Using Experimental and Field Approaches to Identify Predictors and Drivers of eDNA Transport and Removal in Streams and Rivers

Flow shapes the physical attributes and biological processes of streams and rivers, while also transporting materials downstream. Thus, foundational stream ecology concepts such as the river continuum concept, solute spiraling, and the organic matter processing continuum provide a rich context to inform our understanding of the factors that control the fate and transport of materials in streams and rivers. My dissertation utilized approaches from stream ecology to investigate the mechanisms controlling the transport of an organic particle, environmental DNA (eDNA), which is a mixture of genetic material released by an organism that is detectable in water, soil, air, or other media. The use of eDNA as a sampling tool, especially in aquatic habitats, offers insights into the detection of invasive and/or rare species and enables biodiversity assessment without conventional sampling approaches. In recent years, the use of eDNA has moved beyond species presence/absence with attempts to estimate target organism location, biomass, and/or abundance based on eDNA concentrations, but most of this work has been conducted in standing waters (i.e., ponds, lakes). Moreover, our understanding of the environmental factors impacting eDNA removal (i.e., how rapidly eDNA is removed from the water column by the combination of uptake, decay, and physical removal) in streams and rivers is limited. My dissertation explores critical uncertainties about how the characteristics of eDNA interact with environmental factors to determine the fate of eDNA in flowing, freshwater environments. Using experiments in indoor mesocosms, outdoor experimental streams, and natural systems, I found that both biotic and abiotic factors interact to control eDNA removal from the water column. First, I used recirculating stream mesocosms to explore the impact of benthic substrate conditions (including biofilm) and light availability on removal of varying sizes of eDNA particles. Overall, I found that eDNA removal rates were highest for mesocosms with biofilm-colonized substrate, and among eDNA size classes, I saw that larger particles (>10 µm) were removed faster than small particles (0.2-1.0 µm) with removal of larger particles being controlled by deposition into the substratum while removal for smaller particles was driven by biology. I then used the recirculating mesocosm platform to quantify the impact of temperature on eDNA removal, and found that removal increased at warmer temperatures, particularly for small eDNA particles (0.2-1.0µm). Using flow-through experimental streams, I then investigated how the progression of biofilm colonization influences eDNA transport and found that eDNA removal was faster later in the colonization sequence, a pattern seemingly driven by adsorption of the eDNA to fine benthic organic matter. In another eDNA study, I again used the experimental stream platform, this time comparing eDNA transport between two fish species with known differences in particle size distribution and found variation in transport patterns between the two species, which was driven by differing responses of large versus small particles to environmental conditions. Finally, I examined how seasonal variation in environmental context impacts eDNA transport and removal and found evidence that removal was primarily controlled by physical drivers such as discharge and trapping in the substrate. Overall, my dissertation research emphasized the complex relationship between environmental factors and eDNA removal in small streams. Although additional eDNA studies are needed in a diversity of natural waterways and with other taxonomic groups, my work expanded our understanding of crucial drivers of eDNA transport in fluvial systems and advanced the use of eDNA as a tool for science, management, and monitoring.