Comparison Between Environmental DNA Metabarcoding and Traditional Survey Method to Identify Community Composition and Assembly of Stream Fish

ABSTRACT Environmental DNA (eDNA) metabarcoding has been widely used in freshwater systems, contributing to the advancements in the monitoring of fish diversity and community species composition. Nevertheless, the accuracy and reliability of eDNA metabarcoding in assessing functional structures and revealing the mechanisms underlying fish community assembly remain unclear. In this study, we combined a traditional survey method (electrofishing) and eDNA metabarcoding to conduct fish stock monitoring in the upper reaches of the Huishui stream. We assessed taxonomic and functional structures, as well as community assembly mechanisms, during dry and wet seasons. The results revealed that, compared with electrofishing surveys, eDNA metabarcoding detected a greater number of species and higher functional richness in both seasons. Despite significant differences in fish taxonomic composition between the seasons, both eDNA and traditional methods indicated that environmental filtering dominated the process of fish community assembly in both dry and wet seasons. We showed that eDNA metabarcoding is comparable to the electrofishing method in monitoring the community composition of stream fish and can accurately and reliably determine fish community assembly mechanisms. Combining functional traits and eDNA is a robust approach for monitoring stream fish community compared to taxonomic uncertainty. A comparison of morphology and eDNA‐based analysis was performed. eDNA metabarcoding detected a greater number of species and higher functional richness compared with electrofishing. eDNA metabarcoding can infer fish community assembly mechanisms in stream fish communities.