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ROBERT SIEGEL, host:

From NPR News, this is ALL THINGS CONSIDERED. I'm Robert Siegel.

MICHELE NORRIS, host:

And I'm Michele Norris.

The Chesapeake Bay is the nation's largest estuary. It's also one of the country's most polluted waterways. The bay once teemed with fish, crabs and oysters. Now, every summer, large areas of the Chesapeake turn into dead zones that can't support most marine life.

SIEGEL: This year, the Obama administration announced a new strategy to restore the Chesapeake, that's after 25 years of efforts and billions of federal dollars have failed to do the job.

In two stories - one today and one tomorrow - we're going to hear about the bay's problems. Today, Elizabeth Shogren explores the role of agriculture.

ELIZABETH SHOGREN: For 22 years, Carole Morison raised chickens on Maryland's eastern shore. She quit a year ago, but two huge chicken houses still eclipse her yellow farmhouse.

Ms. CAROLE MORISON: I am warning you.

SHOGREN: She opens the door to one of the houses.

Ms. MORISON: This is a really strong odor of ammonia, and this is after a year of no chickens being in these houses.

SHOGREN: The smell is so strong it's hard to breathe.

Ms. MORISON: You're expelling all of this ammonia into the air. When ammonia comes back down to the ground, it is nitrogen.

SHOGREN: Nitrogen is one of the two main culprits polluting the bay. Ammonia from livestock operations is responsible for six percent of the nitrogen in the bay. But Morison knows her operation polluted in other more direct ways.

Ms. MORISON: Just be careful of the large potholes.

SHOGREN: The hundreds of thousands of chickens she raised each year produced a mountain of manure, which she kept in an open shed the size of a pro basketball court.

Ms. MORISON: I'm looking at a large hole that was left by the heavy equipment they brought in here to scoop up the manure. And in that hole is brown water, which is rainwater mixed with manure. I call it manure tea.

SHOGREN: Morison's chicken houses and manure storage shed were built on such soggy ground that the only way to keep them dry is to surround them with trenches. Most of them are full of water even on a dry day.

Ms. MORISON: This is the ditch right here.

SHOGREN: It's only about 30 feet from Morison's manure shed.

Did you ever see that manure tea in that ditch?

Ms. MORISON: Oh, I've seen it plenty of times.

SHOGREN: And where does this ditch go?

Ms. MORISON: This ditch streams into a small tributary in the back of the property, which runs into the Pocomoke River, which in turn runs to the Chesapeake Bay.

SHOGREN: Morison's farm is on the Delmarva Peninsula, a low-lying stretch of land shared by Delaware, Maryland and Virginia. It separates the bay from the Atlantic Ocean. It has one of the country's biggest concentrations of chicken farms. And many of the 2,000 chicken operations have ditches like Morison's.

Ms. MORISON: And it's no wonder we're failing miserably at cleaning up the bay.

SHOGREN: Lots of the manure is trucked away and used as fertilizers. Still, Morison says there's no way to avoid polluting, that's part of why she quit.

Ms. MORISON: We really got tired of being part of the problem.

SHOGREN: Poultry farms here and in Virginia's Shenandoah Valley are a major source not just of nitrogen, but also phosphorus. These nutrients rob the bay of oxygen and kill the sea grass needed as nurseries for crabs and other creatures.

(Soundbite of flowing water)

SHOGREN: Across the Chesapeake from Morison's farm, University of Maryland professor, Thomas Miller, studies the bay from his lab on Solomons Island. Hundreds of seagulls take flight as we walk out on a pier outside his office.

Professor THOMAS MILLER (Chesapeake Biological Laboratory, University of Maryland): It's not a bad place to be.

SHOGREN: The scene of the Patuxent River flowing into the bay is gorgeous on this clear fall day. Miller says views like this give people a misimpression of the health of the bay.

Prof. MILLER: Until quite recently, there would have been large sea grass meadows and large oyster reefs in front of this area. And now, if you were to look out there from one of our research vessels, you'd find those almost completely gone. Even though the view on the surface looks unchanged, the view underneath the water would be very different.

SHOGREN: Miller gets a glimpse of what's going on below the bay's surface when he surveys fish. He tows a huge net behind a ship.

Prof. MILLER: In most regions of the Chesapeake Bay, when we pull the net back on board the vessel, we may find thousands of fish.

SHOGREN: But his haul is very different if he drags the net in the long stretch of the bay north of here that has very low oxygen in summer.

Prof. MILLER: You can pull a net through that water and come up absolutely empty. And it is really quite startling to bring a net on board with no fish in it at all.

SHOGREN: That's what's known as the dead zone. Animals and fish simply can't survive in that water and have to leave. Miller blames overfishing for nearly wiping out oysters. But he fingers nitrogen and phosphorus for his empty nets. It's not just local farms that cause the trouble. Much of the pollution comes from manure and chemical fertilizers used at farms far from the bay.

(Soundbite of a mooing cow)

SHOGREN: Four hundred miles from Miller's lab, these cows are mooing away at a dairy in rural Candor, New York. What happens on farms here affects the bay, even though most people here never think of their connection to the Chesapeake. Part of the reason it's been such a challenge to clean up the bay is that its watershed is massive. Pollution from six states and Washington, D.C., drain into it.

Mr. BOB AMAN (Dairy Farmer): Everything that flows from here ends up in the bay, if it flows that far.

SHOGREN: That's dairy farmer Bob Aman.

(Soundbite of flowing water)

SHOGREN: The creek that flows through his property dumps into the Susquehanna River, the bay's biggest tributary. About 500 of his cows live in one huge barn and produce 15,000 gallons of manure a day. A worker shovels manure from the ends of the barn, then a machine takes over.

Mr. AMAN: And the paddles take the manure to the center of the barn, then it drops through slats, and it goes to a pit where we pump it into the digester.

SHOGREN: That's a contraption that turns manure into gas, which Aman uses to make electricity. Aman has spent a lot of time and money trying to keep manure out of his stream. But many of his neighbors still spread manure on fields -even when they're covered with snow and can't absorb the nitrogen and phosphorus.

The federal government estimates that about 40 percent of the nitrogen and 45 percent of the phosphorus in the bay comes from agriculture. Aman says at least farmers know they're part of the problem, and they do what they can afford to do to avoid polluting.

Mr. AMAN: We as farmers are getting a little tired of everybody pointing their finger at us. I think we're a little bit of a scapegoat. There's as much pollution coming from lawns and detergents.

SHOGREN: In fact, cities, towns and industrial areas send even more nitrogen and phosphorus to the bay than agriculture does. We'll have more on that tomorrow.

Elizabeth Shogren, NPR News.

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