Environmental DNA (eDNA) for Early Detection of Invasive Aquatic Species & Endemic Fish Surveillance in Desert Spring Systems

Authors: Duane Moser, Victoria Wuest, Michael Schwemm

Year: 2022

Abstract

Aquatic organisms continuously shed DNA into their surroundings. This “environmental DNA (eDNA)” is detectable with exquisite sensitivity through the quantitative Polymerase Chain Reaction (qPCR). qPCR is routinely being used for the tracking of coldwater fish (e.g. salmonids) and to infer the invasion of the Great Lakes by Asian carp from the Mississippi River system. Much less is known, however, concerning the efficacy of these approaches for detection of warm-water species. Spring-fed systems of the US Great Basin are home to a diversity of endemic and/or threatened aquatic organisms. The fortunes of these organisms are tied to hydrologic variables and competition/predation from invasive species (e.g. introduced fishes and red swamp crayfish (Procambarus clarkii)). However, molecular detection approaches are just beginning to be applied for the management of sensitive desert aquatic ecosystems. Our proof-of-concept study is in progress and endeavors to optimize sampling (e.g. high-volume filtration) and DNA extraction protocols to maximize method sensitivity. Concurrently, published and custom-designed molecular probes (qPCR primer sets) targeting mitogenome targets are being evaluated to demonstrate that endemic fishes (e.g. Moapa dace (Moapa coriacea) and Warm Springs pupfish (Cyprinodon pectoralis nevadensis)) and invasive species (Red Swamp crayfish, blue tilapia (Oreochromis aureus), and red shiner (Cyprinella lutrensis)) can be quantitatively monitored in two priority ecosystems (the Muddy River and Ash Meadows in Southern Nevada). In parallel, the work aims to confirm the presence or absence of invasive tilapia and red shiner (Muddy River) and red swamp crayfish (Ash Meadows) in reaches where they have recently been removed. Initial work with published qPCR primer sets targeting Eurasian dace performed well for Moapa dace, but also amplified Western mosquitofish (Gambusia affinis, tissue and environmental DNA extracts). This lack of specificity led us to develop and test new primer sets for dace and red swamp crayfish. Calibrations of the new primers, using tissue (fin clips), timed microcosm tests, and environmental sampling support a high level of sensitivity (~1 individual in 100,000 L of water) and specificity for Moapa dace and mosquitofish. Detection of red swamp crayfish was also improved through primer optimization. A watershed-scale eDNA survey for Moapa dace was conducted in parallel with a traditional snorkel survey in the headwaters of the Muddy River. eDNA analysis was still underway at the time of abstract submission and results will be presented in the session. The results from this preliminary study support qPCR-based eDNA monitoring as a cost-effective and high-sensitivity approach for the periodic surveillance of both endemic fishes and potential invaders in desert aquatic ecosystems.