Contribution of eDNA Metabarcoding to Model Ecosystems: Case Study of Threatened Peri-Urban Mediterranean River

Abstract

Simple Summary Freshwater ecosystems on Mediterranean islands host vital wildlife but face growing threats from climate change and human activities. Conventional monitoring methods are often stressful to wildlife, labor-intensive, and miss elusive species. Our study surveyed vertebrates across three representative sampling stations along Sicily’s Oreto River using environmental genetic material continuously shed into the water. While constrained by limited spatial and temporal replication, analyzing water samples provided a spatial snapshot of biological diversity. The results revealed distinct community compositions: upper sections showed synanthropic wildlife signals, middle stretches were characterized by a high proportion of farm animal signals that indicate potential agricultural land use, and lower reaches yielded genetic signatures of endangered native species alongside alien species. Additionally, marine fish DNA in all the sites suggested potential anthropogenic inputs, such as food waste or municipal effluents. In conclusion, collecting waterborne genetic signals provides a fast, non-invasive, and effective way to characterize aquatic biological assemblages. While direct water quality parameters were not measured, this approach offers a practical complementary tool to support biodiversity monitoring, potentially manage land use responsibly, and inform local conservation priorities.