26 July 2010 Last updated at 07:28 ET

Voyage to the bottom of an oily sea

By David Shukman Environment correspondent, BBC News, Florida

It's not for the claustrophobic, the seasick or anyone fearful of venturing underwater, but the mini-submarine operated by the Harbor Branch Oceanographic Institute offers an unparalleled glimpse into the potential impact of the Gulf of Mexico oil spill.

I'll admit it: I feel a little nervous preparing to board the craft for a dive. Its inelegant name, Johnson-Sea-Link II, does not inspire confidence.

Nor does the sight of it: the sub looks ungainly, like a giant insect with a bulbous head fitted to a body crawling with intestinal tubes and cables. I'm told it is capable of taking four people down 3,000ft (914m) but my first thought is who'd want to?

The submarine is being used on an expedition to investigate the spill, mounted by the Cooperative Institute for Ocean Exploration, Research and Technology (CIOERT), a US government-funded coalition of universities and research bodies.

Although the wellhead is 200 miles away off the Louisiana shore, the Gulf's currents could easily bring oil or dispersant chemicals here to the fragile coral reefs and valuable fishing grounds off the west coast of Florida.

Climbing inside the tiny machine, on the rear deck of the research vessel Seward Johnson, must be similar to entering a spacecraft - cramped, switches everywhere and air-conditioning and carbon dioxide scrubbers emitting a loud hum.

I sit in the right-hand seat, chief pilot Don Liberatore is already in the left-hand one, both of us facing a clear, curved window of acrylic that's a reassuring 13cm thick.

Don is busy with his pre-launch checks, running through a series of procedures with the support team on the ship. I try to avoid knocking into the myriad levers and buttons clustered around me.

Then comes Don's safety briefing. The sub has an exemplary record: it's conducted thousands of successful dives. There's a second operator in a smaller chamber at the rear. But I feel a sense of dread as he explains what to do if both of them are incapacitated.

Flick these three switches in a row to blow the ballast tanks or, failing that, open this blue valve and then those two other valves and you'll shoot up.

I convince myself that I'll remember all this but in reality there's a maze of hundreds of switches and valves and I'm the sort of person who can't recall where I've put my own pen let alone rescue a stricken sub from the seabed.

Into the deep

Minutes later, hatch firmly closed, we are lifted off the deck. A giant crane hoists us into the air and down over the stern of the ship where we swing in the swell.

A few sharp lurches follow and then there's a blast of foam as we drop at speed beneath the surface, waves splashing over the canopy, surf breaking around us.

Don releases several vigorous streams of air and we descend. It's quiet and we're soon beyond the surge of the waves, slipping into a darkening, tranquil blue towards the coral on the ocean floor.

It's like scuba diving without any of the hassle, clouds of marine snow streaming past us.

Soon, a reef is looming out of the gloom, its jagged twists and folds teeming with fish. This is a healthy scene, no hint of oil or dispersant doing any damage.

Apart from the hum of the ventilation, the only sound is the constant flick of the switches Don uses to control the nine little electric motors.

As we hover over the beds of coral, grouper and angel-fish idle near us, untroubled as our bubble rides along at a top speed of just over one-mile-per-hour.

At various points, Don manipulates the sub's mechanical arm to collect samples of corals, sponges and sea-fans, which he lowers into an array of collection boxes.

Directing the choice of specimens is Don's wife, Professor Shirley Pomponi of the Habor Branch Oceanographic Institute, who's with the second crewman in the sub's rear chamber.

Over the intercom, she describes the reef as in "far better shape" than she expected but warns of the potential unseen impacts of the spill.

'Invisible threat'

One aim of the expedition is to measure the state of the reefs before any oil or dispersant may arrive - so that future changes can be measured. Another is to devise new techniques for assessing the vulnerability of coral.

A snapshot of the genetic make-up of coral cells can indicate whether the organisms are responding to the invisible threat of a toxin, such as oil or chemical dispersant.

As we traverse the reef, Professor Pomponi explains that analysing the samples should shed light on early indicators of the stresses the corals may have to cope with.

"It's unlikely we'll see oil all over these corals," she says.

"I'm more worried about what we don't see - the long-term effects of microscopic particles of oil entering the food chain.

"That's the real concern - and that's what we need to investigate."

After two hours, it's time to return, a gentle process until we reach the dazzling light of the surface and some tumultuous waves. For a while, we're tossed around like a beach ball caught in a storm.

The approach of the Seward Johnson can't come soon enough, a diver plunging into the waters in front of us to attach a tow-line.

Soon we're hoisted into the air once more. Down on the deck there's a welcoming party and I catch sight of cameraman Rob Magee and producer Rozalia Hristova.

The hatch opens and warm Gulf air surges in. The samples are rushed to the lab, and I hear myself talking with the crazed speed of a traveller back from an alien world.