Determining the influence of substrate heterogeneity on the measurement and transport of environmental DNA (eDNA) using Notre Dame’s Linked Ecosystem Experimental Facility (ND-LEEF)

Background/Question/Methods

Sampling for environmental DNA (eDNA) is a non-intrusive method to detect the presence of invasive species without direct observation, which allows for earlier detection and more rapid response than conventional sampling methods. However, our current understanding of how eDNA is transported and persists in flowing waters remains imprecise. There is little previous study on how the unique transport properties of suspended eDNA particles in flowing water may impact the probability of eDNA detection. To improve understanding of fine-scale eDNA transport in streams, we conducted experimental releases using common carp eDNA, and modeled the impact of stream substrate heterogeneity and substrate size on eDNA transport and retention. Using a short-term eDNA addition, we estimated transport distances in four 50m experimental streams at ND-LEEF (discharge=2L/sec) with varying substrate size (1cm pea-gravel vs. 10cm small cobble) and complexity (homogenous 50/50 mix vs. alternating sections). We also compared the standard eDNA detection method using quantitative PCR (qPCR) with a new detection technique based on Light Transmission Spectroscopy (LTS), which offers the capabilities of field-based eDNA detection. LTS uses target-specific genetic tags attached to polystyrene beads to detect species-specific eDNA and measures wavelength-dependent transmittance through aqueous samples based on the diameter of nanoparticles in suspension. 

Results/Conclusions

Using qPCR detection techniques, we measured particulate retention of eDNA, expressed as an uptake length (S_w), which is the mean transport distance traveled before being removed from the water column. Uptake lengths of eDNA ranged from 6-57m and differed among streams with varying substrate; eDNA particles traveled furthest in cobble, moderate distances in mixed substrate and alternating substrate, and shortest distances in pea-gravel reaches. Differential retention of eDNA particles confirms that eDNA dynamics in flowing waters are not longitudinally constant along stream and river continua, and retention may be habitat-specific, which may complicate interpretation of eDNA detection in flowing waters. Additionally, results from LTS confirm that the platform can give an accurate positive/negative detection signal with high species specificity, and can be optimized for field-based detection. Robust techniques that accurately measure eDNA from invasive species in streams/rivers can inform species management, allowing for rapid responses to invasion, yet questions remain about species detection vs. source location in flowing waters.