The effect of flow velocity on eDNA and eRNA concentration

Across the globe, freshwater ecosystems have experienced a decline in biodiversity resulting from increasing anthropogenic pressure. Over the past decennia the scientific community has developed new and efficient biomonitoring techniques to register these shifts in biodiversity. A promising technique is the capture and analysis of eDNA and eRNA (environmental DNA and RNA; i.e. eNA). eNA constitutes the genetic material released by a host species into the environment in different forms, such as mucous, skin tissue, scales and saliva. However, in lotic ecosystems, such as streams and rivers, detected eNA concentrations can currently not be translated into the spatial and temporal distribution of the associated species. This is due to the lack of knowledge about the processes (e.g. transport and degradation) that influence eNA presence between the moment of release by its host, and the capture of the eNA by the practitioner.

The authors have conducted a set of laboratory experiments to shed light on these processes (i.e. transport and degradation). The objective was to test the influence of flow velocity on concentrations of both eDNA and eRNA. In an annular flume (depth = 19.7 cm; Ø = 3.7 m), which features counter-rotating bottom and top components, we performed eDNA and eRNA degradation experiments under four different flow rates, each with a duration of seven days. The source of eNA originated from water previously inhabited by wildtype zebrafish (Danio rerio). The tested angular velocities of the top lid (ν_{t top lid}) are 0.00, 0.35, 1.05 and 1.80 m/s with corresponding velocities of the bottom component in a constant ratio (ν_{t top lid}/ν_{t bottom}) as to reduce secondary circulations in the cross section of the flume. Flow velocity measurements were taken using an acoustic Doppler velocimeter (ADV) across the depth of the flume. During the experiment, abiotic measurements (of pH, temperature and conductivity) as well as water samples were taken. eDNA and eRNA concentrations (in copy numbers per volume) were gathered from these water samples by means of ddPCR, targeting a species-specific 73 base pair fragment in the Cytochrome c Oxidase subunit 1 gene. The abiotic measurements are consistent over the duration of the experiment (average conductivity of 520.1 µS, average temperature of 20.3 °C, average pH of 8.3). Concerning the eNA results, a decrease in both eDNA and eRNA concentrations can be noted over the span of the experiment regardless of the rotation speed. Additionally, eRNA concentrations generally decreased in concentration at a higher rate than eDNA concentrations. These experiments advance the understanding of eNA degradation in lotic ecosystems, and bring forth new directions of research to improve inference in eNA-based biomonitoring.