The oil that spewed into the Gulf of Mexico during the Deepwater Horizon disaster three years ago killed off millions of amoeba-like creatures that form the basis of the gulf's aquatic food chain, according to scientists at the University of South Florida.

The die-off of tiny foraminifera stretched through the mile-deep DeSoto Canyon and beyond, following the path of an underwater plume of oil that snaked out from the wellhead, said David Hollander, a chemical oceanographer with USF.

"Everywhere the plume went, the die-off went," Hollander said.

The discovery by USF scientists marks yet another sign that damage from the disaster is still being revealed as its third anniversary looms. Although initially some pundits said the spill wasn't as bad as everyone feared, further scientific research has found that corals in the gulf died. Anglers hauled in fish with tattered fins and strange lesions. And dolphins continue dying.

The full implications of the die-off are yet to be seen. The foraminifera are consumed by clams and other creatures, who then provide food for the next step in the food chain, including the types of fish found with lesions. Because of the size of the spill, the way it was handled and the lack of baseline science in the gulf, there's little previous research to predict long-term effects.

The disaster began with a fiery explosion aboard an offshore drilling rig on April 20, 2010. It held the nation spellbound for months as BP struggled to stop the oil, but the spill has largely faded from national headlines. The oil is still there, though.

Weathered particles of oil from Deepwater Horizon are buried in the sediment in the gulf bottom and could be there for as much as a century.

"These are not going away any time soon," Hollander said.

USF researchers dug up core samples from the gulf bottom in 2010, 2011 and 2012, and they plan to return this year and next to compare what they found. Their examination uncovered the massive die-off, according to researcher Patrick Schwing. They also noted an absence of microscopic worms that are normally seen in those areas. The researchers could not estimate how many square miles the die-off covered.

In the core samples, they could see that most of the grayish sediment on the bottom built up gradually over centuries, said Isabel Romero, a researcher working with Hollander. But on top they found a large, dark clump of sediment from the time of the 2010 disaster. The amount registered as 300 times the normal amount of oil-based particles found on the bottom.

The oil in the sediment samples definitely came from the 2010 disaster, Hollander said. The substance bears the same chemical signature as Deepwater Horizon oil.

Effects on fish

That's also the chemical signature of the substance that has clogged the livers of red snapper and other fish found with lesions. The fish livers were trying to screen out the impurities but could not cope with the quantities, he said.

"We're seeing lots of connections with fish diseases," Hollander said. "We're seeing compromised immune systems."

The diseased fish began turning up a few months after BP was able to shut off the flow of oil in July 2010. The discovery of fish with lesions faded out the following year, said Steve Murawski, a USF fisheries biologist who has overseen a project that examined 7,000 fish caught in the gulf.

Scientists are now looking for more subtle effects in red snapper, such as reductions in the number of large fish and a decline in the total population, Murawski said. They are looking for any genetic mutations, too, he said.

"If they get sick, that's one thing," Murawski said. "But if it changed their genes so that they're less resistant to disease or have lower weights, that's a big deal. That would be a real game-changer if true."

BP spokesman Craig Savage said, "No company has done more, faster to respond to an industrial accident than BP did in response to the Deepwater Horizon accident in 2010. As a result of our $14 billion cleanup effort, BP-funded early restoration projects as well as natural recovery processes, the gulf is returning to its baseline condition — the condition it would be in if the accident had not occurred."

But USF oceanographers and biologists are finding lingering effects of Deepwater Horizon. That's no surprise to the biologists, who recall that eight years passed after the Exxon Valdez oil spill before the herring population crashed from immune system problems.

"I spent a lot of time in the marshes in Louisiana," Murawski said. "You can still find a lot of oil in there."

Why soiled sediment?

One intriguing question is why some oil settled into the sediment on the bottom of the gulf a mile deep and stayed there. Hollander says that may be the work of two factors. One is the dispersant called Corexit that BP used to try to spread the oil out so it wouldn't wash ashore. The other is the Mississippi River.

BP sprayed Corexit directly at the wellhead spewing oil from the bottom of the gulf, even though no one had ever tried spraying it below the water's surface before. BP also used more of the dispersant than had been used in any previous oil spill, 1.8 million gallons, to try to break up the oil.

Meanwhile, the spill coincided with the typical spring flood of the mighty Mississippi, which sent millions of gallons of freshwater cascading in to push the oil away from the coast.

The Corexit broke the oil droplets down into smaller drops, creating the plume, Hollander said. Then the smaller oil droplets bonded with clay and other materials carried into the gulf by the Mississippi, sinking into the sediment where they killed the foraminifera.

In some areas where the die-off occurred, he said, the tiny creatures came back, but in others the bottom remains bare. Meanwhile, some of the burrowing kind are digging down into the contaminated sediment — and stirring it up all over again.

Craig Pittman can be reached at craig@tampabay.com.