eDNA Techniques Research Articles

Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species

AbstractAccurate knowledge of the distribution of rare, indicator, or invasive species is required for conservation and management decisions. However, species monitoring done with conventional methods may have limitations, such as being laborious in terms of cost and time, and often requires invasive sampling of specimens. Environmental DNA (eDNA) has been identified as a molecular tool that could overcome these limitations, particularly in aquatic systems. Detection of rare and invasive amphibians and fish in lake and river systems has been effective, but few studies have targeted macroinvertebrates in aquatic systems. We expanded eDNA techniques to a broad taxonomic array of macroinvertebrate species in river and lake systems. We were able to detect 5 of 6 species (Ancylus fluviatilis, Asellus aquaticus, Baetis buceratus, Crangonyx pseudogracilis, and Gammarus pulex) with an eDNA method in parallel to the conventional kicknet-sampling method commonly applied in aquatic habitats. Our eDNA method showed m...

The use of environmental DNA in invasive species surveillance of the Great Lakes commercial bait trade.

Over 180 non-native species have been introduced in the Laurentian Great Lakes region, many posing threats to native species and ecosystem functioning. One potential pathway for introductions is the commercial bait trade; unknowing or unconcerned anglers commonly release unused bait into aquatic systems. Previous surveillance efforts of this pathway relied on visual inspection of bait stocks in retail shops, which can be time and cost prohibitive and requires a trained individual that can rapidly and accurately identify cryptic species. Environmental DNA (eDNA) surveillance, a molecular tool that has been used for surveillance in aquatic environments, can be used to efficiently detect species at low abundances. We collected and analyzed 576 eDNA samples from 525 retail bait shops throughout the Laurentian Great Lake states. We used eDNA techniques to screen samples for multiple aquatic invasive species (AIS) that could be transported in the bait trade, including bighead (Hypophthalmichthys nobilis) and silver carp (H. molitrix), round goby (Neogobius melanostomus), tubenose goby (Proterorhinus marmoratus), Eurasian rudd (Scardinius erythrophthalmus), and goldfish (Carassius auratus). Twenty-seven samples were positive for at least one target species (4.7% of samples), and all target species were found at least once, except bighead carp. Despite current regulations, the bait trade remains a potential pathway for invasive species introductions in the Great Lakes region. Alterations to existing management strategies regarding the collection, transportation, and use of live bait are warranted, including new and updated regulations, to prevent future introductions of invasive species in the Great Lakes via the bait trade.

Molecular Detection of Vertebrates in Stream Water: A Demonstration Using Rocky Mountain Tailed Frogs and Idaho Giant Salamanders

Stream ecosystems harbor many secretive and imperiled species, and studies of vertebrates in these systems face the challenges of relatively low detection rates and high costs. Environmental DNA (eDNA) has recently been confirmed as a sensitive and efficient tool for documenting aquatic vertebrates in wetlands and in a large river and canal system. However, it was unclear whether this tool could be used to detect low-density vertebrates in fast-moving streams where shed cells may travel rapidly away from their source. To evaluate the potential utility of eDNA techniques in stream systems, we designed targeted primers to amplify a short, species-specific DNA fragment for two secretive stream amphibian species in the northwestern region of the United States (Rocky Mountain tailed frogs, Ascaphus montanus, and Idaho giant salamanders, Dicamptodon aterrimus). We tested three DNA extraction and five PCR protocols to determine whether we could detect eDNA of these species in filtered water samples from five streams with varying densities of these species in central Idaho, USA. We successfully amplified and sequenced the targeted DNA regions for both species from stream water filter samples. We detected Idaho giant salamanders in all samples and Rocky Mountain tailed frogs in four of five streams and found some indication that these species are more difficult to detect using eDNA in early spring than in early fall. While the sensitivity of this method across taxa remains to be determined, the use of eDNA could revolutionize surveys for rare and invasive stream species. With this study, the utility of eDNA techniques for detecting aquatic vertebrates has been demonstrated across the majority of freshwater systems, setting the stage for an innovative transformation in approaches for aquatic research.

Needles in a haystack

In the late 1960s, an Air France pilot and his family took a holiday in swampy Louisiana in the southeastern USA and were intrigued by the giant bullfrogs, Rana catesbeiana . The family introduced a dozen of the animals to a pond in the Bordeaux region of southwestern France, inadvertently starting a major invasion that affected thousands of lakes and creeks with devastating effects on the native fauna. “They eat everything and if you go to a pond where there are bullfrogs, there are no other amphibians […] because bullfrogs prey on other animals or because they are spreading a disease—chytridiomycosis—that is absent from some European areas,” said conservation biologist Francesco Ficetola of the Department of Environmental Sciences at the University of Milano–Bicocca in Italy. “There was nothing like them in Europe,” he added. As part of his postdoctoral research, Ficetola studied the frog invasion in Europe at the Universite de Savoie and the University of Grenoble in France. To monitor their distribution, he pioneered the use of environmental DNA (eDNA) to detect R. catesbeiana without observing the animals themselves. He and his colleagues took water samples, extracted eDNA and used primers monomorphic to nearly 400 bullfrog samples to demonstrate their presence in wetlands, even in low densities. ![][1] “The significance was that we were able to detect the presence of the species without seeing or hearing the species,” Ficetola said. The eDNA technique has further potential: “As the environment can retain the molecular imprint of inhabiting species, our approach allows the reliable detection of secretive organisms in wetlands without direct observation. Combined with massive sequencing and the development of DNA barcodes that enable species identification, this approach opens new perspectives for the assessment of current biodiversity from environmental samples” (Ficetola et al , 2008). According to David Lodge, a biologist … [1]: /embed/graphic-1.gif