“There’s lots of uncertainty,” said Charles R. Fisher, a professor of biology at Pennsylvania State University, who is leading a federal study of the dark habitats and who observed the nearby community. “Our best hope is that the impact is neutral or a minor problem.”

A few scientists say the gushing oil — despite its clear harm to pelicans, turtles and other forms of coastal life — might ultimately represent a subtle boon to the creatures of the cold seeps and even to the wider food chain.

“The gulf is such a great fishery because it’s fed organic matter from oil,” said Roger Sassen, a specialist on the cold seeps who recently retired from Texas A&M University. “It’s preadapted to crude oil. The image of this spill being a complete disaster is not true.” His stance seems to be a minority view.

Over roughly two decades, the federal government has spent at least $30 million uncovering and investigating the creatures of the cold seeps, a fair amount of money for basic ocean research. Washington has provided this money in an effort to ensure that oil development does no harm to the unusual ecosystems. Now, the nation’s worst oil spill at sea — with tens of millions of gallons spewing to date — has thrown that goal into doubt.

The agency behind the exploration and surveying of the cold seeps is none other than the much-criticized Minerals Management Service of the Department of the Interior — not its oil regulators but a separate environmental arm, which long ago began hiring oceanographers, geologists, ecologists and marine biologists to investigate the gulf seabed and eventually pushed through regulations meant to protect the newly discovered ecosystems.

The minerals service is joining with other federal agencies to study whether the BP spill is harming the dark habitats. Scientists say ships may go to sea as soon as July, sending tethered robots down to the icy seabed to examine the seep communities and take samples for analysis.

It is a bittersweet moment for scientists like Dr. MacDonald of Florida State University, who has devoted his career to documenting the ecosystem’s richness and complexity. In an interview, he said the sheer difficulty of trying to fathom the ecological impacts of the spill had left some of his colleagues dejected.