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

Abstract

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.

Faeces of generalist predators as ‘biodiversity capsules’: A new tool for biodiversity assessment in remote and inaccessible habitats

“…This is not limited to faecal samples; other sources of environmental DNA have also been used to assess biodiversity, with successes and limitations. For example, environmental DNA from water samples has been used to assess vertebrate and invertebrate biodiversity in stagnant and running-water ecosystems (Ficetola et al, 2008;Goldberg et al, 2011;Hajibabaei et al, 2011). Thomsen et al (2012) proposed a simple model that estimates population abundance based on animal body size and DNA degradation rate, for two amphibian species in a closed freshwater system and under controlled conditions.…”

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

“…2. Detection of low density populations: The detection of eDNA for species or populations that are at low densities (e.g., threatened or endangered taxa) or are visually evasive (e.g., madtom catfishes) appears promising (Goldberg et al, 2011;Takahara et al, 2012;Takahara, Minamoto & Doi, 2013). For example, the chucky madtom (Noturus crypticus), a United States federally endangered species, was last observed in 2004 despite intensive, survey efforts using traditional sampling methods (i.e., seines and snorkel surveys).…”

“…Distributions of organisms and biomass in freshwater systems have been correlated with eDNA concentration (Takahara et al, , 2013. Thus eDNA concentration has been used as a proxy for population distribution in amphibians (Ficetola et al, 2008;Goldberg et al, 2011), fishes (Mahon, Jerde, Galaska, Bergner, Chadderton, Lodge, Hunter, & Nico, 2012;Minamoto, Yamanaka, Takahara, Honjo, & Kawabata, 2012) and reptiles species (Piaggio et al, 2013). In marine species no studies have been conducted to determine the relationship between eDNA concentration and species distribution, abundance and biomass.…”

“…Persistence estimates have been determined for different taxonomic groups: from 15 to 30 days for fresh water fishes (Dejean et al, 2011& Takahara et al, 2012a, 15 to 30 days for amphibians (Ficetola et al, 2008;Goldberg et al, 2011), 0.9 to 7 days for marine mammals (Foote et al, 2012), 21 days for mudsnails (Goldberg, Sepulveda, Ray, Baumgardt, & Waits, 2013), and 14 days for reptiles (Piaggio et al, 2013). In addition to density, size and life history features of the target taxa, eDNA persistence can be influenced by other biotic factors such as bacterial and fungal concentrations (Dejean et al, 2011).…”

Discovering hidden biodiversity: the use of complementary monitoring of fish diet based on DNA barcoding in freshwater ecosystems

“…2008; Goldberg et al. 2011) has been successful. An alarm system for control of biological invasion of Asian carp has been developed by the U.S. Army Corps of Engineers using water eDNA (Darling and Mahon 2011).…”