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From the Louisiana shore, the Gulf of Mexico may seem like a murky sacrifice to our thirst for oil and gas, but that's not the case when you get far offshore. The waters turn crystal clear and in places, marine life thrives along the seafloor.

Last month, scientists set out on an expedition to find out how those ecosystems are doing after the BP oil spill.

NPR's Richard Harris joined them.

RICHARD HARRIS: If you want to know what's going on at the bottom of the Gulf of Mexico, you've got to go down there and look. And that's just what biologists have been doing with the help of a little white submarine named Alvin.

(Soundbite of submarine)

HARRIS: This three-person sub dived almost every day from the stern of the research vessel Atlantis, gradually edging toward ground zero, the BP well head.

(Soundbite of submarine)

Unidentified Woman: Marcus, could you give him a hand getting this one out?

HARRIS: As the Alvin comes back on board, scientists huddle around its collection basket to see the day's haul. This one has plexiglass cylinders filled with mud from the bottom, strange red rock samples, and seawater in special pressure vessels.

(Soundbite of lab)

HARRIS: Andreas Teske, from the University of North Carolina at Chapel Hill,´┐Żlooks appreciatively at the day's treasure.

Professor ANDREAS TESKE (Marine Sciences, University of North Carolina at Chapel Hill): It was one of the best dives.

HARRIS: Teske explored a habitat you would never expect to find nearly a mile under the sea: mussel beds, orange and white bacterial carpets that spread across the seafloor, fish and shrimp and sea cucumbers, and all around an underwater lake. Yes, a lake on the seafloor made up of super salty water: brine.

Prof. TESKE: You could see the surface of the brine pool just like the surface of a garden pond, totally clear. And then within the brine pond, some animals that fell in pickled, sand crabs and others. So once they fall in, and they don't manage to climb out quickly, that's it.

HARRIS: Scientists dubbed this spot Dead Crab Lake on behalf of the hapless crabs that stumbled into the brine and pickled themselves in the process.

Expedition leader Samantha Joye is from the University of Georgia. She first learned about this rich and otherworldly habitat about 15 years ago when she took her first deep dive in the Gulf.

Professor SAMANTHA JOYE (University of Georgia): I had never heard of such things. I had never really imagined that they existed. And it was just a pretty spectacular first dive. It's a little lake you could've walked around with your dog, but it was under, you know, 1,600 feet of water.

HARRIS: This spot, about 20 miles from the BP oil well, seemed to be out of harm's way. But Joye says there are more than 1,000 biological hot spots like this in the Gulf of Mexico. And she's here to figure out what the oil spill might do to them. The next day, she and colleague Ian MacDonald from Florida State University emerge from the Alvin talking about an even stranger place - a place where oil and gas seeps naturally from the seabed.

Professor IAN MACDONALD (Florida State University): So, what a cool site - Oil Mountain.

HARRIS: MacDonald and Samantha Joye saw worms that actually live in ice made from frozen methane and water. The worms didn't seem to mind being slathered with crude oil from the natural seep.

Prof. JOYE: We actually got footage of a crab chomping on what we think are ice worms. It was just mind-boggling. I've never seen an invertebrate, like, living in crude oil. But these guys were in the crude oil, happy as could be.

Prof. MACDONALD: So here's a site that's been oily like this, you know, seeped in oil, saturated in oil for 20,000 years probably, where the ecology, the organisms, the microbiology is completely adapted to dealing with this oil.

HARRIS: But MacDonald says that seep is putting out maybe a barrel a day -vastly less than what spewed from the BP well. And that raises a question.

Prof. MACDONALD: What happens to the natural ecosystem? How does that respond? How do the organisms cope with that?

HARRIS: To answer that question, the scientists will need to move closer to the wellhead. Joye will get to see for herself on her next dive. And our story continues with that tomorrow.

Richard Harris, NPR News.

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