Abstract
The ability to accurately assess biodiversity is a critical first step towards establishing effective conservation and management plans. But, assessment of biodiversity using conventional monitoring programs is often constrained by limited funding and a lack of taxonomic expertise. Environmental DNA (eDNA) metabarcoding may be a useful tool to efficiently catalogue biodiversity in areas that cannot be easily assessed using other methods. In this study, we evaluate the potential of eDNA metabarcoding for assessing fish biodiversity and distribution in the Kumbe River, Papua Province, Indonesia. The method involved in-situ eDNA collection at four sites followed by DNA extraction, amplification, and next-generation sequencing of the mitochondrial Cytochrome-b gene. A total of 23 species were detected, three of which comprised 92% of sequence reads detected; Melanotaenia goldiei (32.03%), Craterocephalus randi (31.19), and the invasive tilapia Oreochromis niloticus (28.77%). Five species detected in water samples including M. goldiei, C. stercusmuscarum, O. niloticus, Neoarius graeffei, and Arius arius were detected in previous studies that used conventional surveys. We also provide the first evidence of 18 additional species in the Kumbe River of which 69.56% are native species. Based on these results, we conclude that environmental DNA metabarcoding is a promising rapid, non-invasive and cost-effective method for assessing fish biodiversity in Papua.