Metabarcoding data of the fish community within Tuckahoe Creek, a tributary of the James River, Virginia, USA.

Electrofishing is currently the most common method used to assess freshwater fish communities. Although conventional electrofishing practices are considered effective there are inherent limitations. One alternative method for evaluating fish assemblage dynamics is the sequencing of environmental DNA (eDNA) extracted from water samples. Although eDNA sampling has become more common in recent years, its routine application in fish community surveys across diverse taxa and habitats remains relatively novel, and more comparisons between eDNA and traditional sampling methodologies are needed demonstrate eDNA’s applicability. In this study, two distinct metabarcoding primers were assessed simultaneously for the detection and concentration of fish species using eDNA against synoptic electrofishing surveys. This research was conducted within a species-rich, stream fish assemblage that is supported by a complex of dynamic abiotic habitats. The findings of this study were analyzed alongside a series of historical fisheries observations from the same watershed, with datapoints that originated in 1869. The comparisons made in this study suggest that metabarcoding outperforms electrofishing for the purpose of determining both long-term and immediate community-level species richness in fish assemblages, particularly when using multiple detection primers. Metabarcoding was most useful in detecting numerically uncommon species of fish. Further, our results indicate great potential in determining relative species abundance from metabarcoding sample composition when compared to the associated electrofishing samples.