Assessment of fish biodiversity in four Korean rivers using environmental DNA metabarcoding

Md Jobaidul Alam; Nack-Keun Kim; Sapto Andriyono; Hee-Kyu Choi; Ji-Hyun Lee; Hyun-Woo Kim

doi:10.7717/peerj.9508

Assessment of fish biodiversity in four Korean rivers using environmental DNA metabarcoding

PeerJ. 2020 Jul 14:8:e9508. doi: 10.7717/peerj.9508. eCollection 2020.

Authors

Md Jobaidul Alam¹, Nack-Keun Kim¹, Sapto Andriyono², Hee-Kyu Choi³, Ji-Hyun Lee⁴, Hyun-Woo Kim^{1

4}

Affiliations

¹ Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan, Republic of Korea.
² Department of Marine, Fisheries and Marine Faculty, C Campus Jl. Mulyorejo Surabaya, Universitas Airlangga, Surabaya, East Java, Indonesia.
³ Molecular Ecology and Evolution Laboratory, Department of Biological Science, College of Science & Engineering, Sangji University, Wonju, Republic of Korea.
⁴ Department of Marine Biology, Pukyong National University, Busan, Republic of Korea.

Abstract

Environmental DNA (eDNA) metabarcoding is a cost-effective novel approach to estimate biodiversity in an ecosystem. In this study, the MiFish pipeline was employed to test if the system methodology is sufficiently reliable to estimate fish biodiversity in Korean rivers. A total of 125 unique haplotypes and 73 species were identified at the species level from 16 water samples collected from a single survey in four Korean rivers (Hyeongsan, Taehwa, Seomjin, and Nakdong). Among the four rivers, the highest species richness was recorded in the Seomjin River (52 species), followed by the Taehwa (42 species) and Hyeongsan (40 species) rivers. The Nakdong River (26 species) presented the lowest species richness and number of endemic species, presumably due to its metropolitan location and anthropogenic impacts, such as dams or weirs. We were also able to detect that five exotic species (Carassius cuvieri, Cyprinus carpio, Cyprinus megalophthalmus, Lepomis macrochirus, and Micropterus salmoides) are widely distributed in all surveyed rivers, a situation that might be problematic in terms of conservation. Our findings indicate that the eDNA metabarcoding technique is one of the most cost-effective scientific tools available for the management and conservation of the freshwater fish resources available in Korea. However, the low number of 12S sequences of endemic species in the database and low resolution of the MiFish region for differentiating several taxa should be upgraded for their wide use.

Keywords: Biodiversity; Korea; MiFish pipeline; Next-generation sequencing; eDNA metabarcoding.

Grants and funding

This research was a part of the project titled “Long-term change of structure and function in marine ecosystems of Korea”, funded by the Ministry of Oceans and Fisheries, Korea. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.