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DNA Techniques Allow Scientists To Become Pollution Detectives

GAINESVILLE—Just when you thought you’d heard enough about DNA testing from the so-called “Trial of the Century,” University of Florida researchers are using the same science to police polluters.

With the oft-mentioned DNA “fingerprint” test, scientists at UF’s Institute of Food and Agricultural Sciences are able to accurately point the finger at who is polluting water bodies by isolating E. coli bacteria in water samples and testing it for resistance to antibiotics and by testing its DNA.

“E. coli is present in the digestive tracts of all warm-blooded animals,” said Mark Tamplin, a professor of home economics at UF/IFAS. “By testing the E. coli (present in fecal matter) for antibiotic resistance and looking at the DNA chains, we can tell if it is human pollution or animal pollution. Different animals will have different E. coli and will have greater DNA patterns because there are more animal species. Humans have fewer DNA patterns.”

Tamplin and his research team, working with a grant from the U.S. Department of Commerce’s National Estuarine Research Reserve System, studied pollution at two sites in Florida: Rookery Bay near Naples on Florida’s southwest coast, and Apalachicola Bay, an oyster-harvesting area in North Florida.

About 90 percent of all Florida oysters are harvested in the Apalachicola Bay area. Lee Edmiston, research coordinator at the Apalachicola Bay reserve who helped collect water samples for the two-year survey, said bacteria from pollutants causes fecal coliform counts to rise. When the counts get too high, the state, fearing illness from consumption of raw oysters, closes the bay to oyster harvesting.

“There’s always been a question as to whether the bacteria was natural or manmade,” Edmiston said. “There was never a way to differentiate that before this research.”

Initial testing pointed the finger in both directions, the UF scientists found.

“Both entities, human and animals were polluting, but wildlife causes a significant amount of pollution in Apalachicola Bay,” Tamplin said.

From their testing in the bay, UF scientists have developed a database of more than 1,000 E. coli strains that will serve as a model for testing in other water bodies.

“E. coli is a very convenient organism to test for,” Tamplin said. “We use E. coli to measure the probability of other harmful bacteria in the water. We hope to be able to have folks send us water samples and to run these tests on it for them. We think this type of test could be used all over the country to detect pollution in water.”

Despite hours of complex testimony in the O.J. Simpson trial, the DNA “fingerprint” testing used by the UF scientists is fairly simple to understand, Tamplin said. Picture a thread that represents one person or animal. By taking one thread from one entity and another thread from someone else and then applying an enzyme to it, the enzyme will cut each thread in different places.

“Then, we look at the number of cuts and where they are to determine if it is a person or an animal,” Tamplin explained. “What we start to see are patterns that emerge and they are different in humans than in wildlife.”

Edmiston said knowing where the pollution came from could help save time and money spent devising solutions to protect the environment.

“Down the road, these techniques could be used to help us manage our problems,” Edmiston said. “There is good potential here to help us develop management plans for different sources of pollution.”