Environmental DNA in different media reveals distribution characteristics and assembly mechanisms of fish assemblages in a complex river–lake system

Abstract

Abstract. Capture-based methods are commonly used for biomonitoring fish assemblages in freshwater. The recent advancement in environmental DNA (eDNA) metabarcoding provides a sensitive, cost-effective, and non-intrusive alternative to traditional methods. Nevertheless, the effectiveness of this approach in river–lake systems has yet to be assessed, and there is ongoing debate regarding the selection of sampling media. In this study, we investigated fish assemblages based on traditional approaches and the eDNA metabarcoding method by analyzing water and sediment from 30 locations along the Baiyang Lake and its inflow rivers (China). The results showed that 21 species were identified based on traditional methods, and a total of 29 species were detected using eDNA, with 22 species found in river water eDNA, 25 species in lake water eDNA, and 27 species in surface sediment samples. Nine benthic fish species were detected exclusively in sediment. The community composition of rivers and lakes revealed by water eDNA is similar, reflecting the biotic homogenization in this river–lake system. A neutral community model (NCM) analysis based on lake water and river water eDNA showed that fish assemblages were not dominated by random processes (5.3 % and 2.7 % concordance with the neutral model, respectively), while analysis of surface sediment eDNA showed more support for random processes (50.2 %). Temperature was the main environmental factor correlated with water eDNA, while NH3–N and TP were the main factors correlating with sediment eDNA.