eDNA Metabarcoding to Monitor Fish Communities in a Large River Floodplain

Abstract

Freshwater ecosystems are highly biodiverse and provide essential services that support both ecosystem health and economic sustainability. Despite their ecological significance, these ecosystems are disproportionately affected by the global biodiversity crisis. Large river floodplains constitute a fundamental component of freshwater ecosystems, sustaining fish biodiversity, growth, and reproduction. Yet, these floodplains face mounting threats from anthropogenic pressures, including physical modifications and land conversion for agriculture. In this context, there is an urgent need for scalable biomonitoring methods to more effectively assess floodplain ecosystems, which present methodological challenges due to their heterogeneous and dynamic nature. Traditional fish monitoring methods, however, are often invasive, costly, and resource-intensive. In contrast, environmental DNA (eDNA) metabarcoding presents a noninvasive, cost-effective, and scalable alternative. This study compares eDNA metabarcoding and electrofishing for fish community biomonitoring in the floodplain of Lake St. Pierre, the largest floodplain habitat along the St. Lawrence River. We assessed the effectiveness of these methods in monitoring fish community diversity and composition, as well as the influence of floodplain sectors and a gradient of land use from natural wetlands to annual (row) crops. eDNA metabarcoding detected a broader range of species than electrofishing, while both methods consistently identified abundant species. The two methods yielded uncorrelated diversity indices and distinct community compositions. Fish eDNA community composition was strongly associated with floodplain sectors, whereas land use within these sectors had a weaker influence on community diversity and composition. Our findings highlight eDNA metabarcoding as a valuable tool for characterizing broad patterns of fish communities in floodplain ecosystems. This method provides an additional tool to traditional methods for monitoring and conserving threatened floodplain habitats. However, careful consideration of study scale is essential to ensure effective conservation outcomes in these hydrologically dynamic environments.