DNA in the water spares team critter-counting

Scientists have used DNA from the waters of Puget Sound to characterize the amount of animal life along highly urbanized shorelines and in more remote areas with fewer humans.

As animals, plants, and microbes shed cells and produce waste, they drop traces of their DNA everywhere—in the air, soil, and water. Researchers can now capture the cells of animals, sequence their DNA, and identify which species were present at a point in time. Think of it as genetic fingerprints that leave a trace of past activity.

“We can go out, take a sample of water, and the DNA from thousands of species appears.”

The study, published in the journal PeerJ, uses genetic markers to understand the impact urbanization has on the environment—specifically, whether animal diversity flourishes or suffers.

“It is now possible to use genetic traces in water samples to look at the effects of human activities on ecosystems,” says lead author Ryan Kelly, an assistant professor of marine and environmental affairs at the University of Washington. “It’s totally remarkable to me that what appears to be plain water can tell you all of this information about what animals are present.”

Using environmental DNA—or eDNA, for short—the researchers found that urban Puget Sound shorelines support a denser array of animals than in remote areas. In particular, clams and other mud-dwellers congregate more densely along urban beaches—a surprising finding, Kelly says.

Get the ocean’s ‘fingerprint’ in a water sample

“Clams and other things that live in mud seem to like living near cities, which is really interesting,” Kelly says. “It suggests that maybe humans are subsidizing mudflats, or it may just as well be the converse—maybe humans tend to live in really protected areas that are the same environment clams happen to like.”

While urban beaches in Puget Sound had more abundant fauna, these areas were also more homogenous in the kinds of species that lived there, the researchers found, suggesting a tradeoff between different kinds of diversity between more- and less-urban areas.

Genetic tools allow researchers to paint a representative mosaic of animal life in particular areas without having to physically count critters. In conventional ways of measuring environmental impacts, scientists choose a select number of species and count how many they see before and after development. Or they might survey a small section of shoreline and try to document everything they find.

These methods are inherently time-consuming and probably don’t fully capture what is present, Kelly explains.

“We can go out, take a sample of water, and the DNA from thousands of species appears,” Kelly says. “This way, we don’t have to decide if we are going to count snails or orcas when we look at environmental impacts. Instead, we can just look at what’s there.”

The researchers collected liters of water from urbanized and remote beaches around Puget Sound, then filtered out cells larger than bacteria. They then extracted DNA from these cells, using a molecular tool to detect animal genes.

After sequencing the DNA, they could identify specific animals present where the water was collected. They detected more than 1,600 unique genetic signatures—many representing different species—across Puget Sound, including porpoises, salmon, starfish, barnacles, eagles, and humans.

Meet the unfamiliar fish of Salish Sea

Kelly and his collaborators have spent years testing and refining the process of obtaining eDNA in water. They first worked in the Monterey Bay Aquarium, a controlled setting where they could make sure their DNA sampling was actually detecting the creatures living in the water. In subsequent work, they found that an animal’s DNA tends to stay within a few hundred feet of where it was initially deposited; it remains in the water for one to two days.

The methods described in this study could be used to evaluate the effects of humans and development in other urban waterways, such as Chesapeake Bay or the Hudson River. Scientists in the Midwest have started using eDNA as a surveillance tool to monitor lakes for invasive Asian carp.

As genetic traces become more reliable, they could take the place of expensive, time-intensive environmental impact statements or environmental monitoring, the researchers say.

“I’m excited because I think if you can make it easier for people to do these sorts of broad scale surveys, they will do it. It’s a much more powerful method,” Kelly says.

Additional coauthors are from the University of Washington, Oregon State University; and the National Oceanic and Atmospheric Administration’s Northwest Fisheries Science Center. The David and Lucile Packard Foundation supported the work.

Source: University of Washington