Distance, flow, and PCR inhibition: eDNA dynamics in two headwater steams

Environmental DNA (eDNA) detection has emerged as a powerful tool for monitoring aquatic organisms, but much remains unknown about the dynamics of aquatic eDNA over a range of environmental conditions. DNA concentrations in streams and rivers will depend not only on the equilibrium between DNA entering the water and DNA leaving the system through degradation, but also on downstream transport. To improve understanding of the dynamics of eDNA concentration in lotic systems, we introduced caged trout into fishless headwater streams and took eDNA samples at evenly spaced downstream intervals. This was repeated 18 times from mid-summer through autumn, over flows ranging from approximately 1 to 96 L/sec. We used qPCR to relate DNA copy number to distance from source for each sampling event. We found that regardless of flow, there were detectable levels of DNA at 239.5 m. The main effect of flow on eDNA counts was in opposite directions in the two streams. At the lowest flows, eDNA counts were...