Environmental DNA metabarcoding: Current applications and future prospects for freshwater fish monitoring

Abstract

Fish, as the top predators in freshwater, greatly contribute to maintain ecosystem stability. There has been a sharp decline in freshwater fish stocks due to multiple factors, both natural and anthropogenic. Effective and accurate monitoring of freshwater fish is necessary to inform on ecosystem health and guide environmental management practices. Traditional survey methods are gradually unable to meet the growing monitoring needs. Environmental DNA (eDNA) metabarcoding provides a high sensitivity, fast and affordable approach for surveying and monitoring of aquatic biology. However, due to the limitations of incomplete databases and non-standardized procedures, the use of eDNA techniques for monitoring freshwater fish remains less mature compared to traditional fish monitoring methods. To systematically review the current applications and future prospects of the eDNA metabarcoding for freshwater fish monitoring, this article: (i) summarizes relevant researches on freshwater fish monitoring using eDNA technology (e.g., methodologies, resource surveys, habitat assessments, etc.) over the past decade. (ii) outlines the methodology of eDNA metabarcoding in freshwater fish monitoring, proposes a standardized process for eDNA methods, and suggests ways to eliminate detection errors. (iii) analyzes the current challenges of the eDNA metabarcoding application in resource surveys and ecological quality assessments of freshwater fish. The eDNA technology can be used as a better alternative or supplement to traditional survey methods for monitoring the diversity, biomass, population distribution, and spawning behaviors of freshwater fish, in particular, it has a prominent advantage in monitoring endangered and rare fish species. (iv) investigates the application of eDNA technology in investigating the impact of human activities and invasive species on freshwater fish, and emphasizes the eDNA's potential in assessing the impacts of water projects (e.g., dam construction or removal, water diversion project) on fish habitats, and the effectiveness of fish passage and invasive fish control efforts. (v) discusses the future prospects of eDNA-based freshwater fish monitoring, both in terms of technology and application. This review provides a guidance for the future development and application of eDNA technology in freshwater fish monitoring and ecological quality assessments.

Keywords: Anthropogenic influences; Ecological quality assessment; Fish community; High-throughput sequencing; eDNA.