Two researchers, Dr. Derek Lovley, of the University of Massachusetts in Amherst, Massachusetts, and Dr. Dimitri Deheyn, of the Scripps Institution of Oceanography, have conducted research in San Diego Bay that challenges some prevailing wisdom regarding pollution in the bay.

Deheyn, 32, is from Belgium, though he has worked at Scripps since 1999. There are two chairs in his small, cluttered office overlooking the Scripps Pier, but the gray-eyed, strong-faced scientist stands while he discusses his work. "I have been studying the contamination of the bay," he explains, "particularly with metals. You have a lot of heavy metals in the bay, and heavy metals are pollutants that can be found in sediment and in water as a result of industry, of shipyards, or from paint on vessels. So you expect to have a lot of those metals in the bay."

Deheyn continues, "[In San Diego Bay] you have a lot of zinc, iron, chromium, copper -- a lot of copper because it is used in vessel paint. Because copper is so toxic, it protects the boat from all those little species of organisms that will ordinarily attach to the boat. If they try to do so, they die because the copper kills them. But the copper diffuses from the paint into the water and then goes into the sediment. That is the general behavior of a contaminant. It will rarely stay suspended in the water. It has to combine with something, and so it will usually combine with something in the sediment or with an organism."

More than a century of heavy use as a commercial and naval harbor, plus seasonal urban runoff, have formed a steady source of pollution for the bay. And the pollution tends to stay in the bay, Deheyn explains, "because it is a closed bay. There is no opening in the back of the bay, and there is no water flowing into the bay, no fresh water. There is no real river. So basically the only way for the water to be renewed in the bay is by tidal exchange. With the cycle of high tide and low tide, you have an exchange of water. And so on average we would say that, around Point Loma and Shelter Island, it takes between two and ten days for the water to be renewed in that part of the bay. If you threw a buoy in the bay at Harbor Island, it would take 2 to 10 days for the buoy to go out. But, in the back of the bay [south of the Coronado Bridge], it takes between 20 and 100 days. But that doesn't mean that the sediment will be transported with the water. And the sediment is where the pollutant accumulates because, as I told you, once you put a chemical in the water, the chemical has to combine to something, whether it is an organism or a sediment."

Because of the rapid water renewal in what Deheyn calls the front of the bay, from the mouth to the bridge, accepted wisdom has been that the water was cleaner there than in the back of the bay. Deheyn believes his research shows that idea to be only half-true. "It doesn't take into account," Deheyn says, "the notion of what we call 'bioavailability,' which is the availability of the pollutants to be absorbed by organisms. In the back of the bay, the bottom is very muddy. You can stick your arm into it right up to your shoulder. And the water is very turbid. You have all of these little particles of sediment suspended in the water. Those little particles have actually very strong power to combine with the pollutants. And so when a pollutant is in the water, in the back of the bay, it will bind to the particle and then stay bound to it, and then eventually it will sink. In the mouth of the bay, you don't have a lot of particles. Many times you can see very far down. There is much better visibility than in the back of the bay. And at the mouth of the bay, the bottom is sand, not mud. And the sand particles are bigger than mud. The particles are coarse. And because they are bigger, they don't have such a great power to combine with the pollutants. That means that you have pollutants available in the water. They will maybe combine a little bit with the sediment, but they will rather combine to something that is better for them, and that will be an organism."

And once combined with an organism, the contaminant then enters the food chain. Deheyn has demonstrated his hypothesis with the help of tiny starfish known as brittle stars. With a body the size of a dime, the brittle stars can light up their comparatively long legs. "It's known as bioluminescence," Deheyn explains. "It's a self-defense mechanism. If a crab approaches, the brittle star lights up, which kind of stuns the crab, and the brittle star can move away. If the crab recovers and catches him, the brittle star can release most of his leg, like a lizard's tail, and then it will regenerate."

Deheyn's experiment, funded by a $30,000 grant from the San Diego Foundation, was to place caged brittle stars "in the mouth of the bay and the back of the bay. We use bioluminescence as an indicator of toxicity because it is controlled by the nervous system, and a common toxic effect of metals is damaged nervous systems. When I analyzed the light production of the brittle stars I put in the front of the bay, the bioluminescence was decreased in a week. In the back of the bay, the brittle stars did just fine. They were living in that mud, and they accumulated some metals but not much. And the light production was just fine. They were normal after weeks. When I compared the amount of metals that they accumulated -- the ones in the front, in the mouth of the bay -- they accumulated about twice as much metal as those in the back. So even though there are more metals in the back bay, there is more available metal in the mouth of the bay."

While Dr. Deheyn is studying metals in the bay, Dr. Lovley is studying a different form of pollution. "What we've been doing for a number of years is looking at the potential for polycyclic aromatic hydrocarbons to be degraded in the absence of oxygen. There's very little oxygen available to microorganisms in sediments or in the mud at the bottom of harbors. It was thought that once polycyclic aromatic hydrocarbons got into the sediments that microorganisms would not be able to degrade them, because they needed oxygen in order to break them down. But -- and we first saw this in San Diego a number of years ago -- we saw in sediments from the bay that organisms had the potential to oxidize these polycyclic aromatic hydrocarbons to carbon dioxide, which of course is harmless, using sulfate naturally present in the sea water. Now that I'm in Massachusetts, we had better access to Boston Harbor sediments, and we more carefully looked at the degradation of the polycyclic aromatic hydrocarbons that are present in the sediments. We also for the first time looked at some of the larger polycyclic aromatic hydrocarbons that are of most concern -- some of the nastiest ones, the biggest ones -- and found that they were degraded."

Like the metals, the primary cause of polycyclic aromatic hydrocarbons is shipping. "Most of the sites that we looked at were fairly heavily contaminated with some kind of petroleum input and creosote from wooden pier pilings. Those are the major sources, though they come from a variety of sources."

Lovley's research over the past nine years has been funded by grants from the Office of Naval Research. "We've had three different grants," he says. "They're typically in the range of $300,000 to $400,000 for three years."

The next step in his research, he explains, "is sequencing a genome of one of the organisms -- they're known as sulfate reducers -- that can carry out this reaction. We're getting more into the molecular biology of the organisms themselves because now we know that they do it, but it's not understood how they do it. Once we know, maybe we can change conditions a bit to promote their activity. With environmental restoration, which is the stuff that I've worked on, the more we understand about the microorganisms, the better we can manipulate their activities to speed up contaminant degradation."

Lovley's research challenges another prevailing notion: that you have to dredge in order to remove contaminated soils. "I think that's one of the major outcomes of this," he says. "It just shows that there's a greater self-purification capacity in these environments than was previously recognized."

Asked about dredging in relation to contaminants, Deheyn answers, "Once the metals are bonded to the sediment -- and they are deep, like a few feet below the bottom -- they are not available. So a starfish, a crab, whatever, would not be exposed to the sediment that is down there below. So the sediment could be highly toxic, but the water could be clean, and the organism that is living in it could be noncontaminated and would not be exposed to toxicity. If you start digging, mixing everything back into the water, the chemical bond between the contaminant and the sediment will be loosened, and the chemical might be released into the water looking for something else to bond to. It is like starting the whole pollution process again. But you also have to keep in mind that the bay naturally fills up with sediment, and ten years from now, if you don't remove sediment, you will be able to walk across the back of the bay."