Pollution sleuths: researchers use DNA fingerprinting test to trace water pollution sources

Like police detectives trying to solve a crime, those who test for water pollution look for clues.

COLUMBIA, Mo., March 22, 2001 — Like police detectives trying to solve a crime, those who test for water pollution look for clues.

However, finding the guilty party often is difficult because most tests can identify the presence of pollution, but not the source. To solve this problem, University of Missouri-Columbia researchers are using a "fingerprinting" test that can trace water pollution back to its source using DNA from bacteria.

According to Andrew Carson, MU professor of veterinary pathobiology, the presence of fecal E. coli bacteria - microbes that live in the intestines of their host until they are excreted - commonly is used to determine if water pollution is caused by human or animal waste.

"Typically, these organisms are non-pathogenic, which means they do not produce disease," Carson said. "However, their detection in water warns of the potential presence of disease-producing strains of E. coli, salmonella or hepatitis virus that also can be found in human or animal waste."

In order to track fecal E. coli water pollutants back to their host source, Carson's laboratory is applying a DNA pattern recognition technique. This novel approach is based on the premise that each host species harbors particular types of E. coli bacteria in its intestinal tract that have unique DNA patterns, or "fingerprints." By comparing the E. coli fingerprints found in water samples with E. coli DNA patterns from known-host species, possible sources of water pollution can be identified.

"This technology, known as ribotyping, was first reported in 1988, but only recently has it been applied to water quality," Carson said. "Others scientists have used it to distinguish between human and non-human sources of water pollution, but we are now able to distinguish among a variety of animal and bird host species using DNA fingerprints."

To date, Carson's laboratory has identified specific DNA fingerprints for fecal E. coli from eight common hosts: humans, cows, pigs, horses, dogs, chickens, turkeys and migratory geese. This technology has allowed Robert Broz, director of the MU Water Quality Program, to help communities in the Long Branch Watershed in north-central Missouri and the Shoal Creek Watershed in southeast Missouri's White River Basin identify and solve pollution problems that threaten their water supplies.

"Without a test such as this, time and energy are wasted when attempting to find where water pollution originates," Broz said. "With this new form of technical assistance, we can now make science-based decisions that relate to solving the problems."

Carson said his laboratory continues to add to its database of known-host bacterial DNA patterns, which will help to further improve the test's accuracy. Many states have sent water samples for analysis, and Carson expects that his laboratory and the fingerprinting technique will contribute significantly to the current nationwide water quality movement.

Carson's most recent article on the application of DNA fingerprinting is in-press with Applied and Environmental Microbiology. The U.S. Geological Survey and MU funded the ongoing project.

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