Assessing freshwater fish biodiversity of Kumbe River, Papua (Indonesia) through environmental DNA metabarcoding
Arif Wibowo
A * , Kurniawan Kurniawan A , Dwi Atminarso A B , Tri Heru Prihadi C , Lee J. Baumgartner B , Meaghan L. Rourke B D , Satoshi Nagai E , Nicolas Hubert F and Anti Vasemagi G H
+ Author Affiliations
- Author Affiliations
A Research Center for Conservation of Marine and Inland Water Resources, National Research and Innovation Agency, Jalan Raya Jakarta-Bogor Km. 48 Cibinong, Bogor, West Java 16911, Indonesia.
B Gulbali Institute for Agriculture, Water and Environment, Charles Sturt University, PO Box 789, Albury, NSW 2640, Australia.
C Research Center for Fisheries, National Research and Innovation Agency, Jalan Raya Jakarta-Bogor Km. 48 Cibinong, Bogor, West Java 16911, Indonesia.
D New South Wales Department of Primary Industries, Narrandera Fisheries Centre, Narrandera, NSW 2700, Australia.
E Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, Yokohama, Japan.
F Université Montpellier (UMR) 5554 Institut des sciences de l’évolution de Montpellier (ISEM) (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, Montpellier cedex 05 34095, France.
G Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden.
H Estonian University of Life Sciences, Institute of Veterinary Medicine and Animal Sciences, Tartu, Estonia.
Pacific Conservation Biology 29(4) 340-350 https://doi.org/10.1071/PC21078
Submitted: 25 December 2021 Accepted: 29 July 2022 Published: 25 August 2022
© 2023 The Author(s) (or their employer(s)). Published by CSIRO Publishing. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND)
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.
Keywords: biodiversity, eDNA, freshwater fish, Indonesia, metabarcoding, Papua, river, tropical.
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