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Redondo Beach
Washington state’s Redondo Beach is one of the urbanized sites where environmental DNA samples were taken. (Credit: Joe Mabel via Flickr / CC BY-SA 3.0)

A novel method for analyzing the DNA left behind in the waters of Puget Sound shows that urban shorelines tend to harbor a wider array of marine life than less developed shorelines.

That outcome came as a surprise to the researchers from the University of Washington, Seattle’s Northwest Fisheries Science Center and Oregon State University. In a study published this week by the journal PeerJ, they reported that bivalves and gastropods – clams and snails – were particularly widespread.

“Clams and other things that live in mud seem to like living near cities, which is really interesting,” lead author Ryan Kelly, a UW assistant professor of marine and environmental affairs, said in a news release.

The analysis was conducted using water sampled from eight sites around Puget Sound in 2014. Four of the sites rated highly on a scale of urbanization, based on how built up the shoreline was. The four others weren’t nearly as developed.

160915-fig1-dna
This chart shows where eight sets of water samples were taken for DNA analysis. The urbanized sites were Big Gulch Creek (BG), Pipers Creek (PC), Sinclair Inlet (SI) and Redondo Beach Cold Creek (RB). Less urbanized sites were Clearwater Casino (CC), Clinton-Whidbey (CW), Manchester (MA) and Shingle Mill Creek (SM). Credit: Kelly et al. / UW via PeerJ

Researchers took the water samples and filtered out the biological cells that were bigger than bacteria. Then they extracted DNA from those cells for sequencing.

Such “environmental DNA” is typically left behind when organisms shed cells and produce waste. Researchers found more than 1,600 different kinds of genetic signatures – including the signatures of fish, porpoises, eagles and humans.

In every case, they found that the urbanized shoreline site showed a wider array of marine animals than the less urbanized site with which it was paired. However, the urban beaches were more homogeneous in terms of the kinds of species living there. The less urbanized sites were more likely to harbor quirkier species.

The study wasn’t designed to determine why different areas have differences in diversity, but the researchers came up with a few possible explanations.

It may be that urban development tends to create offshore habitats that clams and other mud-dwellers like. For example, the outflow of nutrients from urban watersheds may promote a particular kind of marine diversity.

“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,” Kelly said.

In any case, Kelly and his colleagues see environmental DNA analysis, or eDNA, as a valuable tool for assessing marine diversity without having to count the actual animals.

“We can go out, take a sample of water, and the DNA from thousands of species appears,” he said. “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 method isn’t perfect: Some species that were known to exist at the Puget Sound sampling sites didn’t leave a trace in the eDNA analysis. Nevertheless, eDNA is already proving its value.

The U.S. Fish and Wildlife Service is using the technique to track the spread of Asian carp through lakes and rivers in the Midwest. Similar efforts are gearing up to monitor zebra mussels and other invasive species.

In addition to Kelly, the authors of “Genetic Signatures of Ecological Diversity Along an Urbanization Gradient” include James O’Donnell, Natalie Lowell, Andrew Shelton, Jameal Samhouri, Shannon Hennessey, Blake Feist and Gregory Williams.

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