The Identification and Quantification of Marine Fish from Environmental DNA in Sulawesi Waters (Makassar Strait, Flores Sea and Bone Bay), Indonesia

The emergence of environmental DNA (eDNA) represents a recent methodological breakthrough for evaluating the presence of aquatic vertebrate species. This approach offers a relatively simple method with significant implications for conservation biology. Our study aim was to augment our understanding of marine fish biodiversity in Sulawesi waters. We employed eDNA metabarcoding to investigate fish biodiversity within Sulawesi waters, specifically focusing on the Makassar Strait, Bone Bay, and Flores Sea. The eDNA was extracted from 4-liter water samples obtained from the surface (0-1m depth) and the water column (15 m depth) at five distinct sites across the study area. Methodological reliability was evaluated using a primer set (MiFish-U) to estimate fish diversity in Sulawesi waters. Analysis of nine water samples collected from Sulawesi waters revealed the presence of 36 marine fish taxa identified to the species level, representing 18 families across 13 orders. The majority of these taxa were associated with reef habitats, indicating the prevalence of coral reef ecosystems in the region. Among the surveyed regions, Bone Bay exhibited the highest species richness with 27 taxa, followed by the Makassar Strait with 14 taxa and the Flores Sea with 12 taxa. This investigation facilitated the estimation of fish diversity utilizing eDNA metabarcoding, thereby furnishing valuable baseline data.