On the Gulf of Mexico (CNN) -- Ten miles off the coast of Louisiana, where the air tastes like gasoline and the ocean looks like brownie batter, Louisiana State University professor Ed Overton leans out of a fishing boat and dunks a small jar beneath the surface of the oil-covered water.

"God, what a mess," he says under his breath, scooping up a canister of the oil that's been spilled into the Gulf of Mexico.

Even though Overton has been studying oil spills for 30 years, he's not sure what he'll find in that sample. That's because, just below the surface, the scope and impact of one of the biggest environmental disasters in the history of the U.S. remains a mystery.

And that terrifies some scientists.

It's been five weeks since an oil rig exploded and sank, rupturing a pipeline 5,000 feet beneath the surface of the Gulf of Mexico. Some clues about what so much oil -- perhaps 22 million gallons of it -- will do to the environment have become obvious:

Dolphins have washed up dead. Endangered sea turtles have been found with oil stuck on their corneas. Lifeless brown pelicans, classified as endangered until recently, have been carried away in plastic bags. Beaches in Grand Isle, Louisiana, are spattered with gobs of sticky crude. And when the moon rises over the coast there, the oil-soaked ocean sparkles like cellophane under a spotlight.

But what's really going on in the depths of the ocean and in the all-important root systems of coastal marshes may prove to have more impact in the long term, and scientists know much less about what's happening in these invisible reaches of the Gulf ecosystem.

As one oceanographer put it, a Chernobyl-sized catastrophe could be brewing under the sea. Or the environment here may be dodging a huge bullet.

"It's kind of like falling out a window," Overton said of the confusion. "We don't know how hard that ground is gonna be until we hit bottom. We don't know if we're going to land in soft shrubs and live -- or if we're going to hit a rock."

If scientists' worst fears are realized, the oil plume in the Gulf could choke off and kill coastal marshes in the productive Mississippi Delta and barrier islands, turning these verdant tufts of life -- which look like hairy putting greens floating out on the water -- into open ocean. That would snap the region's marine food chain, exposing and starving all kinds of organisms.

Overton said the impacts of such an occurrence would last for a century.

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Equally frightening, the oil also could spawn a massive oxygen-free "dead zone" deep in the Gulf's waters, which would suffocate all marine life on the ocean floor. Samantha Joye, an oceanographer at the University of Georgia, said that if that happens, the dead zone could change marine chemistry in the Gulf of Mexico forever.

"I think it's sort of out of sight, out of mind," she said of the deep-water impacts.

Whether either of those scenarios comes to pass depends on what's taking place beneath the surface of the water.

Scientists now are scrambling to understand what's going on.

Joye recently embarked on a two-week mission to take water samples at the bottom of the ocean.

Researchers know almost nothing about what the oil and chemical dispersants used to try to break up the oil will have on life below the Gulf's greasy surface, Joye said on her boat in Gulfport, Mississippi, just before heading out toward the epicenter of the spill.

"I don't think we know what's going on yet, and it's a month into this thing," she said.

Bacteria eat oil and in the process also chew oxygen out of the ocean. There's so much oil in the water, the bacteria may deplete oxygen reserves until deep-water fish like grouper and snapper and "benthic" communities of sea tubes and oysters suffocate, she said.

Joye will be dropping a huge testing kit -- it's as tall as a person and looks like a stick of dynamite -- several hundred feet into the oil plume to see what's happening. Initial tests show that the bacteria are depleting oxygen levels, she said.

And if the ecosystem at the bottom of the ocean goes, commercially important fish and crustaceans on the surface probably will feel the effects, too, she said.

"It's hard for me to imagine anything worse, honestly," she said of the Gulf oil spill. "It's going to dramatically alter the system."

The roots of the Gulf coast's marshes, also hidden from view, are another focus for scientists. Much public attention has been paid to the migratory birds that nest on the marshes and to the shrimp and fish that use their tangled roots as a nursery, hiding their vulnerable young from bigger fish that swim in open waters.

But the marsh grasses themselves and the less-sexy microorganisms that are the basis for the marsh food chain are easily suffocated and killed if exposed to oil, said Roger Helm, a marine ecologist and chief of the environmental quality department at the U.S. Fish and Wildlife Service. Meanwhile, these unseen "little guys" -- the plankton, diatoms and the like -- "are the basis for everything that's going on out there," he said.

"How this is going to affect the food web long-term, it's a great toxicological experiment," he said.

There are several reasons for the widespread scientific confusion.

Perhaps the best is that nothing like the Gulf oil spill has ever happened before.

Many have compared it to the 1989 disaster in which the Exxon Valdez tanker spilled oil off the coast of Alaska. About 260,000 barrels -- a smaller amount than what's gone into the Gulf -- were released into the environment in that case, and it happened rather quickly. The Gulf spill has dragged on over weeks and hasn't stopped.

A better comparison, some scientists say, is the IXTOC I oil well disaster in Mexico in 1979. But, in that case, little research was done to understand the spill's impact on the Gulf of Mexico, Overton said. So there is no real-world scientific precedent that could be used to understand what's happening now.

BP, the company that was leasing the offshore oil rig that exploded and sank April 20, is handling the environmental cleanup. It's doing so in a way that adds further question marks to the environmental situation.

BP has released more than 28,000 gallons of chemicals on the ocean, according to the U.S. Environmental Protection Agency, in hopes these "dispersants" will break up the oil and minimize its impact on the environment. Such a huge amount of dispersant has never been released deep into the ocean before, according to the EPA, and some independent researchers and the EPA have questioned whether those chemicals may be making matters worse.

The EPA's chief, Lisa Jackson, recently told National Public Radio's "All Things Considered" that the agency is doing "science on the fly" to try to understand what's happening.

Other efforts to mitigate the environmental disaster are equally complicated.

Workers have put plastic booms, which look like elongated strings of childhood floaties, around select barrier islands in hopes of keeping the oil off brown pelican nesting grounds and sensitive marshes. On a recent National Wildlife Federation tour of Barataria Bay, off the Louisiana coast, at least one boom was broken, and another was caked in oil.

The scope of the contamination is daunting. More than 100 miles of Louisiana coast have been hit by the oil, according to CNN reports.

Cleaning up that huge mess along the coast -- which continues to grow -- may prove to be a near-impossible task, said Maura Wood, a senior manager for the National Wildlife Federation's coastal restoration program. Each clean-up option comes with drawbacks, she said, but she remains hopeful that scientists will be able to figure out a way to tackle the problem.

Other scientists are upset that more research wasn't done in advance to understand the environmental impacts of a deep-water spill like this one before it happened.

"It just irritates the piss out of me that we were not prepared for a situation like this and didn't have studies on these issues," said Overton, the LSU professor, adding that he and other scientists "should have raised more hell" about the lack of information about oil-spill response methods and about the marshes themselves.

He said the government should "siphon" a small amount of oil company revenues and put the money into more research about what happens to the environment after a major oil spill.

As Overton rode a fishing boat back to the Louisiana coast on a recent rainy morning, chocolate water spewing from its wake, he said there may be a faint silver lining in an otherwise dire situation.

Perhaps scientists will learn from this oil spill, he said. And maybe they'll learn enough that they can do better next time.