Watch children’s first reactions at a dairy farm and you’ll see their hands quickly going up to their faces and their fingers pinching their nostrils shut.

“What’s that awful smell,” they’ll ask the farmer.

For a farmer who hasn’t hosted groups of students before, the first expression crossing his or her face might be one of puzzlement, but then quickly replaced by a smile or chuckle of understanding.

“It’s manure,” the farmer will tell the children, who are still so overwhelmed by the smell that they don’t immediately notice the dairy calves put in special pens in front of them to see.

“Manure,” they ask. “What’s that?”

By the time the farmer explains what it is  — cow poop, oh, yuck — and why it’s so good for the crops the farm grows, the kids’ interest has begun to flag. They’ve gone on to other questions such as how old are the calves and what do they eat. They might even be given bottles filled with milk so they can feed the calves.

And so it goes with raw manure, an unpleasant-smelling byproduct of livestock operations but one that has the sweet smell of success for farmers who depend on it to nourish their crops.

The up side of raw manure
Farmers use raw manure on their fields because it is an excellent source of nitrogen (N), phosphorus (P) and potassium (K), which are all nutrients necessary for plants to grow and thrive. It also returns organic matter and other nutrients such as calcium, magnesium and sulfur to the soil, thus building soil fertility and quality. In other words, it helps crops grow and keep soils healthy.

Another plus is that raw manure, which has been used to grow crops for centuries, costs less than chemical fertilizers. And better yet, livestock farmers who also grow crops have plenty of it on hand, at no cost to them. Many times, it is shared between neighboring farms.

In the case of organic farms, which aren’t allowed to use many chemical fertilizers, manure is especially important, although some conventional farmers also use raw manure to fertilize their crops.

Western Washington organic dairy farmer Charlie Dykstra said that without it, organic crop farmers would have to buy their own fertilizer.

“Personally, I think organic vegetables would be about twice as expensive in the stores if dairy manure wasn’t used as a fertilizer,” he told the Skagit Valley Herald.

Raw manure’s downside
As most farmers know only too well, raw manure can harbor  potentially deadly foodborne pathogens such as E. coli, Salmonella, Listeria monocytogenes and Campylobacter.

Because of this, raw manure has the potential to contaminate crops that are typically eaten raw such as carrots, strawberries, green peppers, tomatoes leaf lettuce and spinach, to name just a few, merely by coming into contact with them. People who eat contaminated produce raw can become ill, sometimes even suffering kidney failure, and in extreme cases, death.

Yet, the U.S. Department of Agriculture, as well as a great many health officials, advise people to eat as much fresh produce as possible. And therein lies the dilemma.

An example is the current outbreak of E. coli O157:H7 infections associated with romaine lettuce. As of mid-May, 172 people in the United States have been confirmed with infections. One person in California died and 20 of the victims have developed severe kidney failure known as hemolytic uremic syndrome (HUS.) The outbreak has affected people in 32 states and four Canadian provinces. Six confirmed outbreak cases are reported in Canada.

According to a study done by the Center for Science in the Public Interest in 2015, fresh produce was responsible for most of the foodborne illnesses in the U.S..

In the organization’s study of outbreaks that occurred between 2004 and 2013, the consumer advocacy group found that fresh produce, such as cilantro, cucumbers, cantaloupes and peppers, caused 629 outbreaks and almost 20,000 illnesses.

Such statistics spurred Congress to approve the Food Safety Modernization Act, which was signed into law in 2011. The goal of the Act is to prevent outbreaks of foodborne illnesses instead of reacting to them.

No surprise then that the types of fresh produce that are typically eaten raw came under the regulatory spotlight in what is commonly known as the Produce Safety Rule.

Not all fresh produce is subject to the rule, but the vast majority of it is. Raw manure figures into the Produce Rule picture in a big way. Pathogens living in animals’ intestines can contaminate produce that’s growing in the fields treated with raw manure.

Despite that, some produce growers said the Food and Drug Administration went too far in January 2013 when it proposed that the Produce Rule include a minimum nine-month interval between the application of raw manure to produce growing fields and the harvest of food from those fields. The FDA proposal said the interval would reduce the potential pathogen problems that come with raw manure. Composted manure would have been subject to a 45-day minimum pre-harvest application interval.

The proposed manure regulation sent shock waves through the farming community with many farmers asking if the FDA knew anything at all about agriculture. According to a USDA survey, farmers reported using raw manure as a fertilizer on nearly 16 million acres of cropland.

In the world of agriculture, nine months is a long time to wait, especially for crops that are harvested in much less time than that, which is commonly the case with produce. Also, many farmers rely on crop rotation to prevent infestations of bugs and plant diseases. Having to wait nine months would put some of them out of business, according to comments on the proposed rule.

Back to the drawing board
The FDA got enough negative comments on its initial proposal that the agency’s top officials decided to come up with another plan.

But, because of the complex topic — involving manure coming from a variety of animals being applied to a wide variety of soils used to grow many different foods with all kinds of farming practices in a wide range of locations with varying weather conditions — the agency estimates it will take from 5 to 10 years before a final rule will be in place.

As part of its decision to defer the nine-month interval, the FDA acknowledged the lack of comparable scientific evidence needed to support any such time frame, which means that more research needs to be done before the agency can come up with a feasible regulatory approach that’s based on science.

For that reason, FDA is developing a risk assessment that takes a wide range of variables into consideration. It is also working with USDA and other stakeholders to conduct research on this topic.

Things are going well, said David Ingram, Food and Drug Administration Consumer Safety Officer Division of Produce Safety.

“It’s really amazing. We have a great deal of robust research on this — one of the largest data sets ever compiled. We’ve committed several millions of dollars to understanding this better,” Ingram said.

From this research, the agency will be creating a mathematical model that can be used to predict the survival behavior of the bacteria in question — foodborne pathogens such as E. coli in the produce growing environment, for example.

When the FDA proposes a regulation establishing an application interval for untreated biological soil amendments of animal origin, such as raw manure and compost, people will have the chance to comment on it before it is finalized.

Ingram said that growers are rapidly becoming food-safety specialists, which he attributes in part to Food Safety Modernization Act activities.

“When you go visit a farm, you see that every farm is different,” he said. “FDA has been dedicating significant resources to understanding the complexity and variety of growing conditions and understanding grower concerns. Through stakeholder engagement, including educational farm visits, we are learning a lot and taking all of this information back home. We are making every effort to offer flexibility and feasible regulations that will help the farmers reduce the potential for foodborne pathogen contamination in their operations.”

But what about now?
So what’s a farmer to do in the meantime? Turns out that the FDA has some “indirect” advice on this. And it turns out that certified organic farmers were ahead of the game.

Samir Assar, director of FDA’s Division of Produce Safety, put it this way, when asked about minimizing the chance of contamination from raw manure: “ . . .  we believe it would be prudent for farmers to comply with the USDA’s National Organic Program’s standards related to raw-manure use while the research and risk assessment is ongoing.”

The standards call for a 120-day interval between the application of raw manure for crops in contact with the soil and 90 days for crops not in contact with the soil. And no waiting time will be required for properly prepared compost.

The California Farm Bureau took a similar tack in its comments about this: “History does not demonstrate a problem with the NOP’s 120-day interval; if it did, we would see a greater incidence of contamination in organic produce, which we do not. Given 15 years of following this standard without major problems, it is reasonable to assume, as numerous studies state, that this standard is suitable.”

Or as Michele Jay-Russell, microbiology researcher at University of California at Davis’s Western Center for Food Safety, said: “There’s no evidence that it isn’t working.”

However, she also said that there are still questions about whether the National Organic Program standards will work in all climates and with all farming practices and in all soil conditions, to name just some of the variables involved. And that’s why the USDA has funded a wide array of research projects in various parts of the country, some of which she’s participating in.

In the end, said Jay-Russell, “We’re hopeful that it (any future ruling on soil amendments) will fit the needs of public health and be flexible enough for farms.”

Anne Schwartz, an organic farming pioneer who farms in Western Washington, said that for organic farmers, raw manure is a good source of organic matter and fertility for the soil.

“It’s a wonderful tool,” she said.

She’s pleased that as part of FDA’s risk assessment that research on this will be conducted..

“Right now, the organic standards do seem reasonable,” she said. But I’m pleased to hear about the research that’s being done. It’s absolutely good for farmers to have solid information. They don’t want their customers to get sick.”

Food safety attorney Bill Marler said that following the NOP standards won’t protect farmers should someone become sick from eating produce from their farms.

“If the product makes someone sick, they could be sued,” he said, highlighting how important it is for farmers to be diligent about following food-safety practices throughout the entire growing, harvesting, packing, storing and transportation food chain.

Another tip: Farmers need to calculate the runoff risk of manure when applying it to their fields. Water quality is an important factor in this. Ditches leading to streams and rivers and/or irrigation systems could transport the pathogens to other locations that are growing crops. (Some state regulations don’t allow any runoff at all.)

Do plants take up bacteria?
In some of the comments about the original proposed time interval for raw manure to be applied to the soil before a crop can be harvested, several groups pointed to what they perceive as the danger of plants taking up bacteria and transporting them into the edible parts of the plants.

However, some research has shown that this doesn’t happen under realistic agronomic conditions in the field — that the bacteria goes no farther than the roots.

But Trevor Suslow, food safety specialist in the Department of Vegetable Crops at University of California-Davis said this isn’t a slam dunk — more research is needed.

“This is certainly true in the area of produce safety and applies to the polarizing views of the relevance of root uptake and systemic transport of human pathogens in crops such as lettuce. leafy greens, and tomatoes,” he said.

Stepping back from the issue of root uptake, Suslow said that the the FDA has been facilitating a lot of very needed and timely research of pathogen persistence in soils following application of untreated biological soil amendments of animal origin. This research will be presented in several technical sessions at the annual conference of the International Association for Food Protection, set for July 8-11 in Salt Lake City.

What about compost?
Simply put, compost is decayed organic matter. It can be made up of all sorts of “ingredients” — leaves, vegetable scraps, or unused garden or crop material. Compost can also be made from raw manure. It takes time and a certain amount of heat for all of these ingredients to break down into the final product.

According to the University of Minnesota Extension Service, soil that is regularly amended with compost becomes “wonderfully dark and crumbly and often requires much less fertilizer compared to soil that has not yet benefited from regular helpings of compost.” It is the heat generated during the composting process that kills such undesirables as weed seeds and pathogens.

The FDA provides for several ways to make properly “treated” compost from raw manure. The options require a certain amount of time and a certain amount of heat, both of which contribute to killing any harmful bacteria in the manure.

FDA’s Ingram pointed to another benefit of compost: It holds the nitrogen in the soil in a mineralized form, which means it is less susceptible to washing out of the soil during a rainfall or during irrigation events. Instead, it slowly leaches into the soil, enriching it over a period of time instead of all at once.

“Properly prepared compost can be a safe and effective soil amendment for any growing operation, and the benefits go beyond plant nutrient demand,” he said.

“Proper use of manure and compost is essential from both a production and environmental standpoint,” says the University of Minnesota Extension’s website.

Even so, fresh raw manure will generally have a higher N (nitrogen) content than compost. For some crops, an ample supply of nitrogen is essential for good yields.

Ingram said that during three summits held on soil science — two of them last year and one early this year — the term “soil health” came up frequently. He sees that as a good thing.

The summits were called, he said, “because we realized we’d need to have some sit-down sessions with the industry.” The events were so successful, in fact, that that other groups have even started to create some of their own.

Ingram also said that FDA is trying to figure out how to help growers move toward using treated biological soil amendments of animal origin, such as compost. But the biggest hurdle is the cost of transportation. How is all of the manure and compost going to be transported back and forth from the farm?

“That’s a big concern,” he said.

Is FDA trying to eliminate raw manure?
When FDA’s Samir Assar was asked if the FDA had already made up its mind that raw manure should not be used, he pointed out that the agency has already provided for certain ways that raw manure can be used as a soil amendment in compliance with the produce rule.

“There are important public health concerns that we have a responsibility to address,” he said, “but at the same time we recognize that the use of raw manure is an extremely complex and important issue. There are differing views and strong beliefs. We take those seriously.”

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