In California's Protected Waters, Counting Fish Without Getting Wet Using divers to monitor whether life is returning to the 100 or so marine protected areas is pricey. Now, advances in DNA sequencing mean scientists just need a seawater sample to do a marine census.
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In California's Protected Waters, Counting Fish Without Getting Wet

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In California's Protected Waters, Counting Fish Without Getting Wet

In California's Protected Waters, Counting Fish Without Getting Wet

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  • <iframe src="" width="100%" height="290" frameborder="0" scrolling="no" title="NPR embedded audio player">
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Advances in genetic testing have revolutionized everything from our health care to crime investigations. Now genetic testing might even help protect marine life in the waters off California. From member station KQED, Lauren Sommer reports.

LAUREN SOMMER, BYLINE: Diver Dan Abbott is unloading his scuba gear on a beach in Monterey, his tank, flippers and a waterproof clipboard. It's covered in tally marks because he just spent the morning counting fish.

DAN ABBOTT: One fish, two fish, red fish, blue fish, yeah, kind of (laughter).

SOMMER: Or, in all seriousness...

ABBOTT: Pile perch, black perch, blue rockfish, kelp rockfish.

SOMMER: One-hundred-fifty fish in all. Abbott's diving with a team from Reef Check California, a group of volunteers out here doing underwater surveys, counting everything in the kelp forest.

ABBOTT: It gets a little challenging because you're floating. You're swimming. You're looking. You're counting.

SOMMER: He's trying to answer a question. Are there more fish here now than there were eight years ago? That's when this kelp forest became part of a huge experiment to restore marine life. It was set aside as a marine protected area where there's little or no fishing allowed.

ABBOTT: You know, to give the fish and the invertebrates a chance to come back.

SOMMER: There are more than 100 protected areas off California, covering 16 percent of state waters. And the only way to know if they're working, if marine life is coming back, is for Abbott and others to keep checking year after year. That's expensive, and, for a while, the state was funding the work.

ABBOTT: But the monitoring efforts that have gone on have been cut back in the recent years.

SOMMER: What would really help is a way to count marine life without all the fieldwork. That might actually be possible.

JESSE PORT: Let me just show you - I can show you - our bottles are over here.

SOMMER: Jesse Port is showing me around his lab in a basement on the Stanford University campus, where he works.

PORT: Maybe I'm an environmental genomicist.

SOMMER: If Port sounds hesitant, it's because his field is brand new. He studies the environment through DNA testing, the same kind developed for human health.

PORT: These are, like, Nalgene one-liter bottles.

SOMMER: Port fills these bottles with seawater, which he says is all he needs to know exactly what's been swimming through it.

PORT: So all organisms shed their DNA.

SOMMER: Whales, fish, seals, they all leave cells behind.

PORT: Their skin, their scales, their waste, all of this gets into the water.

SOMMER: It's like a soup of genetic information. Port collects the cells and sequences the DNA, all the DNA.

PORT: And we get 150 million sequence rates. And that's a lot of information.

SOMMER: He ends up with a spreadsheet that tells him what DNA is there - humpback whale, check, rockfish, check. Port can do this because DNA sequencing has gotten so much cheaper.

PORT: This was just not possible five, 10 years ago.

SOMMER: He first ran DNA tests in a large tank at the Monterey Bay Aquarium, a good test case because he knew exactly what's swimming in there. But he got back results he didn't quite believe.

PORT: Things like turkey. We picked up chicken DNA in these tanks.

SOMMER: Turns out the poultry was in the feed some of the fish were getting. But it raised some big questions, like how do you know if a DNA comes from a fish or from something it ate miles away? Port is still figuring it out. But if DNA testing proves out in the ocean, it could be revolutionary.

PORT: You can cover such a larger area by taking water samples rather than having divers do that all themselves.

SOMMER: Something that could help California's conservation funding go a lot farther, ensuring its marine protected areas really are working. For NPR News, I'm Lauren Sommer in San Francisco.

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