community structure of coral fish from three different marine protected area reef zones (utility zone, open access zone, core zone) around Lombok Island using eDNA metabarcoding. Biological community composition, richness, and diversity were evaluated based on reads from mid-column water and sediment samples. A total of 58 species were identified from the eDNA samples using the Multiplex Barcode Research And Visualization Environment (mBRAVE) pipeline. The Shannon–Wiener index (H') showed significantly higher species diversity in the core zone than the utility and open access zones. There was no significant between-zone difference in community structure (ANOSIM, R = 0.11   F) = 0.001, p < 0.05). Based on the high number of fish species detected in this study, eDNA can be recommended as an alternative tool or as a complement to visual survey methods for biological monitoring and diversity assessment of remote reefs, with less stringent requirements in terms of field conditions (e.g. visibility) and taxonomic expertise.