Dateline   |  August 01, 2010

What lies beneath Gulf Coast waters?

BP is planning to soon begin a new procedure that it hopes  will permanently seal the leaking oil well in the Gulf. The vast slicks of oil haven't been seen for days, but what scientists say may be even worse – and what could affect even more people – is what's below the surface. Kerry Sanders went underwater to find out: what lies beneath.

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This content comes from Closed Captioning that was broadcast along with this program.

>>> bp is planning to soon begin a new procedure that it hopes will permanently seal the leaking oil well in the gulf. the vast slicks of oil haven't been seen for days but what scientists say may be even worse and could affect even more people is what's below the surface. carrie sanders went under water to find out what lies beneath.

>> reporter: for more than 100 days , the images from the gulf of mexico have been heart-breaking. birds, marine mammals and fish devastated as the oil spread. the destruction on the sea surface and shoreline was there for all to see, but now scientists have serious concerns about what may not be visible. we had a unique opportunity to learn what lies far below the surface. we joined researchers from florida atlantic university 's harbor branch oceanographic institute on their expedition last month and headed out into the gulf from st. petersburg, florida. the team's goal, to assess the current health of the reefs around the florida peninsula looking to locate any any oil but also to try to document a healthy ocean before any oil might get here. even though the ship is 230 miles from the broken well, there are fears the oil has spread this far. what they're most worried about is invisible to the naked eye . dr. shirley pomponi is the mission's chief scientist .

>> we're concerned about the oil that we can't see. my fear is that those droplets could get into the food chain .

>> reporter: the most basic research is on water quality .

>> going down.

>> reporter: collecting samples at various depths that will be sent to an onshore lab and tested for traces of oil. but their best tool for undersea exploration is harbor branch's four-person submarine. nearly 100 miles off the florida coast with chief pilot don libertori at the helm we descended looking for any evidence of the oil spill .

>> this is dive number 3791.

>> roger that one. look at that.

>> oh, we've got a bunch of dolphins right out in front of us. that's an unusual occurrence.

>> so we're now at 146, 147 feet and we're dropping down. we are on the bottom. it looks like we have one to 0.2 of a knot current. we're down to 214 feet. the submersible here was built in the '70s and actually designed to go up to 3,000 feet.

>> get the sonar going.

>> reporter: i've been scuba diving more than 25 years but this was different. inside the sub, every sense was shut down but sight, and what an amazing sight it was.

>> we're going to go ahead and take a digital still of it.

>> reporter: as far as we can see, everything down here looks normal. the fish, starfish and crabs just what you'd expect to see at these depths, but that's only part of the story. these researchers are more worried about what we might not be able to see. scientists in the second chamber of the submersible just behind us direct much of the work.

>> harry, will you please remind don to take a sediment sample?

>> reporter: the mechanical arm digs into the sea bed , collecting sand that will be tested for traces of oil from the deepwater horizon. the sponges that grow on the reefs of your particular interest to the team.

>> you're taking the sponges because they filter so much water. is that your canary in the coal mine if there is one?

>> we're going to see short-term evidence or near-term evidence of oil, it's going to be in things that filter out the water like sponges.

>> reporter: the sub collects samples from the sea floor for more than two hours. the good news, no visible signs of any oil. once safely back on board the research vessel , the specimens were rushed to a wet lab for identification and preservation for later analysis.

>> and then this thing is a sea squirt .

>> reporter: it will be weeks before they know if there is any evidence of oil. but this ocean-going research lab may well be doing double duty. think of it as csi the gulf, with the likelihood of lawsuits, the scientists are careful to maintain meticulous chain of custody records on all their samples.

>> the data that we're collecting, the samples that we're collecting will be subpoenaed. and say, okay, we may be called upon at some point in time one year from now, two years from nou, ten years from now to defend how we collect the data as well as how we analyze the data.

>> reporter: closely monitoring the research is dr. larry robinson . he's the assistant secretary for conservation and management of noaa, the government agency responsible for protecting the oceans and atmosphere.

>> if there's damage there, is it noaa and the federal government 's responsibility to hold bp responsible?

>> that's absolutely correct. part of this mission was to get an assessment, particularly with the deep corals, so that if there is any eventual impact to those corals we can i don't say that in our damage assessment to hold the responsible party, bp , accountable.

>> how do you say with confidence that if you find the damage here, you can prove that it is damage resulting from deepwater horizon's oil spill .

>> one of the things we have the ability to do is fingerprint the oil from the deepwater horizon spill.

>> reporter: despite the damage, the oil has done elsewhere in the gulf, coral reef kolgs dr. voss sees reasons for hope.

>> i think we can be cautiously optimistic. environments are very resilient. the different kind of genes that are present within organisms has allowed them to persist, to bounce back from catastrophic earthquakes, asteroids, volcanos. life is persisting here.