Manure & Nutrient Management Programs

Manure is a valuable source of plant nutrients but also a potential pollutant. Proper management of nutrients from commercial fertilizers and organic sources is important to protect our environment and to have economically and environmentally sustainable livestock operations. NIFA works with government agencies and commodity and public organizations that conduct research and carry out extension and education programs to manage manure and plant nutrients.

General Information

Animal production has the potential to negatively affect surface water quality (from pathogens, phosphorus, ammonia, and organic matter); ground water quality (from nitrate); soil quality (from soluble salts, copper, arsenic, and zinc); and air quality (from odors, dust, pests, and aerial pathogens). Manure and other byproducts of animal production, if not carefully managed, will have a significant negative impact on the environment. Agricultural production has been identified by the U.S. Environmental Protection Agency (EPA) as the largest single contributor to water quality impairment for rivers and lakes.

In addition to manures, commercial fertilizers, other waste products, plant residues, and green manures applied to the land can contribute to environmental problems because of excess nutrients, both at the site of application and in surface and ground waters. Nutrients from all sources need to be accounted for and managed in any production system to sustain our farms and protect the environment. Some problems can arise hundreds of miles from these sources. For instance, excessive use of nitrogen fertilizers in the Mississippi and Missouri river basins is thought to be the major cause of the hypoxia problem in the Gulf of Mexico. Although nitrogen and phosphorus are the major environmental offenders, poorly managed fertilizers, wastes, and organic materials can lead to a buildup of nutrients as salts, and the release of toxic compounds such as sulfides and sulfites, boron and selenium salts, and heavy metals. Non-nutrients, such as arsenic, lead, and mercury, can also come from fertilizers and manures.

Animal manures can also be a source of pathogens, antibiotics, and other bioactive compounds such as endocrine disruptors (estrogens). NIFA supports research, education, and extension activities to study, develop, and promote the best management strategies to reduce or eliminate these potentially harmful compounds and pathogens; to prevent their movement into surface and ground waters, onto food products, and into the air; and to determine risks, mechanisms, and processes for their dissemination, proliferation, and control in the environment.

For centuries, animal manure has been recognized as an excellent source of plant nutrients and as a soil "builder" because of its contributions to improving soil quality. When compared to more conventional fertilizer, manure properly applied to land has the potential to provide environmental benefits, including: reduced nitrate leaching; reduced soil erosion and runoff; increased soil carbon and reduced atmospheric carbon levels; reduced energy demands for natural gas intensive nitrogen fertilizers; reduced demand for commercial phosphorus fertilizer, which is a limited resource; and improved productivity of cropping systems.

Manure contains most elements required for plant growth including nitrogen (N), phosphorus (P), potassium (K), and micronutrients. But, it is manure's unique combination of these nutrients with organic carbon that provides its value to crop production and the environment.

First, manure N is more stable than N applied as commercial fertilizer. A significant fraction of manure N is stored in an organic form that is slowly released as soils warm. Commercial fertilizer N is applied in either a nitrate or an ammonium (easily converted to nitrate) form. Nitrate-N is very soluble and mobile and, early in the growing season, it contributes to leaching during excess precipitation or irrigation. Manure N's slow transformation to crop available forms is better timed to crop N needs, resulting in less leaching potential. 

In addition, some manure N is released very slowly, often not becoming available until the second or third year after application, thus providing long-term benefits. High soil organic matter content is considered a measure of a productive soil. Most nutrients that enter the plant root zone are involved in a range of microbial processes during their conversion to plant-available forms. Manure's organic carbon provides the energy source for the active, healthy soil microbial environment that both stabilizes nutrient sources and makes those nutrients available to crops. 

Tilling the soil and harvesting grain and other crops have reduced the organic carbon content of soils. Soil organic content has declined by an estimated 50 percent to 70 percent in the Midwest during the past 150 years. Several long-term manure application studies have illustrated manure's ability to reverse the trend or return soil organic levels back to their original level before cultivation. In addition to the value of soil organic carbon from a nutrient perspective, manure contributes to improved soil structure, which contributes to improved water infiltration and greater water-holding capacity, benefiting crop water stress, soil erosion, and nutrient retention. An extensive review of the literature and historical soil conservation experiment station data at selected locations around the United States suggested that manure produced substantial reductions in soil erosion (between 13 and 77 percent) and runoff (between 1 and 68 percent). Increased manure application rates produced greater reductions in soil erosion and runoff. During years when manure was not applied, a residual benefit of past manure application was noted.

The following research problems areas have been compiled by NIFA faculty who are part of the Animal Waste Working Group and various other state and federal sources, including the various commodity organizations. 


Dead animals (mortalities) are a normal part of any livestock or poultry operation. Problem areas for investigation include possible effects of age and size for processing of dead livestock (dairy, beef, and swine) and poultry production and processing; treatment technologies to safely dispose of dead animals to prevent the spread of diseases; development of treatment technologies to prevent air, soil, or water pollution; recovery of value-added products; and storage techniques.


Processing of the manure to produce a material that has added benefits, both economically and environmentally, will help the animal production industry. Problem areas for investigation include: composted material for use as a soil amendment; combining animal production and processing of waste with other organic wastes to produce a value-added product; processing of animal manures as a feed ingredient; anaerobic digestion to produce fuel (methane), amino acids, and other feed ingredients from animal manures; and production of pharmaceuticals.


Surface and ground water quality can be affected by improper storage, transport, and use of animal manures. Problem areas for investigation include: preventing runoff of land applied manure from entering surface water supplies, infiltration of water containing pollutants reaching ground water supplies, chemical and physical mechanisms for operation of filter strips and buffer strips, modeling movement of manure nutrients in soil, tillage practices to reduce the transfer of manure nutrients to surface or ground waters, cropping practices to minimize water pollution, pre-treatment processes of animal manures to reduce potential for water contamination, and treatment of animal manures to allow direct stream discharge as in municipal facilities. 


Problem areas for investigation include: health effects of odors, gases, and particulates on confined animals and workers in confined facilities; health effects of odors, gases, and particulates on persons living near animal confinement facilities; psychological effects of odors on farm workers and neighbors; development of standards for odor measurements; model atmospheric deposition of the various forms of nitrogen; chemical and biological methods that will control the generation of odors and gases; air dispersion models for gases; mechanisms to control odors and particulates that are discharged from exhaust air of animal confinement facilities; modification of animal feeds to reduce the dust emissions from these feeds; determination of the mechanisms whereby dust particles absorb odors; spatial and construction techniques in building design to reduce the production of odors; treatment techniques to reduce odors and gases from lagoons or storage structures; and techniques to reduce odors and gases from land-applied agricultural wastewaters.


Problem areas for investigation include: mechanisms by which enzymes will allow livestock and poultry to better use the nutrients in the feed; principles for developing grains and forages that will reduce nutrient content of the manure, genetic potential of livestock and poultry for reducing manure output (better feed utilization efficiency), processes that will reduce the nitrogen and phosphorus content of manure, determination of the appropriate crude and equivalent protein content of feeds that will allow efficient animal growth and reduction of the pollution potential of the manure, reduction of the use of feed supplements, re-evaluating current dietary need for species and phase feeding to reduce output, principles for altering livestock and poultry diets that will reduce the odor potential of manure, and factors for processing manures so they may be used safely as an animal feed.


Problem areas for investigation include: effects of handling, storage, and application systems on the nutrient content of manure; estimation of nutrient availability; processes by which manure affects soil physical, chemical, and biological properties; mechanisms by which manure affects crops; economics of manure as a nutrient source; processes that modulate runoff control measures; potential for ground water contamination; and development of crops that use manure nutrients more effectively.


Mechanical, biological, and chemical treatment technologies need to be developed to reduce the pollution potential of animal manures. Problem areas for investigation include: processes to increase the effectiveness of lagoons for waste treatment, principles of aeration for odor control, anaerobic digestion of solids and liquids, cost-efficient methane production, composting, aerobic and anaerobic treatment to control nitrogen losses to the atmosphere, liquid-solid separation as a treatment technology, and mechanisms by which animal wastes can bio-remediate hazardous wastes. 


One of the potential sources of pathogens is animal manures. Some of the organisms that are of concern include: Escherichia coli, Salmonella, Giardia, Campylobacter, and Cryptosporidium parvum. Problem areas for investigation include: survival rate of organisms under various environmental conditions (time, temperature, and moisture); mechanisms of transmission from animal to animal, animal to man, and man to animal; technologies and practices to reduce pathogen transmission; mechanisms of survival; and movement of pathogens in soil and water. There is the potential for the transmission of antimicrobial resistant pathogens or resistance genes in the environment from animals to humans and humans to animals.


Problem areas for investigation include: characterization of social interactions within a community regarding the effect of concentrated animal feeding operations, economic factors of large- and small-scale animal production for rural communities, processes for developing regulations based on the social and scientific factors, how public perception is formed regarding animal production, fairness and consistency of regulation enforcement, and role of local communities in establishing regulations. 


Problem areas for investigation include: economic impact of regulations; economics of small, medium, and large operations; economic considerations when deciding to focus on regulations for animal agriculture versus a comprehensive approach to pollution problems; determining the economic value of air, water, and soil in determining the costs for implementing waste management practices; role of local, state, or federal policies as they affect the economics of waste management; public financing for installing environmental practices; and determining the costs for various treatment practices.



Program Type: 
Grant Program


External Resources

Related Information

Water, Soil