U.S. scientists using sonar and submersibles to map a reefs off Puerto Rico's northeast coast say they have found a 12-foot (3.6-meter) hammerhead shark, an undersea canyon that suddenly plunges 900 feet (280 meters) and an enormous orange-and-brown barrel sponge.

"You could actually live in that thing it was so big," said Tim Battista, the expedition's chief scientist.

Perhaps more significant, however, is what they are not finding: brightly colored coral and many big fish, the absence of which signals a troubled ecosystem.

"We're not seeing those vibrant, rich coral communities that all of us love to see," Battista said.

In the three-week project that wraps up Saturday, Battista and other scientists with the National Oceanic and Atmospheric Administration are mapping an area of 96 square miles (250 square kilometers). The results will help officials determine what sort of rules are needed to protect Puerto Rico's first officially designated marine corridor in the Northeast Great Reserve.

"There is very little information about what exists there now," Battista said. That is partly because the shelf is too deep for scuba diving.

While there are not as many native creatures as scientists had hoped to find, the reefs abound with an invading species, the lionfish. About 100 have been spotted per square acre, ecologist Chris Taylor said. The lionfish, which have no natural predators, have been gobbling up a variety of species and disrupting the balance of the reef ecosystems.

The team aboard the 187-foot (57-meter) Nancy Foster research vessel is studying reefs that were some of those hardest hit in 2005 by a "bleaching event" that occurs when coral loses its color because of external stress such as warm water. That forces coral to expel the tiny algae that live inside and produce oxygen, remove waste and serve as the main food source. Reefs in some parts of the Caribbean are still struggling to recover.

"The reefs are in a significant state of deterioration," said Ernesto Weil, who oversees the coral reef biology, ecology and systematics program at the University of Puerto Rico in Mayaguez.

Scientists worry that the reef could be further threatened by coral-attacking disease as the Caribbean prepares for an anticipated mild hurricane season that could see trade winds dissipate and water temperatures rise. An unseasonably warm winter also may cause coral-attacking diseases to develop earlier than usual, said Richard Appeldoorn, head of the fisheries, biology and coral reef studies program at the Mayaguez campus.

Another big threat is the winding down of the weather phenomenon known as La Nina, which could end this summer and unleash another bleaching event, Weil said.

"What saved us last year was a very strong La Nina," he said, adding that the weather pattern helped cool water temperatures to normal levels for the first time in 11 years.