A Focus on Animal Manure Management

On this page... General Facts about Animal Manure Management Research Needs for Effective Manure Management Resources Animal manure is a food safety concern because of the negative impact it can pose to the environment and public health. If not properly contained or treated, it can lead to waterborne and foodborne illnesses. Waterborne illness may result when contaminated water reaches water municipal systems or is used for crop irrigation and produce washing. Foodborne illness can occur when improperly aged or treated manure is used as fertilizer on fresh fruits and vegetables. Effective management strategies must be developed and tested to limit and prevent microbial risk from animal manure. Pathogens targeted for immediate attention for animal manure are: Cryptosporidium parvum, Salmonella spp., Campylobacter jejuni/coli, and Escherichia coli O157:H7 and other strains. A mission of USDA Agricultural Research Service is to develop manure management strategies and treatment technologies that effectively handle, store, and apply animal manure in agricultural production systems while preventing the microbial contamination of food and water. The ARS National Program 108 Food Safety includes research on animal manure management and prevention of pathogen transmission to food and water. ARS has also incorporated a pathogen research component into National Program 206 Manure and Byproduct Utilization. Research Needs for Effective Manure Management ARS research in animal manure management is divided into five categories: Pathogen Detection, Loading Rates and Survival, Transport and Dissemination, Treatment Technologies, and Risk Assessment. Pathogen Detection research objectives include: Develop methods for sensitive detection and accurate quantitation of pathogens in manure and soil. Develop methods to separate, detect and identify pathogens encountered in environmental matrices such as manure, and soil. Develop new techniques and adapt existing techniques for the detection of pathogens in a manure and soil environment. Standardize sampling and detection techniques for each pathogen in environmental matrices encountered in agriculture for study comparison. Develop sensors (biological, chemical, molecular) for the rapid detection of pathogens in agricultural systems. Loading Rates and Survival research objectives include: Monitor and track the prevalence of pathogens in manure and the life cycle of pathogen transmission from manure to soil and to fruit and vegetable crops. Determine the survival and proliferation characteristics of pathogens in manure and crop environments in order to assess the extent of risk to human health. Determine effectiveness/adequacy of various manure management techniques and the effects it has on reduction of pathogens. Understand the effect of manure composition on pathogen survival upon storage or on soil applications. Determine the role of biofilm formation by pathogens on plants, plant residues, and soil particles on the survival of pathogens originating from fresh and treated manure. Discover what protectants in manure, composts or soils affect pathogen survival. Transport and Disseminationresearch objectives include: Assess effectiveness of agricultural management practices: vegetative buffer strips, riparian zones, and wetlands to intercept the pathogens. Define the technical requirements in using these practices in order to maximize efficacy. Assess the role of wildlife/insect vectors. Identify environmental parameters that impact pathogen transport (soil type, topography, cover crop, tillage, rain fall). Treatment Technologies research objectives include: Determine the effectiveness and rates of pathogen destruction for existing treatment technologies. Determine how environmental factors and manure type affect pathogen destruction rates of various treatments. Develop new methods to handle and treat animal manure during production prior to land use in order to prevent transmission to soil and crops used for human food. Develop process quality criteria guidelines for various pathogen reduction treatments. Develop quality control tests to assess each treatment. Determine useful indicator or surrogate organisms for assessing reduction strategies. Determine which treatment techniques are most cost-effective in reducing the concentration of viable pathogens and parasites form manure prior to land application. Risk Assessment research objectives include: Establish quantitative and human health assessment endpoints in order to evaluate the effectiveness of treatment strategies. Evaluate manure management strategies using a risk assessment process to determine the potential exposure and harm to human health. The USDA/ARS is working to develop manure management strategies and treatment technologies to effectively handle, store, and apply animal manure in agricultural production systems while preventing contamination of food and water supply by pathogens. A focus on key research areas will allow the USDA to develop new or existing methods of pathogen detection, treatment technologies, and assessment; as well as obtain new data and information in these areas. There is a need to increase knowledge and develop new technology and methodology in the following research areas: Pathogen Detection Many techniques have been developed for pathogen detection in a clinical setting or food laboratory, but are not applicable in the complex chemical environment of soil and manure. Detection is hindered by similarities between pathogenic and non-pathogenic strains of bacteria of the same species. For example, non-pathogenic strains of E. coli, found naturally in the digestive tracts of animals and humans, inhibit the detection of the human pathogen, E.coli O157:H7. Current molecular detection techniques such as DNA sequencing cannot be applied in a complex chemical environment of manure and soil. Pathogen survival in manure also needs further investigation. in manure. Loading Rate and Survival Increase data regarding: The extent to which manure is contaminated with a particular pathogen at a specific time. The relationship of pathogen survival to different microbial loads. The survival characteristics of Cryptosporidium parvum oocysts survival in soil. Transport and Dissemination Increase knowledge about: Pathogen dissemination in the farm environment in order to break cycles of animal re-infection and manure contamination. Physical transport routes and potential vectors (birds, insects, surface water, rodents) as modes of contamination. Treatment Technologies Increase knowledge regarding: The effectiveness of pathogen reduction treatment technologies. Previous treatment systems were more concerned with nutrient stabilization, volume reduction and storage. The effectiveness of other existing manure management techniques. Critical control points for manure treatment and application in vegetable crop production currently do not exist. Operational guidelines for current manure treatments which currently do not exist. Pathogen reduction data in order to meet reduction objectives for different volumes of manure. Risk Assessment Develop risk assessment methods which currently do not exist. Develop environmental or human health assessment endpoints, which do not exist. Back to top General Facts about Animal Manure Management Animal manure is recycled and utilized as a natural fertilizer, providing nutrients to soil and crops. Pathogen reduction is a major component of manure containment, treatment and application procedures. In the past, it was secondary to nutrient stabilization, volume reduction, and storage. The large volumes of animal manure generated on livestock feedlots, dairy barns, and other areas of highly concentrated wastes is a concern because of the risk of food-borne and water-borne transmission of bacterial pathogens and parasites to humans. In the farm environment, direct and indirect pathways of pathogen transport from manure to food and water exist. The level of risk that these vectors impose on human health is unknown. The application of raw manure to soil growing fresh produce is a direct route of contamination. Surface water that supplies municipal systems or is used for crop irrigation can be indirectly polluted by runoff to farm ponds, streams and reservoirs. Vectoring by insects, birds, and wildlife is another indirect transport route. For example, wild geese may ingest Cryptosporidium parvum oocysts that are still viable when excreted. The level of risk that vectors impose on human health is unknown. The Federal Food Safety Initiative Consortium has targeted the following pathogens for immediate attention Salmonella spp.; Campylobacter jejuni/coli; Escherichia coli O157:H7 and other strains; and Cryptosporidium parvum. Water-borne transmission of Cryptosporidium parvum is a concern because the parasite can remain viable for months in natural waters and is resistant to many disinfectants. Food-borne transmission of bacterial pathogens that can colonize within food (i.e. wounds to food surface) or within surface biofilms are also of particular concern. Fresh produce is often contaminated by improperly treated manure used as fertilizer or by manure-contaminated irrigation water. Re-colonization or cycling pathogens back to farm animals or animal feed is also a consequence of inadequate pathogen reduction treatments to animal manure. Manure treatments available include both active and passive processes. Passive processes are deep stacking, stockpiling, drying, and storage lagoons. Active treatments are composting, heat drying, digestion, aerated lagoons, and constructed wetlands. Animal feedlots can be a large source of runoff. The EPA regulates the management of such waste contributing areas, known as Concentrated Animal Feeding Operations (CAFOs), in order to minimize water contamination. To reduce runoff of pathogens to surface water some proposed agricultural management practices include vegetative buffer strips, riparian zones, and constructed or natural wetlands. Back to top Resources Manure and Byproduct Action Plan: Component III: Pathogens (USDA/ARS) Food Safety Begins on the Farm: A Grower’s Guide Good Agricultural Practices for Fresh Fruits and Vegetables (Cornell University) Prevention of Zoonotic Pathogen Transmission from Animal Manure to Human Food (USDA/ARS) The Guide to Minimize Microbial Food Safety Hazards for Fresh Fruits and Vegetables In Brief (U.S. Food and Drug Administration and Center for Food Safety and Applied Nutrition) Photos from the Iowa Manure Management Action Group (IMMAG) Back to top

This document was created by Tara Smith. Users are encouraged to provide feedback and comments. This document was created in Jun 2002; Updated in Dec 2005