Discriminating spatiotemporal heterogeneity and environmental drivers of fish assemblages using environmental DNA metabarcoding in mosaic habitat ecosystems

Surveys of fish diversity in complex heterogeneous environments are highly challenging to perform using traditional survey methods. Although environmental DNA (eDNA) metabarcoding has been effectively used to evaluate fish diversity, studies exploring the spatial and temporal variability of fish communities in mosaic habitats and their connection to water quality after ecological project implementation are still scarce. Here, we evaluated the changes in water quality and fish assembles using the traditional method and environmental DNA (eDNA) metabarcoding after Ecological water replenishment (EWR) and the links between fish communities and water quality were established in the Baiyangdian (BYD) ecosystem in the North China Plain. All water quality variables including TN, NH₃-N, COD_Mn and TP showed a conspicuous improvement pattern, and the number of fish species increased notably after EWR. In addition, 6 more introduced fish species were recorded when compared with the historical data before the implementation of the EWR project. Furthermore, the species richness showed a highly significant difference among the four habitats in the summer 2020 and spring 2021 (spring: P = 0.000; summer: P = 0.002), and obvious discrimination of fish communities across two seasons was observed (P = 0.001) with eDNA metabarcoding. The water quality variables driving the changes of fish communities during the same period varied significantly across different habitats, while not all showed noticeable discrepancy in driving cross-seasonal fish community changes. Thus, our study highlights that the continuous EWR improves the water quality and fish richness but potential ecological issues associated with introduced species should be carefully considered after EWR. Our results also confirm that eDNA is a reliable tool for assessing fish diversity and distinguishing spatiotemporal variability of fish communities in mosaic habitat ecosystems.