C. Claiborne Ray of the New York Times asks, when a virulent strain of E. coli from manure contaminates produce, how do farmers clean the soil in their fields?

“Farmers commonly rely on environmental conditions over time to inactivate the pathogenic E. coli,” said Randy W. Worobo, associate professor of food microbiology at Cornell University.

The disease-causing bacteria may come from the feces of deer, sheep, cattle or other warm-blooded mammals, including humans, Dr. Worobo said. Generic E. coli are normal inhabitants of the lower intestine. Pathogenic forms have acquired virulence genes that produce substances like enterotoxins, which cause intestinal illness, and adhesins, which allow for binding to intestinal cells in the hosts.

“It is not a common contaminant of fecal material,” Dr. Worobo said, “but if the host becomes infected with a pathogenic E. coli strain, it can cause illness in the host and be shed in the fecal material along with generic nonpathogenic E. coli.”

Over time, the pathogenic E. coli are inactivated by exposure to the sun; desiccation; poor nutrient conditions; temperature extremes; and competing soil microbes. To hasten the die-off, farmers may turn the soil, evenly distributing the microbes and making sure they are exposed to these conditions.

To keep the microbes out of land used for food production, Dr. Worobo said, farmers rely on animal barriers and specific practices for handling compost and manure.

For more than a decade, 57-year-old roofer and writer Joseph Jenkins has been advocating that we flush our toilets down the drain and put a bucket in the bathroom instead.

When a bucket in one of his five bathrooms is full, he empties it in the compost pile in his backyard in rural Pennsylvania. Eventually he takes the resulting soil and spreads it over his vegetable garden as fertilizer.

"It's an alternative sanitation system," says Jenkins, "where there is no waste." His 255-page Humanure Handbook: A Guide to Composting Human Manure is in its third edition and has been translated into five languages, but it has only recently begun to catch on. His message? Human manure, when properly managed, is odorless. His audience? Ecologically committed city dwellers who are looking to do more for the earth than just sort their trash or ride a bike to work.

Night soil is rumored to be used in the production  of fresh veggies , especially for upscale restaurants, in many large cities.

I’ll stick with riding my bike to work, and thank engineers for sewage treatment.