Assessing freshwater fish biodiversity of Kumbe River, Papua (Indonesia) through environmental DNA metabarcoding

Abstract

Context The ability to accurately assess biodiversity is a critical first step towards effective conservation and management. However, assessment of biodiversity using conventional monitoring programs is often constrained by high cost 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. Aims Here, we evaluated the potential of eDNA metabarcoding for assessing fish biodiversity and distribution in the Kumbe River, Papua Province, Indonesia. Methods We selected four sampling locations and collected seven eDNA samples from each location. We used eDNA metabarcoding of the Cytochrome-b gene to characterise the fish community. Key results A total of 23 species were detected, three of which comprised 92% of sequence reads detected: Melanotaenia goldiei (32%), Craterocephalus randi (31%), and the invasive tilapia Oreochromis niloticus (29%). Only five species that were previously detected using conventional methods were detected by metabarcoding: M. goldiei, Craterocephalus stercusmuscarum, O. niloticus, Neoarius graeffei, and Arius arius. We detected 18 species (70% native) that have never been recorded from the Kumbe River. Conclusions This work has demonstrated that fish biodiversity is substantially underestimated in the Kumbe River. Environmental DNA metabarcoding is a promising rapid, non-invasive and cost-effective method for assessing fish biodiversity in Papua. Implications The findings support future investment in eDNA metabarcoding to characterise the fish biodiversity in Papua. This will assist in allocating the limited resources for conservation and management to areas most at risk from anthropogenic impacts.