Incheon National University study evaluates eDNA metabarcoding for fish diversity assessment

Environmental DNA (eDNA) metabarcoding has emerged as a powerful tool for monitoring aquatic biodiversity, enabling researchers to identify fish species from traces of DNA found in water without the usage of invasive techniques on fishes. Though this technique is gaining attraction, it introduces certain biases and uncertainties during various stages, thereby impacting the production of reliable eDNA results. This challenge necessitates the understanding of strengths and limitations of the technique.

Against this backdrop, in a new synthesis review, Dr. Chang-Bum Jeong, Dr. Bhavya Kachiprath, Mr. In-Cheol Yeo, Ms. Sung-Eun Hong, Ms. Harim Jeong, and Mr. Kyu-Young Shim, all from the Department of Marine Science, Incheon National University, Republic of Korea, evaluated the performance of fish eDNA metabarcoding by analyzing 59 mock community datasets drawn from 30 independent studies. Mock communities are controlled experimental systems in which the exact species composition and DNA concentrations are known, providing a reliable benchmark for testing detection accuracy. The paper was made available online on February 16, 2026, and was published in Volume 36, of the journal Reviews in Fish Biology and Fisheries.

The team assessed how effectively commonly used universal fish primers detected species and whether sequencing read abundance reflected actual DNA concentrations. “One of the most important findings from our research is that eDNA metabarcoding is already highly effective for detecting fish diversity, but its reliability strongly depends on methodological choices such as primer selection and reference database quality,” says Dr. Jeong.

The review found that primers targeting the 12S rRNA gene, particularly Teleo, MiFish-U, and 12S-V5_1, consistently achieved strong species detection and accurate taxonomic identification. The researchers also found that studies using locally curated reference databases achieved substantially higher identification accuracy than those relying solely on public databases. These findings highlight the importance of developing comprehensive regional DNA barcode libraries. As eDNA metabarcoding becomes more widely used, improving these databases could significantly enhance the reliability of biodiversity assessments.

“Another important finding from our study was that methodological choices such as Primer selection, amplification bias, and reference database strongly influence study outcomes,”explains Dr. Kachiprath. By identifying and understanding these biases may help researchers produce robust eDNA results and avoid overinterpreting. The researchers also examined whether eDNA metabarcoding could be used to estimate fish abundance and biomass, a capability that could support fisheries management and conservation efforts. While eDNA metabarcoding reliably answers the question of which species are present, sequencing read abundance showed weak relationships with DNA concentration across diverse fish communities, limiting its usefulness in estimating total fish biomass.

“eDNA metabarcoding is currently much better at answering the question ‘Which species are present?’ than accurately estimating total fish biomass or abundance,” says Dr. Jeong.

Despite this limitation, the review identified stronger relationships between DNA concentration and sequencing reads within individual species or closely related groups, suggesting eDNA metabarcoding may still be useful for tracking relative abundance trends in targeted monitoring programs.

The findings could help researchers select more effective primers, improve regional DNA reference libraries, and develop more standardized eDNA metabarcoding approaches. In the longer term, the work may support more reliable biodiversity assessments for fisheries management, conservation planning, invasive species detection, and ecosystem restoration.

***

Reference
DOI: 10.1007/s11160-026-10040-9

About Incheon National University
Incheon National University (INU) is a comprehensive, student-focused university. It was founded in 1979 and given university status in 1988. One of the largest universities in South Korea, it houses nearly 14,000 students and 500 faculty members. In 2010, INU merged with Incheon City College to expand capacity and open more curricula. With its commitment to academic excellence and an unrelenting devotion to innovative research, INU offers its students real-world internship experiences. INU not only focuses on studying and learning but also strives to provide a supportive environment for students to follow their passion, grow, and, as their slogan says, be INspired.
Website: https://www.inu.ac.kr/sites/inuengl/index.do?epTicket=LOG

About Dr. Bhavya Kachiprath
Dr. Bhavya Kachiprath received her B.Sc. degree in Zoology from Nirmalagiri College, Kerala, India, and her M.Sc. degree in Marine Biology and Ph.D. degree in Marine Sciences from the Department of Marine Biology, Microbiology and Biochemistry, Cochin University of Science and Technology, Kerala, India. Her doctoral research focused on ‘Arctic Fjord microbiome: A metagenome based investigation on microbial diversity and genome mining for functional attributes’. She received the Best Researcher Award (2019-2020) from Cochin University of Science and Technology in recognition of her scientific contributions. She is currently a Postdoctoral Fellow at the Marine Environmental Biology Laboratory (MEB Lab), Department of Marine Science, Incheon National University, South Korea. Her research interests include environmental DNA, toxicogenomics, marine ecotoxicology, and molecular responses of marine organisms to environmental stressors.

About Dr. Chang-Bum Jeong
Dr. Chang-Bum Jeong is an Associate Professor in the Department of Marine Science, College of Natural Sciences, Incheon National University, South Korea. He received his B.S. degree in Environmental Marine Science from Hanyang University, South Korea, in 2012, and his Ph.D. degree in Biochemistry from Hanyang University in 2017. Prior to joining Incheon National University, he served as a SKKU Postdoctoral Fellow at Sungkyunkwan University from 2017 to 2019. He was appointed as an Assistant Professor at Incheon National University in 2019 and has served as Associate Professor since 2023. His research interests include marine molecular ecology, environmental microbiome, molecular ecotoxicology, and ecotoxicogenomics. His recent work focuses on understanding marine environmental responses and ecological processes using molecular and omics-based approaches.

About Mr. In-Cheol Yeo
Mr. In-Cheol Yeo received his B.S. degree in Marine Science from Incheon National University, South Korea, in 2022, and his M.S. degree in Marine Science from the same institution in 2024. He is currently pursuing his Ph.D. degree at the Marine Environmental Biology Laboratory (MEB Lab), Department of Marine Science, Incheon National University, South Korea. His research interests focus on environmental DNA (eDNA)-based marine biodiversity assessment, including microbial communities-plankton-fish assemblages, ecological network analysis, and ecosystem monitoring in marine environments.

About Ms. Sung-Eun Hong
Ms. Sung-Eun Hong received her B.S. degree in Marine Science from Incheon National University, South Korea, in 2024, and is currently pursuing her M.S. degree in the same department at the same university. Her research interests include environmental DNA (eDNA)-based metabarcoding, microbial ecology, and zooplankton ecotoxicology. Her recent work involves biodiversity assessment using field-derived eDNA samples from marine and freshwater ecosystems, as well as laboratory-based toxicity studies investigating the effects of plastic pollutants on copepods and rotifers.

About Ms. Harim Jeong
Ms. Harim Jeong received her B.S. degree in Marine Science from Incheon National University, South Korea, in 2025, and is currently pursuing her M.S. degree at the Marine Environmental Biology Laboratory (MEB Lab), Incheon National University. Her research focuses on environmental DNA (eDNA), particularly sedimentary eDNA applications for reconstructing past marine environments and evaluating present ecosystem dynamics. Her recent work integrates eDNA metabarcoding with environmental and geochemical proxies to investigate long-term ecological changes in coastal and estuarine ecosystems associated with climate change, eutrophication, and hypoxia.

About Mr. Kyu-Young Shim
Mr. Kyu-Young Shim received his B.S. degree in Marine Science from Incheon National University, South Korea, in 2024, and is currently pursuing his Ph.D. degree at the Marine Environmental Biology Laboratory (MEB Lab), Department of Marine Science, Incheon National University. His research interests include environmental DNA (eDNA), marine biodiversity, microbial ecology, and ecological network analysis in coastal ecosystems. His recent research explores spatial and temporal dynamics of marine plankton communities using multi-marker eDNA metabarcoding approaches.