February 15, 2004 | General

Pathogens, Manure And Composting

Steven J. Scheuerell, Alex Cuyler and Nick Andrews
BioCycle February 2004, Vol. 45, No. 2, p. 38
Organic fruits, vegetables, seeds, milk, nuts and meat are found in almost every grocery store within the U.S. —  making the organic industry the fastest growing sector in agriculture. The USDA’s National Organic Standards (NOS) were established to assure consumers (e.g. the “USDA Organic” labels) that organic claims are certified by accredited agencies. The current National Organic Program (NOP) defines organic production as “a production system that integrates cultural, biological, and mechanical practices that foster cycling of resources, promote ecological balance, and conserve biodiversity.”
Organic growers meet these goals by relying on compost, manures and cover crops to serve crop fertility needs and to improve soil quality. The NOP final rule strictly defines how and when organic materials can be used in crop production, with particular emphasis placed on composted and noncomposted animal manures. As defined in the rule in the section on soil fertility and crop nutrient management, the producer must manage plant and animal materials to maintain or improve soil organic matter content in a manner that does not contribute to contamination of crops, soil, or water by plant nutrients, pathogenic organisms, heavy metals, or residues of prohibited substances. Animal and plant materials include: Raw manure must be composted unless it is: (1) Applied to land used for a crop not intended for human consumption; (2) Incorporated into the soil not less than 120 days prior to the harvest of a product whose edible portion has direct contact with the soil surface or soil particles; or (3)Incorporated into the soil not less than 90 days prior to the harvest of a product whose edible portion does not have direct contact with the soil surface or soil particles.
Under the rule, composted materials are to be produced through a process that established an initial C:N ratio of between 25:1 and 40:1; Maintains a temperature between 131°F and 170°F for three days using an in-vessel or static aerated pile system; or maintains a temperature of between 131°F and 170°F for 15 days using a windrow composting system during which period the materials must be turned a minimum of five times.
Immediately after the rules were released, industry professionals and researchers began to question the composting language and characterized it as too prescriptive and out of touch with contemporary knowledge of soil biology, pathogen survival, and farming practices. Farmers who had wanted a program that would officially distinguish their products from those produced through conventional practices considered not participating in the certification process. For many growers, this area of the rule is a departure from the manure management techniques they have relied upon for decades, and one that has driven some farmers to either abandon the use of manure or abandon the organic certification process.
Indeed, the National Organic Standards Board (NOSB) voiced its concern in April, 2002, that the NOP manure standards were overly prescriptive. Specifically, they outlined six areas of concern: C:N ratio is too narrow. Quality compost can be made with C:N ratios as low as 15:1 and up to 60:1; Requirement for turning compost in a windrow system five times is too prescriptive; Terms in-vessel, static aerated, windrow, and raw manure are not defined; Compost tea is not addressed; Vermicompost products are not addressed; and Manures that have been heat treated to eliminate pathogenic organisms without composting are not addressed.
Part of the debate is how and when organic farmers apply untreated or treated manure to their fields. It is well understood that animal manures are both boon and bane. Untreated manure has traditionally been valued for the crop nutrients and organic matter it contains and associated low processing cost compared to treating manure. However, it has long been recognized that depositing untreated manure directly onto the ground can spread a range of pollutants including weed seeds, microbial pathogens, antibiotics, hormones, salts, heavy metals, and organic chemicals.
The greatest direct threat to public health posed by untreated manure is transferring pathogenic bacteria, protozoa and viruses from livestock to human food crops, particularly fresh fruits and vegetables that do not undergo thermal processing before being consumed. The likelihood of contaminating food with pathogens from untreated manure is controlled by a great number of variables including pathogen concentrations, soil properties, elapsed time, farming practices, and plant type and architecture. Although there have been no documented cases of food borne illness caused by applying manure under Best Management Practices, the uncertainties involved in quantifying the associated food safety risk have led regulators to recommend either very long preharvest application intervals or treating manure to dramatically reduce populations of human pathogens before field application.
Manure harbors pathogenic bacteria and viruses that have been flushed from the intestines of warm-blooded mammals including E coli 0:157, listeria, Salmonella, and others. Indeed, over 75 million cases of food poisoning are reported in the United States each year, and sadly, death can occur from the unsanitary condition of food, food wares, and food handlers. Especially at risk are the very young, the elderly, and those with compromised immune systems.
The epidemiology of pathogens is still a topic of research, although several aspects are well-established. First, the overall number of pathogenic organisms that a person is exposed to correlates to the amount of risk. While it takes only several E coli cells to infect a person, it may take tens of thousands of cells of Salmonella in order to become ill. Second, pathogens must adhere to the intestine to become problematic. The availability of adhesion sites is driven by a person’s overall health. Those with a diversity of intestinal biota tend to remain unaffected by pathogens. The ability of pathogens to survive outside the intestine is poorly understood.
Studies are underway at Ohio State University, North Carolina State University, and within the USDA’s internal research arm to examine how pathogens survive in the environment. Studies of pathogen survival and destruction during composting have been well documented (BioCycle, Sept. 2002) and were instrumental in developing the EPA Part 503 regulations that biosolids composting operations must follow. In fact, the similarity between those regulations and the manure composting regulations in the NOP are immediately recognizable.
In June 2003, Oregon Tilth Inc., one of the oldest organic certification organizations in the country, and Oregon State University cosponsored a national summit titled Human Pathogens From Livestock Manure. It attracted over 80 participants from across the nation representing organic growers, organic dairy operators, compost tea makers, compost facility operators, vermicomposters, organic certification agencies, government agencies, scientists, consultants, extension agents, and educators. Summit speakers and participants discussed what is and is not known about how to manage human pathogens in livestock manure to prevent food safety risks when using manure either as an untreated soil amendment or after treatment by aging, heat processing, composting, vermicomposting, or making compost tea. Participants joined focus groups that addressed manure, processed manure, compost, vermicompost, or compost tea. Each focus group summarized key information on educating operators, regulators, and the public; stated how the current NOP standards could be more flexible; and identified gaps in research needed to quantify food safety risks under agronomic conditions.
At the summit, organic growers shared their frustrations over the impact that the composting and manure application standards have had on their operations. Growers had abandoned springtime grazing of cover crops to avoid leaving manure on fields that would be tilled, planted, and harvested that summer. Low-intensity, long-term composting of manures had to be replaced with higher cost, more mechanized systems. Some growers have switched to processed fish fertilizers, increasing cost and reducing local nutrient cycling. Summit participants expressed a desire to adopt regulations based on field studies done on organic farms, and felt the current regulations were generated from laboratory studies not relevant to their ecologically diverse, biologically dynamic soils.
The summit focus groups summarized a great deal of information, with several common themes across all groups. Preeminent was the notion that regulations should be based on the best available science that is carried out under organic field management conditions. There is a need to survey current farm practices to identify what levels of pathogen risk exist from manure and compost application in the field. Composting and livestock manure management standards should protect public health while providing flexibility for growers. Animal production separated from land-based manure decomposition can be a source of environmental problems; integrated farming systems that utilize livestock in proportion to the land’s capacity to process manure have ecological and economic benefits. There is a need for a Federally funded pathogen risk manure management model that incorporates variables such as type of manure, initial pathogen load, storage and handling practices, composting method, application rate, time of year, climate variables, soil type, soil moisture profile, soil management practices, and crop.
Following are key points directed to the NOP specifically related to manure, processed manure, compost, vermicompost, and compost tea. Proceedings from the summit are available at
Manure: The NOP could delegate some manure use regulations to the state to allow for varying climatic and field conditions in different regions. This increased flexibility could promote good agricultural practices while assuring food safety. Quantifying the pathogen risks to water and food crops from soil-applied manure under organic field conditions is needed. Research on plants internalizing pathogens through their roots from manure needs to be done in fields with manure applied at agronomic rates under agronomic conditions. If crop plants do internalize pathogens, which crops are of concern, what are the mechanisms, and how do we minimize this risk?
Processed Manure: Well-established and innovative manure processing methods should be evaluated for pathogen reduction potential. Processes that produce a product equivalent to Class A biosolids for pathogen content should be allowed without preharvest intervals. The processed manure standards recommended by the NOSB have not been adopted by the NOP. Processed manure should be defined as a fertilizer with certified nutrient analysis labeling.
Compost: There is a general concern that if NOP composting standards are too prescriptive they could lead to decreased use of recycled organic wastes, manure disposal problems and reduced soil fertility. Alternative, energy-efficient composting systems should be evaluated for pathogen reduction with reference to the 40 CFR Part 503.32 requirements. Growers would like these systems evaluated: passive (deep stack) composting for extended time periods; passively aerated windrows capped with pathogen free material that utilize pile porosity and perforated pipes; and forced aeration systems for on-farm use. However, given the current allowable practices, there is a need to educate growers and commercial producers of compost on compliant practices under the current NOP standards.
Vermicompost: Although worm castings are the product of worms, vermicompost should not be classified as raw manure in the organic standards. Currently this is not clear. When considering pathogen reduction issues, vermicomposting systems need to take into account feedstock pathogen loads, worm stocking density, worm species, feeding rate, temperature, moisture, and process time. Research is needed that clearly identifies the mechanisms of pathogen reduction inside worms and how this can be optimized during vermicomposting. The U.S. EPA is evaluating existing data on pathogen reduction during vermiculture; the NOP could adopt any PFRP’s that are approved by the US EPA for production of class A biosolids as an organically approved practice.
Compost Tea: At the summit growers asked: What kinds of compost tea are NOP compliant? Does the NOP support the use of NOP compliant compost when making compost tea that will be applied less than 120 days before harvest? Is this affected by the addition of nutrients (i.e. molasses) during compost tea production? The production and use of compost tea is currently in limbo for certified organic producers; conventional growers are not regulated in their use of compost tea. The major concern is adding nutrients to allow bacteria to multiply during compost tea production. If pathogen contaminated compost is used, pathogenic bacteria can multiply alongside beneficial bacteria during compost tea production. Fast, accurate diagnostic kits are not yet available to test compost tea before use. Growers want to know even if a problem existed, how long would pathogens survive once sprayed and what preharvest interval would provide a safe solution? Again, a lack of data on pathogen behavior under agronomic conditions hasn’t allowed a scientifically based decision to be made. Pathogen survival is greatly affected by climatic conditions and plant architecture. For example, lettuce is much more of a concern than storage onions. These issues are currently being investigated by the NOSB Compost Tea Task Force, with a recommendation to the full NOSB expected by March or April of 2004.
Regardless of how the current NOP regulations might change over time, both commercial and on-farm composters need to understand the NOP composting regulations and document their composting process in order to use or sell compost in organic production systems. On-farm composters hope that sufficient federal resources become available to scientifically evaluate alternative composting processes that meet the needs of growers and satisfy pathogen reduction requirements.
The NOP has a difficult balancing act trying to meet food safety issues and the numerous needs of diverse organic farming operations. At the same time, consumers need to be aware that all fruits and vegetables (organic and nonorganic) should be washed prior to consumption because in spite of the NOP, there are many opportunities for exposure to pathogens between the time these food items leave the field and reach the table. The organic community is proud of their excellent food safety track record and want to keep it that way. They also raise the question that if the NOP composting and manure management regulations are necessary for food safety, why aren’t the same requirements placed on conventional growers? If organic food production has a higher production standard with regard to preharvest food safety issues, then should organic producers be allowed to make superior food safety claims?
As the NOP continues to mature, the role of manure management, composting, and added value products such as compost tea will continue to evolve as well. The market for NOP approved soil amendments will continue to grow. To take advantage of this growing market, manure managers and composters will need to stay educated on issues related to food safety and the microbiological quality of soil amendments.
Steven Scheurell is a Faculty Research Associate in the Department of Botany and Plant Pathology at Oregon State University; Alex Cuyler is Chair of the Association of Oregon Recyclers. Nick Andrews is with Oregon Tilth, Inc. and will be presenting the Summit Findings on “Pathogens in Livestock Manure,” at the BioCycle West Coast Conference in Portland, Oregon March 5-7, 2004.

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