A recent NPR story discussed the 
U.S. Food and Drug Administration (FDA)’s proposed rule on raw manure, highlighting the difference of opinion on the subject between FDA and organic farmers. Many organic farmers rely on manure to fertilize their farms because of its nutritive capacity. But FDA considers manure a risk to food safety and wants to limit its use.
Organic farmers argue that raw manure is simply part of a natural cycle: crops strip vital nutrients from the soil, but by feeding those crops to cattle or turkeys, the nutrients cycle back into the manure.
FDA argues that animal waste contains disease-causing microbes, the agency argues, such as salmonella or E. coli which can survive in the soil for weeks or even months and contaminate the 
crops the manure is used to fertilize. While there is little certainty about the actual risk posed by manure, FDA has proposed a rule that would prohibit farmers from harvesting crops like carrots or lettuce for nine months after spreading raw manure on their fields, relying on the old mantra, “better safe than sorry.” The proposed rule is part of the Food Safety Modernization Act (FSMA), which was signed into law on Jan. 4, 2011, and would exempt small farms with less than half a million dollars in annual sales, those selling food to commercial processors with a “kill step,” or those selling the produce to “qualified end users” (non-business consumers in the same state as the farm that produced the food or less than 275 miles from the farm).
The use of raw manure is currently regulated under USDA’s National Organic Program (NOP), which permits harvest 90 or 120 days after application, depending on whether the crop has direct contact with the soil. FDA’s new rule, however, would make it impossible to use raw manure as fertilizer, because most growing seasons are less than nine months. Interviewed for the NPR story, organic farmer Jim Crawford, owner of a 95-acre farm in Houstontown, Pennsylvania, said that raw manure is safe when used according to the NOP rules, and that if he had to wait nine months, his farm “wouldn’t even be able to function.” Not all organic farmers agree with Crawford, though, especially large-scale organic farms, such as California’s Earthbound Farm, also interviewed for the NPR story. Earthbound’s salad greens were the source of an E. coli outbreak in 2006 killing three people and sickening 200 (although the outbreak was not caused by raw manure). Will Daniels, Earthbound’s chief food integrity officer, told NPR that using manure involves risks that Earthbound is not willing to take. “We’ve gone in that direction because we feel that it’s very important to assure that we are not spreading these pathogens in our fields, that could lead to contaminated product,” he says.
The FDA has pointed out that there are alternatives to raw manure, but farmers argue they cost substantially more. Organic farmers can use pelletized processed chicken manure product which has been treated with heat and pressure to kill microbes, or composted manure, the heat from which kills disease-causing microbes.
FDA extended the comment period for 
the proposed rule until Nov. 22 because of issues with the federal government’s electronic system for collecting opinions on its draft regulations, and the agency received more than 17,000 comments by that date.