ON A SUBZERO FEBRUARY day, Mark Powell stops his vehicle on the road a few miles outside Prairie du Sac. He’s been explaining that cows actually enjoy the polar weather—and as if to prove it, a frisky group in the barnyard across the road turns toward us and rushes the fence.

As a USDA soil scientist and CALS professor of soil science, Powell is focused on the ground beneath their hooves. A few years ago he led a survey of manure handling on Wisconsin dairy farms. He and his colleagues knew how much cows left behind—about 17 gallons a day—but had only educated guesses about the ultimate environmental impact of barnyard design. In open yards like this, says Powell, they found that 40 to 60 percent of the manure ends up uncollected. “It just stays there,” he says. In the decade since his survey, the manure challenge has only grown, both in Wisconsin and nationwide. Water quality has been the major concern, but air quality and climate change are gaining.

A few minutes later we turn into the 2,006-acre U.S. Dairy Forage Research Center farm, and the talking points all turn to plumbing. There’s an experimental field fitted to track how well nutrients from manure bond to the soil. Parallel to one barn are nine small yards with different surfaces, each monitored to measure gasses emitted and what washes out with the rainwater.

The manure pit is frozen over, but circumnavigating the complex—shared by CALS and the U.S. Department of Agriculture—we arrive at the southern terminus of the barns. Uncharacteristic ventilation ducts adorn the walls and roofline. Inside are four unique stalls that can contain up to four cows each. The manure trough is lined with trays so that each cow’s waste can be set aside for further experiments. When the cows return from the milking parlor, airtight curtains will drop, isolating each chamber.