28/07/2010 (AOL) - On Day 100, the worst of the BP oil spill appears to be over, although the cleanup remains a huge challenge.

Crude stopped flowing freely from BP's broken well two weeks ago, and the company's new CEO says the well may be permanently capped by next week, raising hopes that the worst environmental disaster in U.S. history has reached the tipping point in the right direction.

"I do believe we're seeing the end of the oil flowing into the gulf," incoming BP CEO Robert Dudley told NPR this week.

Just below the surface, though, pressing problems remain.

The oil no longer seems to be floating in bulk on the water, but that's where it can be most easily collected, and scientists are wondering where millions of gallons of crude might be lurking in the Gulf of Mexico.

"You know it didn't just disappear," Ernst Peebles, a biological oceanographer at the University of South Florida, told The Associated Press.

About 45.7 million gallons of oil have been collected or burned from the water's surface, but more than 107 million gallons gushed from the broken well into the gulf, according to figures cited by the AP. That leaves a lot of oil unaccounted for.

"Less oil on the surface does not mean that there isn't oil beneath the surface, however, or that our beaches and marshes are not still at risk," Jane Lubchenco of the National Oceanic and Atmospheric Administration told reporters Tuesday.

Jeffrey Short, a scientist with Oceana, an environmental advocacy group, told The New York Times that 40 percent of the oil may have evaporated once it reached the surface.

But some researchers fear that the crude has been suspended in underwater clouds that could disrupt the gulf's food chain.

"Now it's time to look at the molecular and microbial food web," Thomas Bianchi, an oceanographer at Texas A&M University, told the AP. "We may be beyond people in white suits and booms."

And many worry that the 1.8 million gallons of chemical dispersant used to help dissolve the oil after the April 20 explosion of the Deepwater Horizon drilling rig may have a devastating impact on marine life, from the largest fish to the smallest organisms.

Bob Shipp, head of the marine sciences department at the University of South Alabama, says the dispersant probably helped push the oil into the water column where it cannot be collected and where it sucks up oxygen needed by marine life.

"We're adamantly opposed to using dispersants," he told The Palm Beach Post this week. "It doesn't destroy the oil. It doesn't remove the oil. It leaves it in the water column, where it can do a lot of damage to all the ecosystem habitats beneath the surface."

Incredibly, as cleanup efforts continued at the site of the Deepwater Horizon rig, news came that a well owned by a different company had begun to leak oil into the gulf.

A tugboat hit a wellhead just off the coast of Bayou St. Denis, La., on Tuesday, sending a stream of natural gas and light oil 100 feet into the air in an accident officials said was relatively minor, especially when compared with BP's gushing well. And thanks to the cleanup boats stationed just miles away, the response to the new leak was swift.

"One of the positive things, I suppose, about having this response going on is we have a significant amount of resources. ... There's skimming equipment close by and booming equipment," Coast Guard Adm. Thad Allen said Tuesday, according to a report in the AFP.

BP, meanwhile, fresh off a change in command, is sounding increasingly confident about its progress in stopping the oil from flowing into the gulf entirely. Doug Suttles, the company's chief operating officer, said BP may be able to begin pumping mud and cement into the broken well with a process known as "static kill" by early next week.

"Ultimately, we've got to make sure this well can never flow again," Suttles said on CBS' "The Early Show" today. "The first step along that path is actually the static kill, which we hope to actually pump at the beginning of next week."

Suttles said the relief wells, which officials say remain the ultimate solution to the leak, are on track to be completed by the middle of next month.

But Allen, who has been leading the federal response to the disaster, said there's far more work to be done. "When you put somewhere between 3 million and 5.2 million barrels of oil into the Gulf of Mexico, I don't think anybody can understate the impact and the gravity of that situation," he told reporters Tuesday.

Suttles called the 100-day mark a "milestone none of us wanted to ever see."

"This has been extraordinarily painful," he said. "There are so many things we have to do to make this thing right."