In California's Protected Waters, Counting Fish Without Getting Wet
Diver Dan Abbott unloads his scuba gear on a beach in Monterey, Calif. — his tank, flippers and a waterproof clipboard covered in tally marks. He spent the morning counting fish: pile perch, black perch, blue rockfish and kelp rockfish are among the 150 fish he spotted.
Abbott is diving with a team from Reef Check California, a group of volunteers doing underwater surveys by counting everything in the kelp forest in Monterey Bay.
He's part of an effort to determine whether there are more fish in the waters now than there were eight years ago. That's when this kelp forest was set aside as a marine protected area, where there's little or no fishing allowed, part of a huge experiment to restore marine life.
There are more than a hundred protected areas off California, covering 16 percent of state waters, and the only way to know if they're working is for Abbott and others to keep checking the marine population year after year.
These monitoring efforts are expensive. For a while, the state funded the work — to the tune of some $16 million. That money has already run out in some regions of the coast.
But thanks to advances in genetic testing, scientists now have another way to count marine life, without the costly and time-consuming field work.
A Soup Of Genetic Information
Jesse Port, an environmental genomicist at the Center for Ocean Solutions at Stanford University, studies the environment through DNA testing — the same kind developed for human health.
Port says all he needs is a liter of seawater to know exactly what has been swimming through it. That's because all organisms — whales, fish, seals — shed their DNA and leave cells behind.
"Their skin, their scales, their waste — all of this gets into the water," Port explains.
It's like a soup of genetic information. Port collects the cells and sequences all of the DNA.
"We get 150 million sequence reads and that's a lot of information," he says.
Port 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. One sample costs $1,500.
"This was just not possible five, 10 years ago," Port says. "And sequencing technology is just going to get better, so this will probably get even cheaper."
A Potentially Revolutionary Breakthrough
He first ran DNA tests in a large tank at the Monterey Bay Aquarium — a good test case because he knew exactly what was swimming in there. But he got back results he didn't quite believe.
"Things like turkey. We picked up chicken DNA in these tanks," he says.
Turns out, the poultry was in the feed some of the fish were getting. But it raised some big questions. How do you know the DNA comes from a fish or from something it ate miles away? Or how do you know the DNA didn't float in on a current?
Port is still figuring these things out, but if DNA testing proves out in the ocean, it could be revolutionary.
"You can cover such a larger area by taking water samples rather than having divers do that all themselves," he says.
That could help California's conservation funding go a lot further — and help ensure its marine protected areas really are working.
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Transcript
RENEE MONTAGNE, HOST:
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. Transcript provided by NPR, Copyright NPR.
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