Problem: You’re a field biologist trying to assess the population of a secretive , imperiled aquatic species—let’s say a salamander—but you can’t find the little devil, so how can you count it?
Solution: Don’t try to eyeball the critters. Collect their DNA from cells they shed into the water.
This ingenious method, developed over recent years, has taken another major step forward with the publication of a paper from University of Idaho researchers in the peer-reviewed PLoS One.
Studying Idaho giant salamanders (Dicamptodon aterrimus) and Rocky Mountain tailed frogs (Ascaphus montanus), the scientists confirmed that environmental DNA (eDNA), which is found in species’ habitats, can detect rare vertebrates even in fast-moving streams, where their shed cells may travel quickly from their source.
The group was led by wildlife resources professor Lisette Waits at the University of Idaho in Moscow, working with postdoctoral associate Caren Goldberg. The paper’s co-authors are David Pilliod and Robert Arkle of the U.G. Geological Survey’s Forest and Rangeland Ecosystem Science Center in Boise.
“The use of eDNA could revolutionize surveys for rare and invasive stream species,” the paper asserts. “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.”
The implications are important for native aquatic species. In the 20th century, 123 extinctions of freshwater animals were documented, and the most catastrophic effects in North America have been on stream-dwelling amphibians, the researchers note. What’s more, streams are increasingly being invaded by such non-native species as crayfish, aquatic mussels, and gastropods.
The challenges in making an inventory of rare stream species are many. Among them are vegetative cover, unclear water, rapid flows, complex topography, and the tendency of such animals to hide in nooks and crannies, and to use camouflage by adapting their coloration to the environment.
Electrofishing, in which fish are brought to the surface by stunning them with electrical charges, can be successful, but it’s time-consuming, often difficult to achieve in streams, and it can damage not only the target species but others as well.
The eDNA technique is quick, inexpensive, and could be applied selectively to many freshwater stream organisms. A kit that aids the identification of a DNA sample by replicating it six times costs only about $10.
“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,” the paper asserts. “This could be due to decreased metabolism during cold weather or changes in behavior of the target species.”
Of course, the use of DNA as a detection technique isn’t new, but before the University of Idaho study, eDNA technology had not been applied to fast-running streams.
For about a decade, scientists have used DNA from feces, urine, hair, feathers, skin, and eggshells to identify land-based vertebrates. They’ve also used eDNA left by microbes in soil and seawater to determine the presence of disease.
The first use of eDNA to inventory aquatic species was in 2008, by a French team working with a frog in a lab and in wetlands. Early this year, another group showed that eDNA analysis could determine the distribution of invasive Asian carp in American canals and waterways.
The eDNA technique relies on mitochondrial DNA (mDNA), found in the tiny structures within cells that convert energy from food into a form cells can use. Most DNA is contained in the nucleus of cells, but mDNA is more durable when cells are shed into the environment.
Scientists aren’t sure why mitochondria have their own DNA, but one hypothesis is that millions of years ago, tiny organisms engulfed by larger ones survived by converting food to energy for the host. Eventually, the larger organism developed into a cell and the smaller one became the mitochondrion.