Environmental DNA for fish monitoring: Progress, challenges, and applications

Fish are critical biological indicators for assessing aquatic ecosystem health and environmental quality. Traditional fish monitoring methods are limited by low efficiency, habitat disturbance and poor performance in detecting rare species, which cannot meet the growing demands of aquatic biodiversity conservation and environmental management. Environmental DNA (eDNA) technology, characterized by non-invasiveness, high sensitivity, and high throughput, has emerged as a promising alternative for aquatic biological monitoring. This review systematically summarizes the technical workflow and research progress of eDNA technology in fish monitoring, including species identification, biomass evaluation and biodiversity investigation. Three major bottlenecks restricting its large-scale application are highlighted: unclear dynamics of eDNA release, degradation and transportation, widespread contamination risks during field and laboratory operations, and incomplete reference barcode databases. Combined with the latest progress in technical standardization and emerging interdisciplinary technologies such as environmental RNA (eRNA), passive sampling and machine learning, we propose an integrated solution consisting of standardized operation protocols, multi-source data fusion and localized database construction. This work aims to promote the standardized application of eDNA technology in aquatic environmental monitoring and provide technical references for biodiversity conservation and ecosystem management in global aquatic ecosystems.