What’s the best way to collect eDNA?

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Across the Midwest Region, there are numerous ways field stations catch fish. Depending on the species, habitat, and the questions being addressed, field crews might use electrofishing, gill nets, trap nets, seines, minnow traps, hook and line, or any number of other methods. Although eDNA monitoring is still a relatively new technique, there are also several ways to collect eDNA, and again, the habitat, the species, and the questions being asked dictate which method might be most effective. For the past few years, the La Crosse Fish and Wildlife Conservation Office and the Whitney Genetics Lab have been working on a study to determine the optimal methods to collect eDNA for Topeka shiners, an endangered floodplain minnow which resides in oxbows in prairie streams. 

The traditional survey method for Topeka shiners (seining) can be time consuming and inefficient, and there is interest in using eDNA as a more effective monitoring tool. To date, much of the eDNA work in the Midwest Region has focused on invasive carp and collection protocols rely on mobile laboratories outfitted with multiple centrifuges for processing water samples. Monitoring budgets for Topeka shiners are significantly less than invasive carp, and eDNA collection protocols need to be affordable for external partners. 

We tested three methods, centrifugation, vacuum filtration, and field filtration, to determine how effective each method was in oxbows in Iowa and Minnesota. All three methods were able to detect Topeka shiners when they were present. Preliminary results suggest that centrifugation may collect more DNA, but filtration methods, particularly field filtration, are much more affordable and still produce high detection rates. This study should provide external partners with an important comparison between eDNA collection methods they can use to develop eDNA monitoring protocols for this endangered species.

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