Organisms perpetually release genetic material in their surroundings, referred to as environmental DNA (eDNA), which can be captured and subsequently analyzed to detect biodiversity across the tree of life. In lotic, dynamic environments, little is known about the specific factors that affect the concentration of eDNA between release by the host and its dissemination into the environment. This gap in knowledge introduces significant uncertainty when applying eDNA as a monitoring tool. Our objective is to provide insight on the factors that affect the eDNA concentrations in ecosystems representative of rivers and streams. To this end, we conducted a series of laboratory experiments in a rotating circular (annular) flume, which allows for extended degradation experiments under conditions of flow. Here, we show that flow velocity impacts the observed eDNA concentration over time. Our results suggest that flow-induced transport keeps eDNA in suspension, reducing eDNA removal from the water column, which increased the observed concentration of eDNA. We observed a temporary increase in eDNA concentration over the early phase of the flume experiment with the highest flow velocity. This increase in eDNA concentration seems to be due to a combination of low eDNA degradation rates and high shear stress, which fragment and subsequently homogenize eDNA particles over the water column. The results of our study show the importance of better understanding and assessing the detection probability of eDNA, both in controlled laboratory and larger-scale environmental conditions.

River restoration is an established method for the rehabilitation of river ecosystems in order to combat the current declines of freshwater biodiversity (Wohl et al., 2005; WWF, 2022). The urgency of restoration is recognized internationally, as the IUCN has proclaimed 2021-2030 to be the ‘Decade on Ecosystem Restoration’ (Cooke et al., 2022). So far only few restoration projects have been evaluated based on monitoring data (England et al., 2021), and there is a need for monitoring techniques to assess restoration practices. The analysis of environmental DNA (eDNA) has gained popularity in the last decades, as it allows for rapid standardized biomonitoring across the tree of life, requires a reduced dependence on taxonomic expertise for species identification, and it is cheaper than traditional monitoring methods. Depending on the organism, eDNA is shed by its host in forms such as mucous, shed skin cells, and faeces. After release, eDNA is exposed to a wide spectrum of environmental variables that may impact its state, transport capacity, fate, and the subsequent inference made by the practitioner (Barnes and Turner, 2016). Our objective is to study how eDNA quantities are affected by flow and sediment transport in river ecosystems.

A monitoring technique capable of assessing the status of an aquatic ecosystem is needed for reversing negative trends in river biodiversity. Recently, an innovative technique for detecting the degree of biodiversity based on environmental DNA traces (mucus, shed skins etc.) has been proposed (Carraro et al., 2020). This eDNA-based biomonitoring relies on the collection and processing of water samples containing genetic material released by organisms. In recent years, the research community has made significant efforts to advance the identification of species from biological samples, for instance by expanding genetic reference databases. However, eDNA technique implementation is hampered by a lack of knowledge about the dynamics of biological traces in rivers. Here, the aim is to investigate the transport of eDNA in water streams, while considering processes such as degradation and spreading.