Adding invasive species biosurveillance to the U.S. Geological Survey streamgage network

Abstract

The costs of invasive species in the United States alone are estimated to exceed US$100 billion per year, so a critical tactic in minimizing the costs of invasive species is the development of effective, early-detection systems. To this end, we evaluated the efficacy of adding environmental (e)DNA surveillance to the U.S. Geological Survey (USGS) streamgage network, which consists of >8200 streamgages nationwide systemically visited by USGS hydrologic technicians. Incorporating strategic eDNA sample collection during routine streamgage visits could provide early-detection surveillance of aquatic invasive species with minimal additional cost. For this evaluation, USGS hydrologic technicians collected monthly eDNA water samples, May-September 2018, from streamgages downstream of reservoirs in the Columbia River Basin thought to be vulnerable to invasive dreissenid mussel (Dreissenidae spp.) establishment. We tested water samples for dreissenid mussel DNA and also for kokanee (Oncorhynchus nerka) and yellow perch (Perca flavescens) DNA; the two fishes were used to assess if streamgages are adequately located to provide early-detection eDNA surveillance of taxa known to be present in upstream reservoirs. No Columbia River Basin streamgage samples met our criteria for being scored as positive for dreissenid DNA. We did detect kokanee and yellow perch DNA at all streamgages downstream of reservoirs where these species are known to occur. Field collection, laboratory analyses, and personnel time required for collection of four eDNA samples at a streamgage site cost US$500-US$600 (net). Given these results, incorporating eDNA biosurveillance into routine streamgage visits might decrease costs associated with an invasion since early detection maximizes the potential for eradication, containment, and mitigation.

Robotic environmental DNA bio-surveillance of freshwater health

“…We used previously published assays, limits of detection and methods therein for analyses of Naegleria spp. 12 , T. bryosalmonae 13 , S. japonicas 15 , O. nerka 7 , and Dreissena spp. 16 ( Table 1).…”

“…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 .…”

A round‐robin evaluation of the repeatability and reproducibility of environmental DNA assays for dreissenid mussels

“…Water was collected by trained technicians from one water body with established zebra mussel populations (San Justo Reservoir, CA), one water body with established quagga mussel populations (Lake Mead, NV), two water bodies with established populations of both zebra and quagga mussels (Lake Michigan, WI, and Seneca Lake, NY), and three water bodies where zebra or quagga mussel presence has not been documented (Jackson Lake, WY; the Yellowstone River, MT; and the Columbia River, OR; Figure 1). The individuals that collected samples varied by location (Table 1), but we trained all field technicians in US Geological Survey (USGS) eDNA sampling protocols (Sepulveda, Schmidt, et al 2019).…”

“…Importantly, we found that multiple assays that each target different genomic locations (e.g., 16s ribosomal subunit, mitochondrial Cyt B and COI regions) were all high performing. Analyzing a single sample with a suite of assays that target different genomic locations has been suggested as a way to improve the accuracy and rigor of eDNA monitoring programs (Farrington et al, 2015 (Sepulveda, Schmidt, et al 2019). Another, more cost-effective, option involves assay suites combined into multiplex reactions, though Gingera et al (2017) did find performance of the DRE16s, ZEBCOI, and ZEBCYT diminished when incorporated into the same multiplex reaction.…”

msocc: Fit and analyse computationally efficient multi‐scale occupancy models in r

“…Environmental DNA (eDNA) surveys continue to gain popularity for detecting invasive, cryptic and rare species (Klymus, Richter, Chapman, & Paukert, 2015; Lodge et al., 2012; Schmelzle & Kinziger, 2016; Sepulveda et al., 2019), as these techniques are often easier, less expensive and more sensitive than non‐molecular detection tools (Eiler, Löfgren, Hjerne, Nordén, & Saetre, 2018; Hunter, Meigs‐Friend, Ferrante, Smith, & Hart, 2019; Sengupta et al., 2019; Sepulveda et al., 2019; Williams, Huyvaert, Vercauteren, Davis, & Piaggio, 2018). These surveys rely on hierarchical sampling techniques to accommodate spatial heterogeneity in the occurrence of DNA within a study region.…”