Field Trials of an Autonomous eDNA Sampler in Lotic Waters

Abstract

Environmental DNA (eDNA) analysis has become a transformative technology, but sample collection methods lack standardization and sampling at effective frequencies requires considerable field effort. Autonomous eDNA samplers that can sample water at high frequencies offer potential solutions to these problems. We present results from four case studies using a prototype autonomous eDNA sampler as part of the U.S. Geological Survey's Rapid Environmental eDNA Assessment and Deployment Initiative & Network (READI-Net) project. These case studies involved short-term deployments of an eDNA autosampler (Smith-Root) across a range of riverine habitats with the objectives of (a) identifying what insights could be gained from high-frequency autosampling and (b) benchmarking these autosamples against manually collected samples. The high frequency autosampling revealed high temporal variability of eDNA concentrations and provided valuable insights about eDNA associations with environmental covariates, such as discharge and turbidity. Benchmarking assessments indicated autosamples had similar detection rates to manual samples and obtained similar or greater eDNA quantities. We did find minimal carryover contamination in autosampler field controls. We conclude that eDNA autosamplers have potential to improve freshwater biosurveillance by reducing logistical sampling barriers, standardizing collection methods, and clarifying the influence of environmental covariates on eDNA results.

Keywords: Rainbow Trout; Round Goby; Spectaclecase; Western Pearlshell; Westslope Cutthroat Trout; invasive; robotic sampler; temporal.

Figure 1

Deployment of the eDNA autosampler in a USGS streamgage on the Hudson River.

Figure 2

Mean and range of eDNA concentrations (five PCR replicates) from 56 samples (black) and two field controls (pink) collected by the autosampler in the Hudson River case study (June 29–July 6, 2023) plotted against a 1-h running average of continuous (15 min) discharge (top panel) and turbidity data (bottom panel). The number of qPCR replicates for a given sample that did not amplify are listed above the x-axes and were assigned a zero for sample mean calculation. Vertical shading denotes periods of darkness.

Figure 3

Estimated relation (with 95% confidence interval) between the proportion of target volume filtered and turbidity from a one-inflated β regression for 56 samples collected by the autosampler in the Hudson River case study.

Figure 4

Mean and range of eDNA concentrations (five PCR replicates) from eight samples and two field controls collected in triplicate using the autosampler, backpack sampler, and manual hand pump in the Hudson River case study. The number of qPCR replicates for a given sample that did not amplify are listed above the x-axis and were assigned a zero for sample mean calculation. Dashed regions denote paired field controls.

Figure 5

Mean and range of eDNA concentrations (five PCR replicates) from 56 samples collected by the autosampler and seven pairs of manual grab samples (Glass: glass-fiber filter, PES: polyethersulfone) in the Cherry Creek case study (August 14–21, 2023) plotted against 1-h water level. Vertical shading denotes periods of darkness.

Figure 6

Mean and range of eDNA concentrations (3 PCR replicates) from 31 samples and 1 field control collected by the autosampler, and 6 paired samples and 1 field control collected with the backpack sampler in the Loggers Creek case study. The number of qPCR replicates for a given sample that did not amplify are listed above the x-axes and were assigned a zero for sample mean calculation. Vertical dashed line indicates a break in the time series. Dashed regions denote paired field controls.

Figure 7

Mean and range of eDNA concentrations (four PCR replicates) from 16 samples collected by the autosampler and nine paired manual centrifuge samples (collected in quadruplicate) during the Lake Trout slurry addition in the Big Piney River case study. Vertical dashed line indicates the time point at which the frozen slurry was added. The number of qPCR replicates for a given sample that did not amplify are listed above the x-axis and were assigned a zero for sample mean calculation.