| Summary: | We compared two sampling methods, eDNA metabarcoding and microscope identification (MSI), for the analysis of zooplankton diversity in reservoirs with its inflow and outflow streams. The dynamic patterns of Cladocera and Rotifera at different time points were similar between the two sampling methods, but there was a slight difference in the Copepoda. Specifically, the members of the Copepoda subclass could not be easily classified using the MSI method, whereas eDNA metabarcoding could detect minor taxa of Cladocera and Rotifera. Upon comparing the list of zooplankton communities in Korea with the gene database of NCBI, only ~56% of the zooplankton genera reported in Korea could be detected based on the 18S rRNA gene. However, eDNA metabarcoding detected a more diverse range of zooplankton despite the lack of genetic information. As water temperature increased after May, the zooplankton diversity decreased according to the MSI method but increased according to the eDNA metabarcoding method. Although eDNA metabarcoding has some limitations, it was able to detect a wider diversity of zooplankton compared to the MSI. eDNA metabarcoding provides a more reliable means to identify zooplankton.
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