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Everyone is surprised at how many times warning signs were posted on Duluth beaches. Research about the source of bacteria has led to a surprising discovery. (MPR/File photo)

For three years the Minnesota Pollution Control Agency has been warning swimmers and kayakers in Lake Superior when bacteria levels are dangerously high. The agency repeatedly posted a few Duluth beaches as being unsafe. A team of researchers has been trying to track down possible sources of the bacteria. What they've found so far is surprising. And it raises a big question about the standard way of testing for beach contamination.

Duluth, Minn. — When the MPCA started testing Lake Superior water three years ago, everyone was surprised at how often they found enough bacteria to prompt a warning that the water could make swimmers sick.

Heidi Bauman runs the beach monitoring program. She says the problem is concentrated at four locations in the Duluth harbor, and so far no one knows what's causing it.

"Our testing only tells us that there's high bacteria counts," she says. "The type of tests we do does not tell us where that bacteria came from."

The sanitary district hasn't found leaks in the sewer system that could account for the high levels.

The problem seems to spike after heavy rains, and Bauman says it may be that runoff from the steep hillsides in Duluth is carrying the bacteria.

But is it from people, or dogs, or birds, or deer? No one knows. Dr. Randall Hicks and his research partners are trying to find out.

In his lab at the University of Minnesota Duluth, Hicks has a special low-temperature deep freeze. It's full of boxes holding tiny tubes. The tubes hold samples of e. coli -- a very common kind of bacteria that live in the intestines of warm-blooded animals. There are a few strains of E coli that can make people sick, but most varieties are not harmful.

The frozen bacteria come from Heidi Bauman's beach monitoring program. Twice a week during the summer, someone collects water samples from 39 beaches along the shore. Randall Hicks and his colleagues separate out the bacteria and freeze it.

Meanwhile in the Twin Cities, another freezer holds tubes full of bacteria from various known sources. Hicks and his colleague Michael Sadowsky have been collecting these samples for five years. They have thousands of samples from different animals.

"We've gotten samples by working with the Wisconsin DNR when they go out and tag terns, and they help us get some gulls that we're able to take swabs from," Hicks says. "We've worked with trappers that are trapping beaver in this region, and they would get us swabs when they'd do the trapping. We work with deer hunters during deer season." Hicks says it's a very time-consuming process just to get the samples.

He and Sadowsky and other colleagues are going to spend the next year trying to match the DNA fingerprints of bacteria collected in the water with the DNA fingerprints of bacteria from known sources.

That could help the Minnesota Pollution Control Agency deal with the problem.

But in the meantime, the team has discovered something that may pose a new challenge.

We all know bacteria live in soils -- they help our gardens grow. But until now, scientists thought E coli only lived in the guts of warm-blooded animals.

Recently researchers found e. coli living in soils in the tropics. And last month, Hicks and his colleagues reported they'd found e. coli bacteria living in soils near Lake Superior. They were surprised to discover the bacteria could survive the cold winters.

"Whether they originally came from a warm-blooded animal or not, some have adapted to environmental areas like sediments and soils, and are self-sustaining populations now," Hicks says.

And that raises a big question about whether it makes sense to use e. coli as an indicator to warn of contamination that threatens people.

"If there's e. coli in these beach sands or sediments that are re-suspended into the water, then obviously the e. coli are not coming from recent fecal pollution from humans, or some animal," says Hicks.

The report was just published in an academic journal, and EPA scientists have not studied it yet.

But EPA spokesman Dale Kemery says the soil bacteria shouldn't make much difference, because the agency already sets a low threshhold for beach warnings.

"EPA is always going to err on the side of protecting the public health," Kemery says.

Results from the DNA fingerprinting should come in about a year.