As it blazed, a dense column of black smoke rose toward the sky. Oily water, the colour of st­rong tea, slopped up the sides of boats. The breeze carried an acrid smell, like gasoline fumes.

Aboard the research vessel FG Wal­ton Smith, anxiety was growing. Five scientists and six students had come to study the oil leak and its effect on the sea. They were not looking for oil on the surface, where it was so thick in places that it was being burned off, but for plumes of fine oil droplets far beneath the waves.

The stakes were high. Two weeks earlier, when some of these scientists had disclosed evidence of undersea oil plumes. Their claim had been greeted skeptically by the government. The scientists’ credibility was on the line.

If the plumes did exist, much of the wisdom about combating oil spills mi­g­ht need to be reconsidered. The plu­m­es would suggest that any future oil le­ak in deep water could be expected to do much of its damage in the sea, not on shore. But where were the plumes?

After a slow start, American science is finally beginning to tackle the oil disaster in earnest. The National Oceanic and Atmospheric Administration, the federal agency charged with monitori­ng the health of the oceans, is sending multiple boats into the gulf. The Natio­nal Science Foundation, another arm of the government, is issuing rapid gr­ants to finance academic teams, incl­uding the one aboard the Walton Sm­ith. BP, the oil company responsible for the spill, has pledged $500 million for research. And scientists like those abo­ard the Walton Smith are getting emergency financing from the government for their studies. The goal of the researchers aboard the Walton Smith was to nail the existence of such deep-sea plumes beyond any doubt.

They sailed this week from Gulfport, Mississippi, and went back to the spot where they had originally disc­overed a large plume. It was no longer there.

All one afternoon, the Walton Smith hopscotched across the gulf. The top scientists on board, Samantha Joye of the University of Georgia and Vernon Asper of the University of Southern Mississippi, peered intently at instrument readouts, hoping for a signal.

Down to the bottom of the sea went a huge apparatus designed to test the water and grab samples of it. The results kept coming up clean.

Then, late in the afternoon of the second day at sea, the entire scientific crew suddenly leapt to attention.

The boat had arrived at a new sampling site, west of the oil leak, and the instruments were travelling once again to the bottom. In a clean ocean, they would be expected to produce fairly straight lines on a graph.

Instead, wild squiggles were showing up. The display looked like one of those seismograph readings taken in the throes of an earthquake. At three different depths, the instruments picked up plumes of material drifting through the deep ocean.

Asper stood back, arms crossed, wa­tching the squiggles appear. “To see so­mething like this is a once-in-a-lifetime thing,” he said. “It’s really remarkable.”

Soon, a giant winch on the rear of the boat hauled special bottles back from the deep, carrying water samples. The younger researchers rushed to the rear deck. Working quickly in a daisy chain, circling the bottles, they filled small vials and other containers, and then hustled back to their makeshift laboratory. Over the next few hours, they filtered some of the water. They shook some samples. They pickled some. They bubbled gases through the water. They refrigerated some vials. Then they got ready to do it all again.

Within a day, word would come that a separate university vessel, the Weatherbird II, had discovered a giant plume stretching in the other direction from the broken well, toward Mobile Bay. It will take weeks of laboratory work to confirm with certainty that the plumes are made of oil droplets, or more likely, some complex mixture of oil and natural gas. If that idea holds up, the existence of these undersea plumes may well turn out to be the major scientific discovery of the great oil spill of 2010.

It could take years for scientists to assess the deep-sea damage fully, if that is even possible. Among other problems, gulf researchers have long been hobbled by a critical shortage of vessels equipped for oceanography.