Chicago River Bacteria

Paddling down the Chicago River seems a long way off, but spring will eventually come and boaters will be back on the river. Just how clean is that river water?  That's what scientists at Argonne National Laboratory west of Chicago want to know.

“We’re actually trying to make a map of all of the bacteria, good and bad, that live in the rivers of Chicago,” said Argonne Environmental Microbiologist Jack Gilbert.

Bacteria levels in the Chicago River have been tested for years by the Metropolitan Water Reclamation District. In a lab at the district’s Stickney plant, scientists test the river water by isolating the bacteria from the water on a thin filter, then transferring the bacteria to a petri dish.

Microbiologist Geeta Rijal says the petri dishes tell the story.

“If you look at the water, it could be clear. Microbes are unseen, hidden inside the water. We visualize it by growing it in a petri dish,” said Rijal. “There's a medium in this where bacteria grow. They love that condition and they multiply, and that's how you see those blue colonies. And we count them, and that gives you, or checks the fecal condition of the waterway.”

But a new study being conducted at Argonne over the next seven years will provide vastly more information about the bacteria in the river.

Gilbert says this is the largest study ever done to measure the level of disease in an urban river system.

“We've come a long way since petri dishes were invented,” he said. “Now we have genomics. We’re able to sequence the genomes of these organisms, and give very, very specific identifications to them. So I can say exactly which species are there.”

Argonne began taking river samples last March, and will continue to sample monthly from March to November for the next seven years. The samples are frozen, the DNA is extracted and processed to make more DNA. The DNA is then sequenced to discover the genome of each microorganism.

Once the DNA from the samples has been sequenced, the data will be fed into Argonne’s supercomputer, MIRA, the fifth fastest supercomputer in the world. That will enable scientists to understand exactly what kind of microorganisms are in the Chicago River.

MIRA then produces a model on Gilbert's computer that maps the relationships of all the bacteria in the river where the sample was taken.

“What we're doing in the Chicago River system is generating a map of their metabolic capabilities: what they eat, what they generate, because that’s incredibly well-linked to how they cause disease,” said Gilbert. “The metabolism of a bacterium is linked to its virulence, how it produces a disease response.”

Gilbert says this information is not available from studying a petri dish.

“The only way we can get at this is by extracting the DNA and the RNA directly from the bacteria, directly from the environment, and analyzing it immediately,” he said.

Once the analysis of where the disease-causing bacteria are located along the Chicago River system, the environmental engineers at Argonne take over.

Cristina Negri has already begun utilizing maps for the Chicago area river system, or CAWS. CAWS includes the north branch of the river, the downtown main stem, the Calumet River, and the Sanitary and Ship Canal. Eventually, these maps will show all the hot spots where disease-causing bacteria exists and where it comes from.

“When you think about sources, you have to think about different things. The first one is, is it coming from humans, is it coming from animals, from geese, from wherever it comes in the animal kingdom?” said Negri. “Who is the host for these organisms? But that is only part of the study. We also have to figure out where spatially it comes from, so if you take a map, we have to identify hot spots or areas that need intervention more than others.”

Argonne’s study will provide critical information to the MWRD as it moves to comply with court orders to begin disinfecting the water it discharges from its treatment plants into the Chicago River, beginning in 2016.

“We are going to be repeating our analysis before the disinfection, after the disinfection, and after the TARP system comes into place. We will actually know the effectiveness of the disinfection, and we will know the relative importance of disinfection versus controlling other sources of contamination in the river.”

Gilbert says there is a clear reason for Argonne’s first of its kind seven-year study.

“It’s very important because my children like swimming, so from my perspective, I want to be able to go fishing and swimming in rivers, and be 100 percent, or at least as clear as it can be, that those waters are good for them and good for me to fish in and swim in,” he said. “So we want to be able to make sure the Chicago River system is the cleanest in the world.”

So the study should finally answer the question Chicagoans have asked for years: when will it be safe to swim in the Chicago River?