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About a third of the material that gushed into the Gulf of Mexico from the BP blowout wasn't oil. It was natural gas. And scientists have been trying to figure out what happened to all of that carbon-rich gas, and whether it's disrupted the Gulf's ecosystems.

Well, a new study concludes that it's gone - quickly eaten by bacteria.

But as NPR's Richard Harris reports, that conclusion is stirring a bit of controversy.

RICHARD HARRIS: While most of the world was focusing on the frightening oil slick spreading across the Gulf of Mexico, John Kessler from Texas A&M University was wondering what was happening to all the methane gas that bubbled out of BP's Macondo well. It had the potential, at least, to deplete oxygen that fish and shrimp need.

He was on an early scientific expedition to the Gulf.

Dr. JOHN KESSLER (Assistant Professor of Oceanography, Texas A&M): We were first out in the middle of June, and it was at that time where we were noticing very large concentrations of methane in the deep ocean.

HARRIS: The methane didn't seem to be bubbling to the surface, and undersea bacteria were eating it - but very slowly.

Dr. KESSLER: This wasn't terribly surprising because most of the places we normally study are fairly active natural methane seeps around the planet. And even in those natural environments, the rate at which methane decomposes is fairly slow as well.

HARRIS: So Kessler, along with many other marine scientists, figured that methane from the blowout would persist in the deep ocean for many years. He and some colleagues returned to the Gulf in August, expecting to find plenty of methane still out there.

Dr. KESSLER: What we were met with was an entirely different story.

HARRIS: They took more than 200 water samples and found, essentially, no excess methane. Two things could have happened to it.

Dr. KESSLER: Did methane itself just dilute out, or was it consumed by some of the indigenous bacteria that are in the water?

HARRIS: There are bacteria in the Gulf of Mexico known for their ability to gobble up methane. And sure enough, Kessler and his colleagues found those bacteria in abundance. They also looked at oxygen levels because these bacteria consume oxygen when they eat methane. And Kessler and his colleagues report in Science magazine that oxygen was also depleted in the deepwater layer where they had originally found the methane.

Dr. KESSLER: All of that oxygen loss could only be explained by a complete consumption of the methane.

HARRIS: So Kessler's paper concludes that in just 120 days, bacteria basically gobbled up all of this methane, and turned it into carbon dioxide and organic carbon.

Ian MacDonald at Florida State University, for one, is not so sure.

Dr. IAN MacDONALD (Professor of Oceanography, Florida State University): I'm not totally convinced by the data that they present here.

HARRIS: For one thing, it seems odd that the methane-eating bacteria usually do their work quite slowly around natural methane seeps, but became super speedy around the oil well. And MacDonald says nobody really managed to trace the deep undersea currents, which could have carried away the methane.

Dr. MacDONALD: It's possible that there was enough flow, enough current movement - water movement through this region, that what we're looking at is not so much the disappearance of gas due to consumption by the microbes, but simply by mixing.

HARRIS: Further tests of the Gulf water can help resolve this puzzle. If bacteria did, indeed, eat up the oil, they should have left behind telltale traces of ancient carbon from these fossil fuels. What we're witnessing here, MacDonald says, is science in progress, so no single study is likely to provide a definitive answer.

Dr. MacDONALD: And the exciting thing about the science that's happening here is that there are alternative ideas, and there are plausible alternative ideas being put forward by very respectable and capable people. And it's - I think it's just going to teach us a lot about this giant experiment, and how the ocean works.

HARRIS: MacDonald and Kessler both agree that the methane findings are reassuring. Whatever happened to the methane, it does not seem to have caused obvious damage to the economically valuable ecosystems near the surface, or near the shore, in the Gulf of Mexico.

Richard Harris, NPR News.

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