eDNA metabarcoding revealed differential structures of aquatic communities in a dynamic freshwater ecosystem shaped by habitat heterogeneity

Freshwater ecosystems have been threatened by complicated disturbances from both natural and anthropogenic variables, especially in dynamic and complex river basins. The environmental DNA (eDNA)-based approach provides a broader spectrum and higher throughput way of biomonitoring for biodiversity assessment compared with traditional morphological survey. Most eDNA metabarcoding studies have been limited to a few specific taxa/groups and habitat scopes. Here we applied the eDNA metabarcoding to characterize the structures and spatial variations of zooplankton and fish communities among different habitat types in a highly dynamic and complex freshwater ecosystem of the Daqing River basin (DRB). The results showed that varied species spectra of zooplankton and fish communities were identified and unique dominant species occurred across habitats. Additionally, markedly spatial distributions of biotic community structures were observed in areas with different habitat characteristics. Natural variables, including geographic distances and gradient ratio, as well as anthropogenic factors of chemical oxygen demand (COD) and organic chemicals demonstrated significant effects but different outcomes on the structures of zooplankton and fish communities. Moreover, the relative abundances of specific aquatic taxa were associated with the gradient of particular environmental variables. This case study verified the distribution patterns and differentiation mechanisms of biotic communities under habitat heterogeneity could be captured by application of eDNA biomonitoring. And habitat-specific and even species-specific environmental stressors would be diagnosed for improving management of complex river basins.