How eDNA will change the way we see the ocean

 

A boat of scientists with the U.S. Fish and Wildlife Service skims across the Illinois River. As the boat passes, hundreds of silver carp rocket out of the river, like a barrage of anti-aircraft fire. This is the densest population of silver carp on Earth. Kelly Baerwaldt, Asian carp and eDNA coordinator for the Fish and Wildlife Service’s Midwest Region, is aboard. Although the sudden shower of fish can be alarming, Baerwaldt stays calm. She’s seen it many times.

Silver carp, indigenous to Southeast Asia, were introduced to fish farms in Arkansas in the 1970s to filter pond water. Floods enabled some carp to escape, and the species quickly spread across the United States. With the ability to consume 40 to 50 percent of their bodyweight in a given day, the Asian carp easily outcompeted native fish species for food and space, destroying ecosystems along the way.

“In one year, 1999, it was the perfect storm,” Baerwaldt said. “You just saw exponential growth. God, they were everywhere. And we were like, ‘What the heck are these things? Where did they come from?’ It’s been insane.”

Now, this invasive species is knocking on the door of the Great Lakes. Baerwaldt and her team collect water samples at points throughout the Illinois river. These samples will be sent back to the lab to analyze the environmental DNA, or eDNA, in the water. It will help biologists determine how close the invasive fish are to muscling their way into the largest group of freshwater lakes on the planet.

Traditionally, if researchers wanted to verify the presence of silver carp, they had to go out and spot one or catch one. With eDNA, scientists can leave the snorkels and fishing gear at home. As fish or other animals swim through a stretch of water, they leave behind waste (i.e. poop) and cellular tissue containing DNA. This DNA is like a short-lived fingerprint that allows scientists to identify individual organisms that have recently passed through the area. After a few days, the DNA degrades and the fingerprint disappears. The presence or absence of the Asian carp, in this case, can be detected with a water sample about the size of a Starbucks Trenta latte.

The FWS spends $30 million a year to keep Asian carp out of Lake Michigan (and the rest of the Great Lakes). The only waterway standing between the lake and the Illinois River is the Chicago Sanitary and Ship Canal. An electric barrier has been installed to prevent the carp from passing through. Raw sewage and antifreeze spill in from nearby wastewater reclamation facilities. Beer bottles, condoms, tampons and other debris from Chicago’s streets collect at the edge of the canal and flow in after a heavy rain, creating an ecosystem in which the invasive carp flourish.

“Chicago Sanitary and Ship Canal is the sewage pipeline for Chicago,” Baerwaldt said. “It’s the grossest place to live on Earth and the Asian carp love it.”

In one water sample, Baerwaldt is able to test for the presence or absence of a few species. The current process is called First Generation Testing and works well if she is looking for specific species determined in advance. The next version of eDNA testing, however, will be able to identify every species that recently passed through the area in the water sample.

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”This is where it all happens,” said Hilary Starks, a lab technician in the Boehm Lab at Stanford University. In the Boehm lab, researchers are developing Next Generation Sequencing for eDNA in the ocean. It is one of many underground labs beneath the engineering quad at Stanford, packed into a space about the size of a football field.

(Editor’s Note: Peninsula Press is a project of the Stanford Journalism Program.)

Shelves crammed with beakers, test tubes, chemical solutions and complicated apparatus separate each lab like rows in a library. Here, Starks analyzes the water samples for the DNA of marine vertebrates using a technique called a Polymerase Chain Reaction (PCR). Because DNA is very small, it must be amplified to be detected. This is the primary goal of PCR, which rapidly copies the vertebrate DNA millions of times. A powerful computer program compares the DNA in the sample to a known database of DNA sequences. Then, the computer spits out a list of all the species found in the sample.

“Using DNA has been around for a long time,” said Eily Andruszkiewicz, a Ph.D. student in the Boehm lab. “It’s not a new technology, but the way that it’s being used right now is new. And it’s kind of exploding.”

In some cases, verifying the existence of endangered species can be counterproductive, because scientists sometimes accidentally kill animals they’re trying to count. “Genetic sampling is way less invasive, way less destructive, and much more cost effective,” Baerwaldt said.

For example, scientists often collect data on freshwater fish biodiversity by sending an electrical jolt into a stream or creek. The shock is intended to stun the fish—so they float to the surface and can be identified—but not kill them. But some inevitably die.

Paying trained scientists to snorkel or scuba dive and manually record fish populations is also costly, and often inaccurate. “If you can get the same information, or potentially more information, just by taking a water sample, that’s very attractive,” Andruszkiewicz said.

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A technology as promising as eDNA doesn’t come without limitations. For instance, observers in the field have an advantage when it comes to estimating a species’ population. An eDNA sample can reveal that sharks and tuna were present in a given area, but it can’t tell you how many swam past.

“One major thing is quantification,” said Jesse Port, a former postdoctoral fellow at the Center for Ocean Solutions at Stanford University. “We’re a long way from there.”

Other big questions that need to be addressed include sequencing errors, PCR bias (it is possible that the PCR process amplifies the DNA of some species better than others) and data interpretation. With eDNA sequencing, there isn’t a way to know exactly where your DNA came from or how long it’s been there. Maybe a sample of DNA drifted a great distance, or came from a dead animal. Sunlight, depth, pH levels and temperature all degrade eDNA in the ocean, but it is unknown which variable degrades it the most or how much the degradation varies from location to location.

“We’re still struggling to identify false positives and false negatives,” Port said. “There’s still a lot that could be better.”

Another issue of managing ecosystems is what to do after you are armed with the knowledge that eDNA provides.

“We can go out and sample all day long but what do you do when you find it?” asked Baerwaldt. “What are you going to do when you get a positive? What are you going to do when you get a negative?”

In one of Andruszkiewicz’s studies, researchers sequenced DNA from the stomachs of twelve cookiecutter sharks from Hawaii. They compared what the sharks were eating to the kinds of species they found via eDNA in the area. It turned out that the eDNA samples were a good indicator of recent meals, so they could assume that the sharks had eaten in the general area.

“It was both cool and gross,” Andruszkiewicz said. “We saw bones and chunks of tissues. One chunk looked like a piece of ahi tuna.”

Such studies are paving a path for understanding and interpreting eDNA. Scientists can’t put eDNA to use unless they trust that it works in the first place.

“It’s awesome to be getting [into the research] at a time when it’s starting,” Andruszkiewicz said. “But it’s frustrating because there’s not a lot of literature. The technology is there, and we can be getting a lot of information, but the question is how we interpret it. What does it really mean?”

For example, in a 2015 study by Port and colleagues, researchers compared the traditional method of visual surveying techniques to eDNA tests in a kelp forest ecosystem. They enlisted divers to survey the kelp forest for fish, and then sampled the water for vertebrate species. The eDNA samples not only detected all of the species that the divers recorded, but also revealed “cryptic species known to occupy the habitats but overlooked by visual methods.” The study was published in the Journal of Molecular Ecology.

Environmental DNA may make the lives of scientists easier or less costly or more efficient, and the implications for policy and environmental management could be significant. But it will also change the scientists. To Port, eDNA has obvious advantages and some less obvious drawbacks. On the downside, it means he does not get to spend as much time being in the place that inspired his interest in marine conservation in the first place: the ocean.

“I think going out and observing fish is not replaceable by any means, but the geographic scope of eDNA is greater and more effective,” Port said. “It’s not something I’d rather be doing, but it’s practical.”

New technologies often involve tradeoffs, and eDNA is no exception. With a transition to genetics as a method of biological monitoring, scientists like Port may end up spending less time outdoors and more time in the lab. They might get to know the ocean better, but they might sacrifice part of themselves in the process.

(Homepage photo courtesy of U.S. Fish and Wildlife Service/NCTC Image Library.)