Seasonal Changes in Fish eDNA Signal Vary Between Contrasting River Types

Abstract

Due to the societal reliance on goods and services provided by river systems and their close proximity to settlements, few modern-day rivers are without significant anthropogenic modifications. The natural river hydrology is often altered as a consequence of pumping water for flood alleviation, retaining water for irrigation, and modifying channels for navigation. In recent years, water pumping stations have been found to have several adverse impacts, including fish mortality (direct and indirect) and habitat fragmentation. More broadly, modern-day river systems face a myriad of anthropogenic flow and channel modifications, with varying impacts on different fish life stages. To manage such risks in line with policy, knowledge of the overall fish community and priority species present is required. It is therefore important to understand the robustness of developing survey strategies across differently managed river systems. This study investigates the seasonal patterns of environmental DNA (eDNA) metabarcoding fish detections from water samples taken across three differently managed river types over a one-year period. We observed some significant seasonal variation in detection rates and fish communities; however, this variation was not consistent among river types. Despite this, we found comparatively poor fish communities upstream of pumping stations all year round, with pumped catchments containing significantly fewer species than the adjacent main river channel and our regional control site. Finally, we highlight that seasonal variation in detectability for the overall fish community may not always reflect that of priority species. In our case, we found favorable European eel (Anguilla anguilla) detection in the summer months across all river types. It is therefore recommended that rather than focusing on overall detectability, policy-driven targeted surveys should be designed with priority species ecology in mind.