Manure Management Strategies for Limiting Antibiotic Runoff

Manure Management Strategies for Limiting Antibiotic Runoff

Author: Reagan Uhlmann, UNL Senior, Biological Systems Engineering, University of Nebraska-Lincoln

It is important that farmers and agriculturalists implement practices to reduce the runoff of antibiotics.

Just as people take antibiotics when sick with a bacterial infection, antibiotics are an important tool in livestock production to treat bacterial infections in animals. Concerns do exist, though, about the fate of these compounds and their metabolites in the environment. Approximately 75% of the antibiotics an animal consumes ends up in the manure (Beecher 2018). Although antibiotics themselves do not pose a risk to people or the environment, large amounts of antibiotics have resulted in the development of antibiotics resistant genes which are immune to antibiotics medicine. It should be noted that the relationship of drug-resistant bacteria in people to antibiotic use in livestock is still a highly debated topic.  

This article is written by a University of Nebraska-Lincoln student, Reagan Uhlmann, as part of an Animal Manure Management class in Biological Systems Engineering. It has been reviewed by experts to encourage accuracy of issues presented. The article represents the student’s understanding of the subject addressed at this stage in his career. Rick Koelsch, faculty instructor.

Because livestock manure is often used as a fertilizer input on neighboring cropland, it is important that farmers and manure managers understand the potential risks associated with antibiotic compounds. This includes knowing how to manage land-applied manure to reduce persistence of antibiotic compounds and losses of these compounds via runoff. The potential risks of antibiotic compounds in livestock manure may be addressed in three ways: manure treatment prior to land application, implementation of conservation practices within manure-amended fields, and the limitation of antibiotic consumption. It should be noted that antibiotic runoff is not currently regulated. However, there are regulations implemented by the U.S. Food and Drug Administration that regulate antibiotics fed to animals.   


Manure Treatment via Composting

One method of treatment is to treat the manure before it reaches the field. One way the manure can be treated is by heating the manure. Heating the manure kills the bacteria and reduces the concentration of antibiotics. Composting is one effective way of heating the manure. Composting typically heats the manure up to 60°C which is the ideal temperature for destroying most bacteria. Composting the manure is more effective in antibiotic reduction when the manure is composted over a longer period of time. Not only does composting limit the efficiency of antibiotics, it is also effective in killing harmful pathogens. The survival period of pathogens is dependent on several different characteristics including moisture content and the carbon to nitrogen ratio of the manure. Since the type of antibiotics and pathogens vary so does the amount of time it takes to destroy them. However, for the highest efficiency in activating antibiotics it is recommended that the manure be composted for up to 15 days with at least 5 turns (Martin 2015). Although this is the procedure for the highest efficiency, there are several methods of composting that are successful in limiting antibiotic concentration.


Aerobic Treatment of Manure

Because most antibiotic compounds degrade faster in the presence of oxygen (aerobic environment) than in environments where oxygen is limited (anaerobic conditions), another way of reducing antibiotic efficiency is to use manure treatment processes that are aerobic. Surface aerators or mixers are two options for aerobic manure treatment, but there are many different types of equipment and methods that can be used. A disadvantage to aerobic treatment is that it can have a high initial cost and high operating cost. However, there are several advantages to aerobic treatment other than the destruction of antibiotics. These include the potential reduction of odor, methane, and ammonia. Each antibiotic varies in properties, but overall heat treatment and aerobic processes have been found to decrease the antibiotic activity to safe levels (Thiele‐Bruhn 2003). 


Conservation Practices for Manure-Amended Fields
Conservation practices reduce antibiotic movement to surface waters.  From:  “Manure Phosphorus and Surface Water Protection III: Transport” (Photo by Bahman Eghball)
Conservation practices reduce antibiotic movement to surface waters. From: “Manure Phosphorus and Surface Water Protection III: Transport” (Photo by Bahman Eghball)

 Runoff of antibiotics can also be limited through conservation practices within the fields. Leaching of antibiotics is also an issue, but only runoff transport is addressed in the following conservation practices. One conservation practice is to add vegetative barriers or grass “filter strips” around the edges of fields. These are designed to act as a barrier between the field and bodies of water that may receive surface water runoff from the field.

 Another practice that can be utilized is no-till compared to tilling. No-till practices have been found to increase microbiological activity which helps destroy antibiotics. They also reduce runoff which can include runoff containing antibiotics.

 Manure is better absorbed by the soil and produces less runoff when the soil is warm and dry. Likewise, when manure is applied to saturated and frozen soil it results in larger amounts of runoff. Therefore, application should be limited from the months of November through March when the ground is the coldest. Best Application Tips for Winter Application provides additional ideas to reduce winter application risks. 

 These conservation practices are helpful in reducing runoff of antibiotics, however there are still many types of antibiotics that leach into the soil instead. When antibiotics leach into the soil they are much harder to control. Research has found that there is no correlation between the type of manure application (incorporated, injected, etc.) and antibiotic runoff (Thiele‐Bruhn 2003).


Limiting the Consumption of Antibiotics

 Another way to limit antibiotic runoff is to limit the amount of antibiotics that are initially consumed. Antibiotics end up in manure when they are not fully utilized by the animal, or when the animal is fed an excess amount. By limiting the amount of antibiotics that are fed to animals, it can limit the amount of antibiotics the animal excretes. The U.S. Food and Drug Administration (FDA) has already implemented regulations to limit the consumption of antibiotics. Antibiotics intended for animal feeds are labeled as veterinary feed directive drugs (VFD) and can only be administered by veterinarians. Farmers can help limit antibiotic runoff by only feeding their animals the prescribed amount of antibiotics. If there are ever extra antibiotics, or antibiotics that need to be disposed, they should be dropped off at a medicine take-back site. Take-back sites can either be temporary locations set up nationwide by the U.S. Drug Enforcement Administration or permanent collection sites.


Why is limiting antibiotic runoff important?
Research has found that long-term use of antibiotics promotes the development of antibiotic resistant genes.

Research has found that long-term use of antibiotics promotes the development of antibiotic resistant genes.

The antibiotics from animals can be absorbed by the crops or end up in drinking water. This is due to the manure running off into nearby streams and bodies of waters. Although some antibiotics are due to runoff from livestock industry, there are also issues with misuse or overuse within the human population. The antibiotics are dangerous because they create an environment that allows for an increase in the amount of antibiotic resistant bacteria (ARB). These bacteria are dangerous because they are immune to the medicine that should affect them. Research has found that the long-term use of an antibiotic can promote the development of antibiotic resistant bacteria (“General Background: About Antibiotic Resistance” 2014). Although there is a correlation between antibiotic resistant bacteria and antibiotic consumption, there is no correlation between amount of antibiotics in soil and amount of antibiotic resistant bacteria. Research has shown that antibiotic resistant bacteria occur naturally in the soil and vary based on the environment. Researchers have still not been able to find a link between human and agricultural activity and antibiotic resistant bacteria in the environment. Therefore, the main concern with antibiotics and antibiotic resistant bacteria is potential human consumption due to runoff or leaching. A land grant university group summarizing the current science on antibiotic use in livestock and resistance can be followed at



All antibiotics vary in composition which makes them harder to regulate. However, research has shown that both heat treatment and aerobic processes have been successful in decreasing antibiotic activity. Farmers should be aware of the antibiotics fed to their animals. This is vital in discovering the most efficient way to limit antibiotic runoff. Overall, there are still a lot of questions about antibiotics and antibiotic resistant genes that scientists have not been able to answer. As antibiotic resistant genes continue to be a growing concern, so does the runoff of antibiotics.



Beecher, Cookson. “Managing 'Black Gold': Animal Manure and Antibiotic Resistance.” Food Safety News, 31 July 2018,

“General Background: About Antibiotic Resistance.” Index of /, 2014,

“Inactivation of Antibiotics by Heating in Foods and Other Substrates - A Review.” Journal of Food Protection. 1987 July 30.

Kumar, K, et al. “Antibiotic Uptake by Plants from Soil Fertilized with Animal Manure.” Journal of Environmental Quality., U.S. National Library of Medicine, 12 Oct. 2005.

Martin, Hugh. “Manure Composting as a Pathogen Reduction Strategy.” Ministry of Agriculture, Food, and Rural Affairs. Aug. 2015.

Soren, Thiele-Bruhn. “Pharmaceutical antibiotic compounds in soils- a review.” Journal of Plant Nutrition and Soil Science. 22 April 2003.

Wortmann, Charles, et al. “Manure Phosphorus and Surface Water Protection III: Transport >Factors.” Plant and Soil Sciences E Library: Print Lesson, 2005.


Other Sources for Further Reading: 


Temporary locations on National Drug Take Back Days

 DEA Permanent Drop-Off Locations


This article was reviewed by Mara Zelt, Graduate Student and Extension Assistant; Amy Schmidt, UNL Extension Specialists

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