Research Paper

Utilizing environmental DNA metabarcoding and local ecological knowledge for fish biodiversity assessment in Rivers of Java, Indonesia

¹ Research Center for Conservation of Marine and Inland Water Resources, National Research and Innovation Agency, Cibinong Science Center, Jl. Raya Jakarta − Bogor Km 46, Cibinong, West Java 16915, Indonesia
² Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong Science Center, Jl. Raya Jakarta − Bogor Km 46, Cibinong, West Java 16915, Indonesia
³ Yayasan Diversitas Lestari Nusantara, West Java: Pondok Mitra Lestari, Blok C8/3, South Bekasi, West Java 17424, Indonesia Jakarta: Menara Bidakara 2, Annex Building FL 4, Jln. Gatot Subroto, Jakarta Selatan
⁴ Food and Agriculture Organization (FAO) Representation in Indonesia, Jakarta 10250, Indonesia
⁵ Gulbali Institute for Agriculture, Water and Environment, Charles Sturt University, PO Box 789, Albury, NSW 2640, Australia
⁶ School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Albury, NSW 2640, Australia
⁷ New South Wales Department of Primary Industries, Narrandera Fisheries Centre, Narrandera, NSW 2700, Australia
⁸ Research Center for Veterinary Science, National Research and Innovation Agency, Cibinong Science Center, Jl. Raya Jakarta − Bogor Km 46, Cibinong, West Java 16915, Indonesia

^* Corresponding author: andi071@brin.go.id

Received: 4 December 2024
Accepted: 15 April 2025

Abstract

Knowledge of fish biodiversity in aquatic ecosystems is critical for sustainable management and conservation of inland waters. Indonesia highlights these issues with its rich natural aquatic biodiversity, which is seriously threatened by human development. To inform restoration goals, we examined the fisheries biodiversity in eight coastal rivers in Java (Indonesia) using environmental DNA (eDNA) and local ecological knowledge (LEK). Three replicate 1L water samples were collected and filtered from each river for environmental DNA metabarcoding, targeting the 12S rRNA gene. LEK surveys were conducted with 50 indigenous residents near the eight focal rivers, including fishers, anglers, traders, and farmers. The combined methodology identified a total of 51 fish species, including 32 through eDNA and 30 through LEK surveys. Both methods detected the same eleven species (22%) in total. The eDNA technique revealed 21 species that fishers had not reported, while fishers reported 18 species that eDNA did not detect. The eDNA approach improves biodiversity identification and monitoring, including the detection of aquatic species that are not recorded by fishermen, especially where historical quantitative data are fragmentary. Meanwhile, LEK can supplement eDNA findings by identifying species that eDNA alone may not detect. We recommend this combined approach where traditional fisheries assessments using capture-based techniques are impractical or cost-prohibitive. Our findings highlight its value in guiding adaptive management strategies in resource-limited regions where traditional fisheries assessments are impractical. Enabling targeted conservation efforts helps protect ecologically significant and culturally important species within priority habitats.