You are here

Manure Management on Commercial Layer Operations: Environmental Concerns

Publication Number: P3724
View as PDF: P3724.pdf

Control of ammonia volatilization in poultry houses is a major concern for the poultry industry (Timmons and Harter-Dennis, 2011). Ammonia (NH3) is the major pollutant gas associated with poultry production operations. Bird feces contain uric acid that can be rapidly converted to NH3 in the presence of appropriate microbes (Xin et al., 2011). Ammonia emission is environmentally important because it contributes to the acidification of soil and water and increases nitrogen deposition in ecosystems (Liang et al., 2005).

Excessive NH3 in poultry houses is detrimental to bird performance and welfare. Ammonia generation is largely influenced by nitrogen (N) content in the manure. How that manure is managed in laying hen houses can greatly influence NH3 emission. High-rise (HR) and manure-belt (MB) houses are the two most common housing styles in the egg industry in the U.S. In HR houses, solid manure is stored in the lower level of the building for perhaps a year before removal (Liang et al., 2005). Manure in MB houses drops onto a belt beneath each row of cages and is removed daily or perhaps weekly.

Ammonia’s threat to air quality is not the poultry industry’s only environmental challenge. There is growing concern that land application of manure may pollute both surface and groundwater. Water quality may also be at risk if manure application is mishandled.

In addition, widespread use of antibiotics in animal husbandry has resulted in much concern over antibiotic resistance genes (ARGs). Conventional manure management practices do not completely remove ARGs, resulting in their release to soil and water environments when manure is land applied.

It is critical that producers follow best management practices related to storage and land application of manure to protect not only the environment but also their way of life.

Ammonia Concerns

The common NH3 level recommended for U.S. poultry houses is 25 ppm or less (UEP, 2017). Serious consequences can result from elevated levels of atmospheric NH3 in poultry houses, including:

  • reduced feed intake and growth rate (Carlile, 1984; Charles and Payne, 1966a; Deaton et al., 1984)
  • decreased egg production (Charles and Payne, 1966b)
  • damage to the respiratory tract (Nagaraja et al., 1983)
  • increased air sacculitis (Oyetunde et al., 1978)
  • increase in Mycoplasma gallisepticum (Sato et al., 1973)
  • increase in keratoconjunctivitis (Faddoul and Ringrose, 1950)
  • increase in Newcastle disease susceptibility (Anderson et al., 1964)

Ammonia is an environmental concern because it can enhance acid rain (Xin et al., 2011). Once ammonia is emitted to the environment, it can contribute to the formation of fine particulate matter (PM2.5) that may cause respiratory illness in humans (Fierro, 2000) and contribute to problematic environmental issues, such as an increase in atmospheric haze (ApSimon et al., 1987; NRC, 2003). Based on the sum of nitrogen from manure, eggs, and carcasses, approximately 40 percent of feed N input can be lost to the atmosphere as NH3 (Patterson and Lorenz, 1996). Typical nitrogen losses between excretion and land application for poultry manure stored in deep pits is 25 to 50 percent (MWPS, 1985).

Liang et al (2005) reported NH3 emission for HR houses in Iowa and Pennsylvania reached 317 grams NH3 per hen per year (0.87 gram NH3 per hen per day) for hens fed a standard industry diet and 296 grams NH3 per hen per year (0.81 gram NH3 per hen per day) for hens fed a diet with 1 percent lower crude protein. Ammonia concentrations and emission rates of MB houses were lower than those of HR houses. The frequency of manure removal in MB houses affects NH3 concentration and emission rate. Semi-weekly removal emitted 74 percent more NH3 than daily removal.

In addition to NH3, poultry operations can also be a source of greenhouse gases (GHGs), although poultry’s contributions are much less than those of ruminant animals. The GHGs of greatest concern are carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). The danger to the atmosphere (the global warming potential or GWP) of a GHG is determined by an index that is used to compare a specific gas to a reference gas (usually CO2) in terms of its ability to trap outgoing thermal infrared radiation (Xin et al., 2011). Methane and nitrous oxide have a global warming potential of 23 and 296 times that of carbon dioxide, respectively, making them important in any discussion on climate change, even though their concentrations in the atmosphere are less than 1/100 of that of CO2 (IPPC, 2007).

Poultry and livestock operations are unique facilities. Production and emission of gases and particulate matter depend on a series of complex physical, chemical, and biological processes. Emission rate is influenced by a variety of factors that include diet composition and conversion efficiencies, manure handling practices, and environmental conditions (Xin et al., 2011). Diet composition and the efficiency of its conversion to eggs affect the quantity and physical and chemical properties of layer manure; as do handling practices and environmental conditions (Xin et al., 2011).

Dietary modification offers an effective means to lower NH3 emissions by reducing excessive nitrogen excretion or manure pH without adversely affecting egg production (Xin et al., 2011). Including high-fiber ingredients (e.g., DDGS, wheat mids, soybean hulls) in laying hen diets can lower ammonia emission from manure with no adverse effect on egg production (Roberts et al., 2007a, b). A nutritionally balanced diet with 1 percent lower-than-standard crude protein content can lead to roughly a 10 percent decrease in annual NH3 emission while maintaining hen performance (Liang et al., 2005).

Repeated applications of poultry manure to cropland have the potential to improve soil health characteristics such as soil organic matter and soil fertility (Lin et al., 2018). However, manure applications to cropland have not always resulted in improved soil health indicators (Clark et al., 2017), partially because of difficulties in assessing soil health in short-term studies because of the complex and dynamic nature of soil nitrogen and organic matter. While agronomic benefits are well established, the environmental impacts of poultry manure management have primarily focused on water quality (Harmel et al., 2009; Vervoort et al., 1998).

Effects on Water Quality

Lorimor and Xin (1999) monitored four commercial HR layer houses in Iowa for a year to determine manure production and nutrient concentration characteristics. Manure production was 10.5 tons per 1,000 birds per year at an average moisture content of 41 percent on an “as is” basis. When manure production was combined with nutrient concentrations, the measured nutrient production was shown to be 385-867-551 (N-P2O5-K2O) pounds per 1,000 birds per year. The manure handling system was found to play a significant role in manure moisture content. Manure that was allowed to stay on boards beneath the cages for a period before being moved to storage was significantly drier than manure that dropped directly into storage.

There is concern that land application of manure will pollute both ground and surface water. This has led to increasing demands for more precise manure handling practices to prevent environmental damage resulting from overapplication of manure nutrients. Hen manure is an excellent organic fertilizer, but it does have the disadvantage of a low nitrogen to phosphorus (N:P) ratio. Adding to the problem is that plants require approximately eight times more N than P. Therefore, if poultry manure is applied based on N needs of the crop (as it often is), P is overapplied (Sims et al., 2000; Hoover et al., 2019). This can result in increased soil P levels and lead to P runoff (Pote et al., 1996). P concentrations in runoff water can be high after poultry manure application, even when soil test P levels are low (Edwards and Daniel, 1992, 1993; Moore et al., 2000).

Eutrophication is the biggest water quality problem facing U.S. surface waters (EPA, 1996). Eutrophication can lead to algal blooms and fish kills (resulting from oxygen deprivation) in lakes and rivers. Algal blooms can threaten municipal water systems with taste and odor issues. Phosphorus runoff from hen manure can contribute to eutrophication in freshwater systems (Schindler, 1977).

Best management practices to reduce phosphorus runoff from poultry manure application include:

  • proper nutrient management planning (DeLaune et al., 2004; Edwards and Daniel, 1992, 1993)
  • buffer strips (Chaubey et al., 1993)
  • dietary modifications to lower phosphorus content of diets using phytase enzymes (Plumstead et al., 2007)
  • chemical precipitation of P in manure using compounds such as alum (Moore et al., 2000; Moore and Edwards, 2007; Wilson, 2004)

If mishandled, nitrogen can also be an environmental threat. Runoff nitrogen from manure and atmospheric ammonia can contribute to eutrophication. Nitrate leaching into groundwater is another potential water quality threat. Nitrate leaching from hen manure is dependent on application rate and is recommended to be below 5 tons per acre. You can keep application rates below this threshold by using best management practices and a phosphorus index to determine application rate.

Since the 1940s, livestock production practices in North America have evolved from extensive to intensive systems, concentrating animals, nutrients, and their associated microorganisms within limited geographic areas (McAllister and Topp, 2012). Approximately 39 percent of pathogens currently known to infect livestock are also infectious to humans (Cleaveland et al., 2001). Livestock manure can harbor a wide range of bacterial, viral, and parasitic pathogens that can move from land-applied manure to surface water, leach into groundwater, or contaminate vegetable crops through irrigation (McAllister and Topp, 2012). However, pathogen mobility from intensive and extensive livestock operations is complex, and exposure of adjacent water sources occurs through multiple pathways.

As the global human population approaches 10 billion by 2050, meat and milk production are expected to nearly double (FAO, 2006). More than 1 billion of the population increase is expected to occur in Africa alone (Thornton et al., 2009). In fact, much of this expansion will occur in developing countries already prone to microbial contamination of water. Proper manure handling is one critical control point required to avoid foodborne illness. Best livestock management practices can reduce the release of pathogens into the environment.

Both extensive and intensive production systems can threaten surface waters through microbial contamination. Livestock often have direct access to streams and rivers in extensive systems, while in intensive systems (as with commercial layers), pathogens most often enter surface water by runoff from land-applied manure. This highlights the importance of developing sound manure management practices and a nutrient management plan for your operation.

Many of these practices are simple. Avoid spreading manure in high-risk areas such as steep slopes, bottomlands that are prone to flooding, and fields adjacent to waterways. Consider planting cover crops that inhibit overland water flow and increase soil water-holding capacity. Conservation tillage practices that leave crop residue in the field can reduce runoff and erosion. Buffer strips and set-back distances create a safety zone and help protect streambanks. Soil and manure tests can prevent overapplication of nutrients and loss of these nutrients to the environment through leaching and runoff.

Antibiotic Resistance Genes (ARGs)

Globally, animal husbandry accounts for over half of all antibiotic use (Van Boeckel et al., 2017). Much of this antibiotic use in animal husbandry is for non-therapeutic purposes, such as promoting growth and preventing disease (Woolhouse and Ward, 2013; Zhu et al., 2017). In recent years, most non-therapeutic use in Europe and the U.S. has been phased out, but non-therapeutic use is still prevalent in many parts of the world. This enables bacteria in livestock digestive systems to acquire and maintain antibiotic resistance genes (ARGs) and fosters an increase in the relative abundance of resistant populations (Gullberg et al., 2011). When these ARGs propagate to surrounding environments, antibiotic resistance becomes an environmental pollution concern (Rysz and Alvarez, 2004).

Although current livestock waste treatment technologies are not designed to remove ARGs specifically, the possible removal of ARGs during waste treatment from concentrated animal feeding operations is an area of interest. Currently, one of the most pressing needs is to control ARGs at the source by improving management strategies to reduce the abundance and diversity of ARGs in livestock manure (He et al., 2020). Management changes—including adjusting animal diets to minimize disease occurrence, decreasing human-to-animal interaction, optimizing manure collection methods, increasing frequency of manure collection, and creating confinement areas for sick livestock to reduce the spread of disease—could suppress ARG proliferation and reduce the need for antibiotics (He et al., 2020). In addition, antibiotic alternatives, such as antimicrobial peptides, probiotics, prebiotics, essential oils, and enzymes, show promise for selective microbial control.


While commercial layer manure is an excellent organic fertilizer source, it has a low N:P ratio. If mishandled, excess nutrients can leach into groundwater or run off into surface waters, affecting water quality. Ammonia volatilization may also have a detrimental effect on bird health and the environment if not properly managed. An increase in antibiotic resistance genes is also a possibility if livestock manure is mishandled. While some regions of the world have banned antibiotics for prophylactic use, the practice is still common in many places. Using best management practices and following the nutrient management practices uniquely designed for each livestock operation will lessen environmental concerns associated with poultry and livestock and reduce chances of overapplying manure nutrients.


Anderson, D. P., C. W. Beard, and R. P, Hanson. 1964. The adverse effect of ammonia on chickens including resistance to infection with Newcastle disease virus. Avian Dis. 8:369–379.

ApSimon, H., M. M. Kruse, and J. N. B. Bell.1987. Ammonia emissions and their role in acid deposition. Atmos. Environ. 21:1939–1946.

Carlile, F. S. 1984. Ammonia in poultry houses: A literature review. World’s Poult. Sci. J. 40:99–113.

Charles, D. R., and C. G. Payne. 1966a. The influence of graded levels of atmospheric ammonia on chickens. I. Effects on respiration and on the performance of broilers and replacement growing stock. Br. Poult. Sci. 7:177–187.

Charles, D. R., and C. G. Payne. 1966b. The influence of graded levels of atmospheric ammonia on chickens. II. Effects on the performance of laying hens. Br. Poult. Sci. 7:189–198.

Chaubey, I., D. R. Edwards, T. C. Daniel, and D. J. Nichols. 1993. Effectiveness of vegetative filter strips in controlling losses of surface-applied poultry litter constituents. Paper No. 932011. ASAE Meeting, Spokane, WA. American Society of Agricultural and Biological Engineers. St. Joseph, MI.

Clark, K. M., L. Boardman, D. Staples, et al. 2017. Crop yield and soil organic carbon in conventional and no-till organic systems on a claypan soil. Agron. J. 109:588–599.

Cleaveland, S., M. K. Laurenson, and L. H. Taylor. 2001. Diseases of humans and their domestic mammals: Pathogen characteristics, host range and the risk of emergence. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 356:991–999.

Deaton, J. W., F. N. Reece, and B. D. Lott. 1984. Effect of atmospheric ammonia on pullets at point of lay. Poult. Sci. 63:384–385.

DeLaune, P. B., P. A. Moore, Jr., D. K. Carman, A. N. Sharpley, B. E. Haggard, and T. C. Daniel. 2004. Evaluation of the phosphorus source component in the phosphorus index for pastures. J. Environ. Qual. 33:2192–2200.

Edwards, D. R., and T. C. Daniel. 1992. Potential runoff quality effects of poultry manure slurry applied to fescue plots. Trans ASAE 35(6):1827–1832.

Edwards, D. R., and T. C. Daniel. 1993. Effects of poultry litter application rate and rainfall intensity on quality of runoff from fescuegrass plots. J. Environ. Qual. 22:361–365.

EPA. 1996. Environmental Indicators of Water Quality in the United States. EPA 841-R-96-002. Office of water (4503F), US Environmental Protection Agency, US Government Printing Office, Washington, DC.

FAO (Food and Agriculture Organization of the United Nations). 2006. Livestock’s long shadow: environmental issues and options. FAO. Rome.

Faddoul, G. P., and R. C. Ringrose. 1950. Avian keratoconjunctivitis. Vet. Med. 45:492–493.

Fierro, M. 2000. Particulate matter. Available at:

Gullberg, E., S. Cao, O. G. Berg, et al. 2011. Selection of resistant bacteria at very low antibiotic concentrations. PLoS Pathog. 7(7):e1002158.

Harmel, R. D., D. R. Smith, R. I. Haney, and M. Dozier. 2009. Nitrogen and phosphorus runoff from cropland and pasture fields fertilized with poultry litter. J. Soil Water Conserv. 64(6):400–412.

He, Y., Q. Yuan, J. Mathieu, et al. 2020. Antibiotic resistance genes from livestock waste: occurrence, dissemination, and treatment. npj Clean Water 3:4.

Hoover, N. L., J. Y. Law, A. M. Long, R. S. Kanwar, and M. L. Soupir. 2019. Long-term impact of poultry manure on crop yield, soil and water quality, and crop revenue. J. Environ. Manage. 252:109582

IPPC (Intergovernmental Panel on Climate Change). 2007. Climate Change 2007: Mitigation of climate change. Contribution of working group III to the fourth assessment report of the intergovernmental panel on climate change. Cambridge University Press, Cambridge, UK.

Liang, Y., H. Xin, E. F. Wheeler, et al. 2005. Ammonia emissions from U.S. laying hen houses in Iowa and Pennsylvania. Trans. ASAE 48(5):1927–1941.

Lin, Y., D. B. Watts, E. van Santen, and G. Cao. 2018. Influence of poultry litter on crop productivity under different field conditions: a meta-analysis. Agron. J. 110:807–818.

Lorimor, J. C., and H. Xin. 1999. Manure production and nutrient concentrations from high–rise layer houses. Appl. Eng. Agric. 15(4):337–340.

McAllister, T. A., and E. Topp. 2012. Role of livestock in microbiological contamination of water: Commonly the blame, but not always the source. Anim. Front. 2(2):17–27.

Moore, P. A., Jr., T. C. Daniel, and D. R. Edwards. 2000. Reducing phosphorus runoff and inhibiting ammonia loss from poultry manure with aluminum sulfate. J. Environ. Qual. 29:37–49.

Moore, P. A., Jr., and D. R. Edwards. 2007. Long-term effects of poultry litter, alum-treated litter, and ammonium nitrate on phosphorus availability in soils. J. Environ. Qual. 36:163–174.

MWPS (Midwest Plan Service). 1985. Livestock Waste Facilities Handbook, MWSP-18. 2nd Ed., Ames, Iowa. Iowa State University.

Nagaraja, K. V., D. A. Emery, K. A. Jordan, J. A. Newman, and B. S. Pomeroy. 1983. Scanning electron microscope studies of adverse effects of ammonia on tracheal tissues of turkeys. Am. J. Vet. Res. 44:1530–1536.

NRC (National Research Council). 2003. Air emissions from animal feeding operations: current knowledge, future trends. National Academy Press, Washington, D.C.

Oyetunde, O. O., R. G. Thomson, and H. C. Carlson. 1978. Aerosol exposure of ammonia, dust, and Escherichia coli in broiler chickens. Can. Vet. J. 19:187–193.

Patterson, P. H., and E. S. Lorenz. 1996. Manure nutrient production from commercial white leghorn hens. J. Appl. Poult. Res. 5:260–268.

Plumstead, P. W., H. Romero-Sanchez, R. O. Maguire, A. G. Gernat, and J. Brake. 2007. Effects of phosphorus level and phytase in broiler breeder rearing and laying diets on live performance and phosphorus excretion. Poult. Sci. 86:225–231.

Pote, D. H., T. C. Daniel, A. N. Sharpley, P. A. Moore, Jr., D. R. Edwards, and D. J. Nichols. 1996. Relating extractable soil phosphorus to phosphorus losses in runoff. Soil Sci. Soc. Am. J. 60:855–859.

Roberts, S. A., H. Xin, B. J. Kerr, J. R. Russell, and K. Bregendahl. 2007a. Effects of dietary fiber and low crude protein on ammonia emission from laying-hen manure. Poult. Sci. 86:1716–1725.

Roberts, S. A., H. Xin, B. J. Kerr, J. R. Russell, and K. Bregendahl. 2007b. Effects of dietary fiber and low crude protein on nitrogen balance and egg production in laying hens. Poult. Sci. 86:1625–1632.

Rysz, M. and P. J. J. Alvarez. 2004. Amplification and attenuation of tetracycline resistance in soil bacteria: aquifer column experiments. Water Res. 38(17):3705–3712.

Sato, S., S. Shaya, and H. Kobayashi. 1973. Effect of ammonia on Mycoplasma gallisepticum infection in chickens. Natl. Inst. Anim. Health Q. 13:45–53.

Schindler, D. W. 1977. The evolution of phosphorus limitation in lakes. Science 195:260–262.

Sims, J. T., A. C. Edwards, O. F. Schoumans, and R. R. Simard. 2000. Integrating soil phosphorus testing into environmentally based agricultural practices. J. Environ. Qual. 29:60–71.

Thornton, P. K., J. Van de Steeg, A. Notenbaert, and M. Herrero. 2009. The impacts of climate change on livestock and livestock systems in developing countries: A review of what we know and what we need to know. Agric. Syst. 101(3):113–127.

Timmons, J. R., and J. Harter-Dennis. 2011. Superabsorbent polymers as a poultry litter amendment. Int. J. Poult. Sci. 10(6):416–420.

UEP (United Egg Producers). 2017. Animal Husbandry Guidelines for US Egg Laying Flocks. Available at:

Van Boeckel, T. P., E. E. Glennon, D. Chen, et al. 2017. Reducing antimicrobial use in food animals. Science 357:1350–1352.

Vervoort, R. W., D. E. Radcliffe, M. L. Cabrera, and M. Latimore, Jr. 1998. Field-scale nitrogen and phosphorus losses from hayfields receiving fresh and composted broiler litter. J. Environ. Qual. 27(5):1246–1254.

Wilson, M. G. 2004. Development and testing of a liquid alum delivery system for high rise hen houses. MS Thesis. University of Arkansas, Fayetteville.

Woolhouse, M. E. J., and M. J. Ward. 2013. Sources of antimicrobial resistance. Science 341:1460–1461. Available at:

Xin, H., R. S. Gates, A. R. Green, F. M. Mitloehner, P. A. Moore, Jr., and C. M. Wathes. 2011. Environmental impacts and sustainability of egg production systems. Poult. Sci. 90:263–277.

Zhu, Y. G., Y. Zhao, B. Li, et al. 2017. Continental-scale pollution of estuaries with antibiotic resistance genes. Nat. Microbiol 2:16270.

Publication 3724 (POD-10-21)

By Tom Tabler, PhD, Extension Professor, MSU Department of Poultry Science; Yi Liang, PhD, Associate Professor, Biological and Agricultural Engineering Department/Center of Excellence for Poultry Science, University of Arkansas; Jonathan Moon, Poultry Operations Coordinator, MSU Poultry Science; and Jessica Wells, PhD, Assistant Clinical/Extension Professor, MSU Poultry Science.

Print Friendly, PDF & Email

The Mississippi State University Extension Service is working to ensure all web content is accessible to all users. If you need assistance accessing any of our content, please email the webteam or call 662-325-2262.

Select Your County Office


Portrait of Dr. George Thomas Tabler
Extension Professor
Portrait of Dr. Jessica Benoit Wells
Asst Clinical/Ext Professor