Robotic environmental DNA bio-surveillance of freshwater health

Abstract

Autonomous water sampling technologies may help to overcome the human resource challenges of monitoring biological threats to rivers over long time periods and across large geographic areas. the Monterey Bay Aquarium Research institute has pioneered a robotic environmental Sample processor (eSp) that overcomes some of the constraints associated with traditional sampling since it can automate water sample filtration and preservation of the captured material. The ESP was originally developed for marine environment applications. Here we evaluated whether the eSp can provide reliable, timely information on environmental (e)DNA detections of human and fish pathogens and introduced fishes at U.S. Geological Survey streamgage sites in freshwater rivers. We compared eDNA collected via ESP at high frequency (e.g., every 3 h) with manual eDNA collections collected at lower frequency (e.g., weekly). We found that water samples filtered and preserved by ESPs successfully detected the DNA of human pathogens, fish pathogens and introduced fishes. Both ESP and manually collected samples provided similar information about target DnA presence. We suggest that the greatest current benefit of the ESP is the cost savings of high frequency, bio-surveillance at remote or hard to access sites. the full potential of robotic technologies like the eSp will be realized when they can more easily execute in situ analyses of water samples and rapidly transmit results to decision-makers. Invasive species have serious negative effects on regional and national economies 1,2. Thus, early detection is a central pillar of most monitoring programs because the earlier an invader is detected, the more likely control efforts will be effective in limiting invader spread and the resulting economic and environmental damages 3. Environmental DNA (eDNA) sampling has recently emerged as a sensitive, early detection tool because it can detect as little as a single cell from an invasive species by identifying the cellular or extracellular DNA that organisms release into the environment 4. Despite the ubiquity of eDNA in the aquatic environment, eDNA of targeted taxa is not always well mixed, so high detection probabilities often require intense sampling 5,6. Therefore, reliable detection requires trained individuals to manually collect water samples over long time periods or across large geographic areas 7. Autonomous, robotic water sampling technologies present an opportunity to overcome the temporal and human resource demands associated with eDNA sampling. Autonomous robots placed within the environment can conduct high frequency sampling, regardless of location, weather or the availability of human resources. The Monterey Bay Aquarium Research Institute (MBARI) has pioneered a robotic instrument called the Environmental Sample Processor (ESP) that overcomes the constraints of regular travel and work schedules, safety concerns with high water flows, and adverse weather. The ESP is a robotic device that can be programmed to automate water sample filtration an...

Integrating Environmental DNA Results With Diverse Data Sets to Improve Biosurveillance of River Health

“…We applied the data science workflow to two datasets described in Sepulveda et al (2020). In the first dataset used as an example of eDNA early detection programs, autonomous robotic eDNA samplers collected samples at two USGS streamgage sites in the Yellowstone River of Montana (United States): USGS 06191500 Yellowstone River at Corwin Springs MT and USGS 06192500 Yellowstone River near Livingston MT, described below as Corwin Springs and Carters Bridge, respectively (Figure 2).…”

“…Samples were analyzed for DNA of the fish pathogen, Tetracapsuloides bryosalmonae, the causative agent of salmonid fish Proliferative Kidney Disease (PKD), which has resulted in large salmonid mortality events in this region and also in Europe (Hutchins et al, in press). Detections of T. bryosalmonae DNA were rare, as only 5 of 256 samples were scored as positive (Sepulveda et al, 2020).…”

“…Samples were analyzed for Oncorhynchus nerka (kokanee salmon) DNA; O. nerka occur upstream in Palisades Reservoir. Thirty-five of 128 samples were scored as positive for O. nerka DNA (Sepulveda et al, 2020).…”

“…Environmental (e)DNA sample collection and subsequent analyses have revolutionized biosurveillance because inferences can be made about species occurrences sightunseen (e.g., Cristescu and Hebert, 2018). More recently, autonomous robotic eDNA samplers have made it possible to make biological observations match the scale and quality of in situ physical and chemical measurements (Yamahara et al, 2019;Sepulveda et al, 2020). Autonomous robots placed within the environment can conduct high frequency (sub-daily) sampling, regardless of location, weather, or the availability of human resources.…”

“…For eDNA analyses, multiple samples are collected at a location and multiple replicates from each sample are analyzed for the presence of the target organism DNA. Samples taken at the location occupied by a species may not necessarily contain DNA of that target species, just like replicates may lack target DNA even if the DNA is present in the sample (Darling, 2019;Sepulveda et al, 2020). Thus, each sample and replicate may detect the organism's DNA, if present, with some probability.…”