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Exploring freshwater fish biodiversity using eDNA metabarcoding and traditional sampling to assess floodplain waters

Mirna Dwirastina,Muhammad Nizar,Helmizuryani Helmizuryani,Boby Muslimin,Eny Heriyati,Saleh Hidayat,A. P. Prasetyo,Robin Robin,Khusnul Khotimah,Swarlanda Swarlanda,Dewi Apriyanti,Innike Abdillah Fahmi

Published 2025 in Journal of Water and Land Development

ABSTRACT

The floodplains of Bangka Island, which are inhabited by endemic and native fish species, are increasingly threatened by several landscape change and waste pollution. Therefore, the investigation into fish diversity using environmental DNA (eDNA) metabarcoding and traditional sampling is required. eDNA samples were obtained from surface waters of Kurau and Bikang Rivers in Bangka Regency using a metaprobe with sterile gauze (10×10 cm). The extracted DNA products were amplified using Tele02 forward and reverse primers at annealing temperature of 54°C. The resulting polymerase chain reaction (PCR) products were cleaned, attached to adapters, and sequenced with the Next Generation Sequencing Illumina MiSeq platform. The total of 385,661 reads were initially generated using the Divisive Amplicon Denoising Algorithm 2 (DADA2). After the quality control (QC) process, 25.5% of the read (73,301) were retained for analysis. Results of the eDNA metabarcoding showed that species abundance and Shannon–Wiener diversity index were higher in the experiment fishing group (6 and 0.93) compared to those obtained from eDNA data (3 and 0.42). Additionally, both indices were higher in the Kurau River (4 and 0.82) than in the Bikang River (3 and 0.48). Species richness was significantly different between the two sampling methods (p < 0.001). Eighteen fish species were identified through experimental fishing, three using eDNA metabarcoding, and one species was common to both methods. PCA results revealed that the richness of species and effectiveness of sampling technique were significantly affected by water quality. The result of eDNA detection in this research was not better than experimental fishing. Hence, the development of reference for genetic database and optimisation of eDNA technique are required.

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