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The Origin of the Feces: Small Mass. Town Uses DNA Tech to Identify E. Coli Source

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Fingerprinting the DNA of fecal bacteria helped a small town in Massachusetts determine the origin of feces in its harbor.

A recently reported study found that the principal sources of fecal E. coli in the outer harbor of New Bedford were geese and seagulls rather than humans. The New Bedford Harbor Trustee Council had commissioned the study to help it decide whether building a sewer line in the area, which currently has only septic systems, would have an effect on the fecal coliform concentrations in New Bedford Outer Harbor, according to Paul Hall, a senior scientist at Applied Science Associates of Narragansett, RI, which conducted the study.

E. coli concentrations — which indicate fecal contamination, and thus the possible presence of disease-causing bacteria from human waste — have long been above regulatory limits in the area, he said, restricting it for certain activities, such as shell-fishing.

To arrive at their results, researchers at Cape Cod Community College in Barnstable, Mass., analyzed DNA from E. coli found in water samples taken in and around the outer harbor. Also, scientists at Applied Science Associates used computer models of water currents to help them identify which of the 21 sources, which they had sampled over more than one year, contributed mainly to fecal coliform pollution.

Hemant Chikarmane’s team at Cape Cod Community College performed the DNA fingerprinting. The researchers analyzed variations in E. coli DNA encoding ribosomal RNA, a method called DNA ribotyping. The researchers matched the results against a library of E. coli fecal isolates from various animals. Each animal harbors distinct E. coli strains. The analysis revealed that birds account for about half of the fecal coliform in the harbor, followed by rodents, deer, humans, and raccoons.

It might be difficult, though, to use the DNA ribotyping approach in other places since the E. coli library is specific for a certain geographic region. “E. coli from a deer in Massachusetts could be different from E. coli in a deer in North Carolina,” said Hall. Thus, DNA ribotyping could be used only in places where such a library exists, he said.

However, bacterial source tracking in general might be used more often in the future to determine the source of fecal pollution. “Within the environmental sciences, this is kind of a hot topic,” Hall said. “It is important for surface water management issues, particularly in coastal areas, where often in the summer time you have beach closings or regions that get restricted because of high fecals in the water.”

The $130,000 study, published in a report in April, was commissioned and funded by the New Bedford Harbor Trustee Council.

—JK

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