Comparison of fish communities using environmental DNA metabarcoding and capture methods in a freshwater lake: A new set of universal PCR primers

Abstract

Freshwater biodiversity is under pressure from the detrimental effects of climate change, habitat degradation, biological invasion, and overfishing. Environmental DNA (eDNA) obtained directly from environmental samples can be used to evaluate the distribution of aquatic species. We developed a new set of universal PCR primers (16 S 200) for eDNA metabarcoding from mitochondrial DNA sequences. Using the new 16 S 200 primers, we detected the presence of 27 fish species distributed across four families in Lake Gehu, in southeastern China. eDNA metabarcoding and live capture methods identified 16 species in common; however, the two methods identified nine and 12 unique species, respectively. Data from eDNA metabarcoding were more consistent with results from gill net capture methods than from ground cage capture. The present study supports the effectiveness of eDNA for rapidly assessing the species composition of fish communities.This is the first attempt to designed new sets of primers for eDNA-based metabarcoding analysis of freshwater fish in China. Despite pitfalls and limitations, eDNA metabarcoding is a promising approach for assessing fish communities in freshwater lakes. Current applications of eDNA are widespread, but the new technology requires further refinement.The eDNA metabarcoding is an efficient and cost-effective method that can be used in conjunction with traditional survey methods for analyzing fish communities.