USC microbiologist Jed Fuhrman and UCI environmental engineer Stanley Grant were contracted by the city of Avalon in 2001 to figure out what was polluting the bay of the popular tourist destination.

Combining genetic testing and bacterial samples, the scientists found both the concentrations and specific sources of pollution, revealing that aging sewer pipes were leaking human waste into the ocean waters along the shore.

Bird feces and animal waste, among other contaminants, may also have contributed to the pollution, said the researchers.

Their results were posted Jan. 9 on the Research ASAP Web site of Environmental Science & Technology.

“Previously it was thought that all the contamination probably came from animal sources,” said Fuhrman, the McCulloch-Crosby Chair in Marine Biology in USC’s College of Letters, Arts & Sciences. “But our results suggested that some of the contamination came from leaking sewer pipes under the city.”

The leaking pipes in Avalon’s downtown area have since been repaired, and bacteria levels along the shoreline have decreased by more than 50 percent, according to city officials.

The city now is investigating sewer pipes from private businesses and homes to make sure there are no more leaks.

But since the city pipes were fixed, beach closures have declined from 31 in 2001 to 15 in 2002.

“It was like a mystery, and we followed the clues,” Grant said.

Traditionally, beaches are tested for fecal indicator bacteria using methods that provide only general information about the sources of pollution.

Those methods can’t always distinguish, for example, whether the indicator bacteria are from human or animal sources because all warm-blooded animals - including shorebirds - have them in their gut.

Using a method developed by colleagues in Oregon, Fuhrman and Grant used polymerase chain reaction (PCR) - a laboratory technique that amplifies strands of DNA so they are bountiful enough to be tested - to detect a group of bacteria thought to originate only from human waste.

They also used a method to detect human enteroviruses - pathogenic viruses that can be transmitted by water and cause a variety of illnesses - that used PCR with an added step since the viruses have RNA as their genetic material instead of DNA.

Fuhrman said this was the first time, to his knowledge, the genetic tests have been used in a beach study of this kind.

“Many people are interested in knowing when contamination arises from human waste, as opposed to animal waste, because the risk of exposure is thought to be higher,” said Fuhrman.

“Tests such as these help to distinguish human from animal sources. Also, by showing we can look for viruses as well as bacteria, we expand the numbers of indicators available,” he said.

The tests may prove to be new weapons in the arsenal against beach water pollution. But, Fuhrman said, they are still in the developmental phase.

“Other tests that attempt to get similar answers are also being tried and compared by a variety of labs, and there are trade-offs between the cost and sensitivity of the tests,” he said.

Also involved in the study were Alexandria Boehm of Stanford University and Robert Mrse (cq) of UCI.

The study was funded by the state’s Clean Beaches Initiative project, which used Proposition 13 money to fund 38 projects. The initiative’s goal is to reduce health risks and increase the public’s access to clean beaches.

Contact Usha Sutliff at (213) 740-0252.