As I've written at some length before, the story of Chicago is one of a city lifting itself out of its own waste—from the raising of the city, to the tunnel system leading out to the distinctive water cribs on Lake Michigan, to the reversal of the river, to the epic Deep Tunnel project.
Running through the heart of it is the Chicago River, long an industrial artery-cum-sewer that's being reinvented for a 21st-century role as a recreational amenity, reclaimed as the centerpiece of the riverwalk project and next year's Great Fire festival.
But through all this time and effort, we don't really know what's in it. The EPA monitors a handful of things like disease-causing and fecal bacteria, towards making it safer for recreational use suggested by the city's future plans. But there's a whole universe of life within the river that technology has, in the past few years, made it possible to explore. A world of "dark taxa," to use microbiologist Jack Gilbert's phrase, the living equivalent of dark matter: "Some 1.2 million species are scientifically catalogued but the vast majority of life on Earth still exists as 'dark taxa', with perhaps 86% of extant eukaryotic species awaiting even the most basic description."
Much of Gilbert's work centers on investigating metagenomics, the science of biological life that encompasses large biological communities. Gilbert, for example, who works at Argonne and the University of Chicago, is directing the Hospital Microbiome Project, which is documenting the growth of the microbiological world at the university's new hospital.
Now Gilbert and Argonne colleague Cristina Negri, an agronomist and environmental scientist who's done extensive work with wastewater and remediation in Chicagoland and elsewhere, are embarking on a seven-year study of the Chicago River, investigating its dark taxa and how the components of its metagenome interact.
To put it in context, you may have read about recent advances in our understanding of how bacteria interact with the human body—a vast number that live in our "microbiome," especially in the gut. The human microbiome is a tremendously active field of study; scientists are examining its effects on depression, obesity, cancer, and other health outcomes.
And the Chicago River, in its way, is the city's gut. What's in it and how those bacteria interact, in place and over time, is not understood, in large part because the technology that can process the staggering amounts of data that the genomic information contained in a system that large has only become practical (and affordable) in the past five to ten years.
It's a challenging task. Intuitively, you might think of what good and bad things happen in the river just from what we pump into it, which tends to be the same crap, literally and figuratively. But as our understanding of interactions within that biome advances, it complicates the picture.
"It's highly unstable," says Gilbert. "It's remarkable how much instability there is in river systems. They tend to change quite rapidly. From month to month we'll see different types of microorganisms there. And that makes an interesting conundrum when you're looking into river systems for pathogens or known disease-causing bacteria. "Because we're probably pumping into the water the same kinds of disease-causing bacteria every time, but each time they're interacting with a new community of organisms. And it's those interactions we are most interested in deliniating."
Gilbert and Negri expect to keep an eye out for damaging microorganisms, as you'd expect—if the river is indeed going to grow as a place of recreation, targets will be the kinds of bad bacteria that cause skin or intestinal problems. But just as the study of the human biome is finding good organisms that can serve as a defense, Gilbert and Negri also expect to find organisms that could work towards remediation, rather than just those to be eliminated as a part of remediation.
"The idea of microbial ecology is really not on people's minds, normally," says Negri. "We're taught that you have to get rid of germs—we're told you should use disinfecting wipes to clean up your countertop, and all that kind of stuff. I'm a soil person, an agronomist, who works with plants and soil—and the first thing you learn is that life can occur because you have this interaction between organisms, feeding off each other. We're at the cusp of discovering exactly how these interactions are actually useful for us…. You don't just wage a war on the bad organisms, like we did before."
On a larger scale, urban designers are looking at how returning aspects of the Chicago River and waterways like it to their old forms can work with manmade technologies as part of a broader cleanup strategy. Architect Jeanne Gang, for instance, proposes a combination of green tech and wetlands to clean the river. "The next step is to take out the canal—which is a concrete basin—and remediate the area so it can start to operate like a wetland," Gang told Chicago in 2011. "Use nature as technology."
At the vanishingly small, constantly changing level of the genome, Negri and Gilbert's work could have similar implications. "We have to help support the good guys," says Gilbert. "We have an army out there, in the environment, that's ready and more than willing to help protect us. We just have to understand how best to use the army and how to get it to do what we want it to do, so it fits within our framework of human civilization."