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updated 9/21/2010 12:31:39 AM ET 2010-09-21T04:31:39

As BP prepares to finish drilling a relief well this week, the focus in the Gulf of Mexico now turns to two questions: How bad was it? and Will the Gulf ever recover?

The answers to those questions are driving a small army of marine scientists who continue to probe, sample and evaluate the ecological health of a body of water that has been hit hard in the last few decades. Even before the 206 million gallons of oil spilled from the Deepwater Horizon rig, the Gulf faced a barrage of threats.

"It's not a pristine and wild place," said Stan Senner, director of conservation for the Oceans Conservancy. "It's already a stressed ecosystem and we've added another layer to that. These stresses are cumulative."

Senner points to these examples:

- Previous spills. State officials in Louisiana are still tallying the environmental damage from Hurricanes Katrina and Rita in 2005, which led to 540 individual spills and released an estimated 11 million gallons of oil -- bigger than Alaska's Exxon Valdez incident. The assessment was put on hold while agencies scrambled to combat this summer's BP spill.

- Overfishing. The Gulf provides U.S. consumers with one-fifth of their seafood. Top of the food chain species like Atlantic bluefin tuna, sperm whales, sharks and five species of sea turtles all make the Gulf their home. All have been decimated by decades of overharvesting or loss of their food supply.

- Wetlands loss. Coastal wetlands are nurseries for juvenile fish, shrimp and other marine life. But the supply of Mississippi River sediment and sand that keeps them healthy has been dammed and diverted. President Obama and local officials were working on a restoration plan even before the BP spill.

- The Dead Zone. Pesticides and fertilizers from Midwestern farmers flow down the Mississippi and create a low-oxygen "dead-zone" each year toxic to marine life. Scientists say it's much bigger this year, but disagree over whether the spill was the cause.

That's the bad news. The good news is that scientists report marsh grasses are returning and that hundreds rather than thousands of birds were likely killed by the oil. The government's formal assessment of damage won't be ready for some time.

Ian MacDonald is an oceanographer at Florida State University who has been studying the Gulf's undersea ecosystem for the past quarter-century. He calls the spill an "unplanned experiment" whose results won't be known for years. MacDonald says that recent pronouncements by federal officials that the oil had largely disappeared or was naturally broken down by natural forces in the Gulf have proven incorrect. In fact, researchers from the University of Georgia have just discovered oil-soaked sediments covering a wide swath of seafloor near the BP rig.

"The responsible authorities say the problem is gone and then they discover it didn't go away," MacDonald told Discovery News. "But in every case of previous spills, we do see a (environmental) change and it has continued for years. This is a pattern that is repeating itself."

Experts like MacDonald worry about "sublethal effects" on wildlife such as bottle-nosed dolphins that don't die from oil exposure right away, but don't reproduce at the same levels next year; or die-offs of tiny plankton that provide the food for so many larger animals.

The Ocean Conservancy's Senner has seen this ecological drama play out before, when he was Alaska's restoration program manager following the Exxon Valdez spill. He coordinated the post-spill science program for the state and federal trustees that administered the $900 million civil settlement between the governments and Exxon. He saw many animal species that were knocked down by the Exxon oil and failed to rebound.

Based on his experience, he said it will take scientists at least three years to understand the ecological damage from the Gulf spill, and that it will last anywhere from 10 to 20 years.

"The Gulf of Mexico is not dead," said Senner, who has visited the Gulf region several times. "There will be lots of life there, but the ecosystems do change. What comes next may be a different mix of things, some of the more sensitive species may disappear. That would be a tragedy."

© 2012 Discovery Channel

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