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One of the biggest changes recently in America's supermarkets is in the dairy aisle, where Greek yogurt keeps shoving aside its rivals. This thick, protein-rich version of yogurt has become very cool. But the traditional straining process that makes it so thick and rich is also very messy. It leaves behind a thin liquid called acid whey. And getting rid of that whey isn't as easy as you might think, as NPR's Dan Charles reports.

DAN CHARLES, BYLINE: Fage Greek yogurt comes from a ultra-modern, robot-equipped factory in Johnstown, New York. It was built in 2008, and it's already doubled in size.

RUSSELL EVANS: We're supplying yogurt for the whole United States from here...

CHARLES: Russell Evans is director of marketing for Fage U.S.A.

EVANS: ...right from this one plant, from the beaches of California all the way to the islands of Maine, everywhere.

CHARLES: Trucks bring more than a million pounds of milk into this factory every day. Evans explains that because Fage uses the traditional straining process to make their yogurt extra thick, it takes four pounds of milk to make one pound of yogurt. But when I ask him if I could see exactly where the rest of the milk goes, the other three pounds, Evans is stumped at first. Waste management is not exactly his department.

It turns out that the watery stuff that's drained out of the yogurt, the whey, gets pumped into one of the tall storage tanks outside the factory.

EVANS: So I believe that that third, steel silo is where the whey is. It's being collected there.

CHARLES: Getting rid of that whey, though, is complicated. Whey comes in different forms. Cheese factories produce lots of whey, too, but that whey is thicker. It has more sugar and protein in it. So big cheese makers filter out that lactose and concentrated protein and sell it to other food companies. It's a good business.

Greek yogurt factories, though, aren't so lucky. Their whey is thinner and more acidic and nobody's figured out a way to make money from it. But if you just poured it into a river, it would be an environmental crime.

George Bevington, an engineer who deals with waste water treatment, says the whey would set off a boom of bacteria in the river, feeding on the sugar.

GEORGE BEVINGTON: And that means there'd be no oxygen left in the river and that means there'd be no fishies left in the river.

CHARLES: Bevington and I are standing outside Johnstown's waste water treatment plant. And in the distance, less than a mile away, we can see the steel storage tanks of the Fage factory. It's so close the company can pipe most of its whey straight over here for treatment. Not every waste water plant can handle whey, but this one can, because it has what's called an anaerobic digester: a huge tank full of special bacteria that feasts on this kind of waste.

BEVINGTON: Anaerobic digesters love sugar, they love milk, they love beer. Anything you can put in a digester that's high-strength waste, bacteria love to eat it.

CHARLES: And these very helpful bacteria convert it into something useful: Biogas, mostly methane.

BEVINGTON: What we do is, we take this biogas, around 240 cubic feet per minute, we split that to two engines, and we're generating power 24/7.

CHARLES: The generators deliver enough power to run this plant. When Superstorm Sandy came through and the electrical grid in New York started to wobble, engineers here simply cut themselves off from the grid and relied entirely on gas from their own digesters.

It's the best solution, so far, to the whey problem, but it's not perfect. It costs Johnstown's taxpayers more to run these generators than it would cost to buy the same amount of power from the local utility. To cover that extra cost, Fage still has to pay to city to take the whey off its hands.

Also, Fage now puts out more whey than the city's digester can actually digest. So Fage has to do the same thing that even bigger Greek yogurt factory not far away, the Chobani factory, does with its waste. The yogurt makers haul that whey back to farmers.

Farmers like Ken Dibbell, who lives outside the town of Norwich, about ten miles from the Chobani factory. Dibbell mixes the whey together with manure from his cows and spreads it on his hay fields as fertilizer. Some other farmers mix it into their cattle feed. Dibbell gets paid $300 every time he takes a 6,000 gallon truckload of the factory's whey.

KEN DIBBELL: It's a cash cow. And anything you can do on the farm to generate cash, safely, you do it.

CHARLES: But there's a limit on how much each farmer can use: any more than that, and the whey would end up polluting nearby streams. And there's so much whey coming out of these fast-growing yogurt factories in upstate New York, Chobani is hauling that waste a couple of hours, in some cases, just to find farmers who can take it - that gets expensive.

So the State of New York, which is anxious to keep this yogurt boom going, has set up a task force with researchers from Cornell University to look for a better alternative. Maybe it's turning more whey into biogas; maybe it's filtering out those valuable sugars and proteins. There are lots of technologies, one of the researchers said, but the economics are tricky.

Dan Charles, NPR News

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