Application of Environmental DNA in Monitoring Diversity of Freshwater Ecosystems in China (A Systematic Review)

Freshwater ecosystems have been among the most vulnerable habitats globally over the past 50 years. These ecosystems have experienced varying degrees of decline due to a combination of global changes, including anthropogenic activities and climate change in recent decades. As a result, monitoring the diversity of freshwater ecosystems and their biota has emerged as a hotspot area of research in light of this diminishing variety. Environmental DNA (eDNA) has emerged as a powerful, complementary tool, offering a rapid, non-invasive alternative for biodiversity monitoring. eDNA represents an environment-friendly and cost-effective method for identifying and quantifying taxa without harming native species or habitats. The genetic material, consisting of short DNA fragments or cellular components released by aquatic organisms through skin, urine, feces, mucus, and cellular debris into environments like water, air, soil, or sediment, enables species identification and the characterization of community composition. The use of eDNA has expanded significantly in recent years, particularly in freshwater ecosystems in China, demonstrating its utility across various ecological and conservation applications. However, challenges remain, particularly regarding false positives and false negatives, which affect its reliability. This highlights the need for rigorous calibration and validation at each stage of analysis. Additionally, advancing eDNA technology requires a better understanding of the ecological and physical processes that influence eDNA dynamics, including its production, persistence, degradation, and transport. This review provides Chinese researchers, as well as non-molecular biologists, with a clearer understanding of the eDNA metabarcoding concept and its methodological overview.