Monitoring estuarine fish communities: environmental DNA (eDNA) metabarcoding as a complement to beach seining

Abstract

Environmental deoxyribonucleic acid (eDNA) metabarcoding offers advantages over physical capture for identifying and quantifying animals in monitoring programs. In this study, the fish community was sampled at three stations (inner, middle, and outer estuary) in three estuaries in August 2020, and four estuaries in June and August 2021 (Prince Edward Island, Canada) using both beach seining and eDNA metabarcoding. Two 12S primer sets, 12S-160 and 12S-248F, with different amplicon lengths, yielded similar results. eDNA metabarcoding consistently detected species captured by 186 co-located beach seines and revealed additional species. It also detected monthly (June–August), interannual (2020–2021), and spatial shifts in the fish community, distinguishing stations separated by as little as 0.4 km. Positive correlations existed between eDNA metabarcoding species reads and beach seining captures. These findings suggest eDNA metabarcoding complements physical capture methods for characterizing nearshore fish communities in Prince Edward Island’s estuaries. While eDNA techniques lack certain population parameter information provided by physical methods, such as size, sex, and age structure, they offer a more comprehensive diversity assessment and presence–abundance insights, especially in inaccessible environments.