Environmental DNA (eDNA) for Fish Biodiversity Monitoring: A Systematic Review

Introduction: Effective monitoring of fish biodiversity is essential for conservation, fisheries management, and sustainable aquaculture. Traditional survey methods, including netting, electrofishing, and visual censuses, may be limited by sampling effort, habitat accessibility, and species detectability. Environmental DNA (eDNA) has emerged as a promising molecular approach for detecting aquatic organisms from genetic material released into the environment. This systematic review evaluates recent advances, applications, strengths, and limitations of eDNA for fish biodiversity monitoring.

Methods: A systematic literature search was conducted following PRISMA 2020 guidelines using Scopus, Web of Science, PubMed, and ScienceDirect databases. Peer-reviewed studies published between 2020 and 2026 were screened according to predefined inclusion and exclusion criteria. Extracted data focused on eDNA applications in marine, freshwater, and aquaculture systems, methodological developments, and comparisons with conventional fish monitoring techniques.

Results: The reviewed literature suggests that eDNA can provide high sensitivity for detecting fish species, particularly rare, cryptic, invasive, or low-abundance taxa that may be overlooked by traditional sampling methods. Many studies reported that eDNA-based approaches complemented or, in some cases, exceeded conventional surveys in species detection. Recent technological developments, including droplet digital PCR (ddPCR), metabarcoding, long-read sequencing platforms, and machine learning-assisted bioinformatics, have improved analytical performance and taxonomic resolution. However, several factors continue to influence eDNA reliability, including DNA degradation, hydrological transport, environmental conditions, incomplete reference databases, and methodological variability among studies.

Conclusions: Current evidence indicates that eDNA is a valuable and increasingly mature tool for fish biodiversity assessment. Although challenges remain regarding standardization, biomass estimation, and data interpretation, ongoing advances in molecular technologies and bioinformatics are likely to enhance its utility. eDNA is expected to play an increasingly important role in biodiversity conservation, fisheries management, and aquaculture monitoring.