eDNA is ​Fostering a New ​Kind of Fish ​Biology

Quick and inexpensive DNA sampling of a river  or lake can now divulge what fish or other animals live there. This rapidly growing environmental DNA, or eDNA, technology is proving to be a game-changing conservation tool.

By Jim Robbins

A U.S. Forest Service technician heads out to the Blackfoot River in western Montana and pumps water through a small filter, five liters every time she stops. In a single day, she gathers dozens of samples, bringing back to the lab each of the fine mesh filters that the river water passed through.

U.S. Forest Service biologist Michael Schwartz gathers water to be sampled for eDNA  from Rattlesnake Creek in Montana. KELLIE CARIM/U.S. FOREST SERVICE

The filters contain DNA for species — whether brook trout, stone flies, wood ducks, or river otters — that have swum in that stream in the last day or two, up to a kilometer above the sample site. Every insect, fish, or animal continually sloughs off bits of its DNA — in its feces or from its skin — and just a single cell of the invisible, free-floating genetic material can tell researchers which species are present in a river or other water body.

Environmental DNA, or eDNA, is at the center of a brand new kind of fish and wildlife biology, and it is such a powerful tool that it’s transforming the field. eDNA was first used to detect invasive bullfrogs in France a decade ago. It was used in North America for the first time in 2009 and 2010 to detect invasive Asian carp in and around the Great Lakes. Since then, its use has grown exponentially, primarily in marine and freshwater environments.

“You can’t manage a species if you don’t know where it is — even 80-pound Asian carp, because you can’t see them underwater,” said Cornell University biologist David Lodge, who participated in the Asian carp study. “So eDNA is particularly powerful in aquatic systems.”

The DNA is so easy and inexpensive to gather and assay — $50 to $150 to test each sample — that the U.S. Forest Service has launched a project to collect DNA from all rivers and streams across the western U.S. to create an Aquatic Environmental DNA Atlas.

“Environmental DNA is turning out to be an amazing tool in allowing us to detect the distribution of species, a distribution that has been invisible to us in the past,” said Michael K. Schwartz, director of the Forest Service’s National Genomics Center for Wildlife and Fish Conservation in Missoula, Montana. “It has remarkable efficiency.”

Experts say use of the technology is in its early stages and that as it evolves it will become even more powerful, providing an even deeper look into the genetics of aquatic ecosystems, including ocean environments.

The next step in the evolution of the technology would be to estimate the abundance of a species in a river or other water body based on the quantity of DNA found in samples. “That is going to continue to be a research frontier,” said Lodge.

Scientists say that eDNA can be used not only to detect the presence of invasive species in a river, lake, or ocean, but also to help reintroduce native species, to study genetic diversity among fish stocks, and to better manage commercial and endangered species.

Researchers have used eDNA testing to assess populations of bull trout, a threatened species in the U.S. Northwest. WADE FREDENBERG/USFWS

Until now, the primary way to conduct distribution studies was to physically see, count, and describe species, a time-consuming process that is expensive and often hit-or-miss. That leaves huge gaps in the knowledge of where species are, which often confounds species management.

One of the best examples of the transformative nature of eDNA is in assessing the distribution of bull trout across its entire range. Bull trout are a threatened species in the U.S. Northwest, and their habitat is declining because of deteriorating water quality and warming water temperatures. Cold water is essential to their spawning.

By knowing where the fish live, managers can direct funding for protecting and restoring riparian habitat. Until recently, though, the only way to find and count bull trout was to do an electro-shocking census. That means a biologist would take equipment to the river to shock fish in the water and count them as they float, stunned, to the surface. That technique is time-consuming, not always permitted, and can survey only a fairly small area with each census.

With eDNA, a single sample can tell which species have been in a river a kilometer upstream from the sample site within the last 24 to 40 hours — that’s how long the DNA lasts in the water. Tests with caged fish have shown that just three fish in a river can give a 100 percent detection rate, and one fish 85 percent.

Read more at: Yale Environment 360

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