In the months ahead, as scientists try to decipher the effects of the huge oil spill in the Gulf of Mexico, one piece of the puzzle could come from a Temple University researcher who studies deepwater corals and tube worm communities.

Last summer, Erik Cordes and his team were interested in the particles and small creatures that rain from the ocean's surface onto these communities.

So they lowered two collection devices about 1,500 feet to the seafloor nearby. Over the course of a year, a series of collection cups rotate into place - one every three weeks.

It just so happens that one of the collectors is directly under the center of the oil spill. The other is in clear water 85 miles west.

When the team members retrieve the devices this fall, they will analyze what was collected and when. The data will provide a baseline, and then show whether - and how - things changed after the BP oil-rig explosion last month and the subsequent gusher of oil from the ocean floor.

"We'll have real quantitive data on how much of the oil is ending up on the seafloor," said Cordes, an assistant professor of biology at Temple.

For now, no one really knows how much oil will sink, if any. But the more it stays on the surface, the more it will mix with the water and the more likely it is to drift downward, Cordes said.

Storms could mix the oil more thoroughly, and it could attach to particles, which also increase its sinkability.

Meanwhile, over the last 10 years, scientists have established a number of long-term monitoring stations, said Charles Fisher, a Pennsylvania State University deep-sea biologist who also is part of the team.

"We have excellent detailed maps and photo mosaics of coral communities that are underneath that oil spill right now," he said. Others are clear of the spill.

On a trip back to the sites scheduled for November, "we can look at the changes that are occurring naturally, or changes occurring as a result of the spill in the deep sea," he said.

Work in the gulf began precisely because regulators were worried about the effects of drilling in deeper and deeper waters.

Laws in the United States and abroad forbid the disturbance of coral reefs, and they do not specify whether the reefs in question are the gloriously colored, shallow-water tropical reefs most people think of, or the strange and bewitching deepwater reefs that Cordes and others study.

Louisiana State University oceanographer Bob Carney said governments' first real interest in deepwater reefs occurred in Britain, where BP wanted to drill in a formation called the Darwin Mounds.

The area had deepwater coral communities, and in 1999 British courts decided they should be protected.

On that cue, Carney said, the federal Minerals Management Service, which oversees drilling off the U.S. coast, began looking for similar environments in North America.

"There is incredibly little known about the deep sea," said Jeremy Potter, with the Office of Ocean Exploration in the National Oceanic and Atmospheric Administration. He was responding via e-mail from a NOAA research ship off Hawaii.

"Given that energy companies have developed the technology for extraction of oil and gas from deeper and deeper water, it is important for the agencies responsible for regulation to have a much better understanding of the basic ecology of these areas," he said.

In the last decade, aided by sophisticated acoustical equipment and robotic submersibles, they have begun to unlock more of the secrets of the depth.

Cordes, Fisher, and the rest of the team - including researchers from LSU, the Woods Hole Oceanographic Institution, Florida State University, and more - are funded by grants from the service and NOAA.

One of the missions is to map the communities in the Gulf of Mexico so that drillers can avoid them. The oil reservoirs are large enough that drillers can move a mile away from these ecological rich communities and still tap into the same resources.

Two decades ago, researchers discovered communities of tube worms and mussels that, it turns out, are directly tied to the oil reserves. They have been studying them ever since.

Oil, natural gas, and hydrogen sulfide - the stuff that smells like rotten eggs - naturally seep out of a lot of places on the seafloor. And those sites support a specialized community that thrives on these gases.

Mussels have bacteria inside that eat the natural gas. Tube worms, with no guts or mouths, are basically containers for bacteria that get their energy from the hydrogen sulfide and make food for the worms.

Fisher, Cordes, and others often find the communities by looking for small oil slicks visible in satellite images of the gulf.

This was part of a project called "Expedition to the Deep Slope," the first systematic exploration of hydrocarbon-seep communities deeper than 1,000 meters in the Gulf of Mexico, Potter said.

"The scientists' mission was to provide essential information on the ecology and biodiversity of these deep-sea communities to regulatory agencies, like MMS and NOAA, and energy companies, as the quest for oil moves into deeper and deeper water," he said.

Over time, the seeps slow down. Meanwhile, the tube worms alter the microbial process in the sediments on the seafloor. As bacteria break down the hydrocarbons, calcium carbonate begins to precipitate into the immediate area.

As the carbonate rock builds up, coral communities start to develop, Cordes said. One of the largest reefs in the gulf is 250 meters in diameter.

These dark, eerie worlds are populated by different kinds of hard and soft corals, but one of the most common is lophelia - a white, branching species found worldwide.

The reefs are wildly productive, attracting many fish, including species of commercial value. Some studies have shown that these deepwater reefs are almost as diverse as the tropical coral reefs.

But in the no-light environment, they behave entirely differently. There's no photosynthesis, no algae. Instead, their food is delivered either by ocean currents or gravity. The menu is small shrimp and other crustaceans that feed on the dead algae and bacteria sinking from the surface of the ocean far above.

Cordes is hopeful the reef communities won't be harmed by the spill. But they depend on the sweep of the current to remain cleansed, and oil particles could clog their tentacles, polyps, or other feeding apparatus.

"There's the tie right there," Fisher said of the current spill. "The food source for those corals is coming from those surface waters.

"If the rain of food slows down, the corals will be impacted," he said. "If the rain of food is contaminated, they'll be impacted."

Another worry is the emulsifying substance workers have been spraying onto the oil as it gushes from the ocean floor.

This will keep it in the water column longer, said LSU's Carney.

"Instead of a smokestack carrying smoke away, suddenly all the smoke comes and lays down in the city streets," he said.

"There isn't any good answer here so far," he said. "If the choice is oil washing ashore on the Gulf of Mexico and oil killing animals on the deep seafloor, the choice will probably be to kill animals on the deep seafloor.

"It's a choice," Carney said, "not a fix."

Contact staff writer Sandy Bauers at 215-854-5147 or sbauers@phillynews.com Visit her blog at http://go.philly.com/greenspace.