Swine Manure Management: Systems and Best Practices

Swine manure management directly affects herd health, crop nutrient budgets, neighbor relations, and regulatory standing. The system you choose determines how much nitrogen and phosphorus you can recover, how much odor and gas you emit, and what your storage and application costs will be. This article compares the main swine manure management systems, explains how nutrients move through each one, and gives you practical records and checks to keep your operation within environmental limits.

At a Glance

The table below compares the four most common swine manure management systems used on commercial farms. Each system has different strengths for nutrient recovery, odor control, gas emissions, and capital cost.

Core Principles of Manure Management

Manure management starts with understanding what is in the manure and where those nutrients go after excretion. Swine manure contains nitrogen, phosphorus, potassium, and organic carbon. The form of those nutrients changes depending on how you store and treat the manure. Nitrogen is the most volatile nutrient. It can be lost as ammonia gas, nitrous oxide, or nitrogen gas depending on the system. Phosphorus does not volatilize but can move with eroded soil or runoff into surface water. Carbon leaves the system as methane, carbon dioxide, or is retained in the soil when manure is applied to land.

The Food and Agriculture Organization of the United Nations provides international guidance on animal production systems, including manure handling as part of sustainable livestock farming. Their materials frame manure as a resource to be cycled back to crop production instead of a waste stream to be disposed of.

A review in the Journal of Animal Science explains that swine are not the largest source of agricultural greenhouse gas emissions, but feed production and manure management together create a substantial environmental footprint. The same review emphasizes that integrated nutrient management, using precision application of nitrogen, phosphorus, and potassium combined with manure reuse, can significantly reduce nitrogen losses and improve soil organic carbon. This means the decisions you make about manure storage and application are not separate from your crop fertility program. They are the same program.

Swine Production Systems and Manure Characteristics

The housing system you choose determines the physical form of the manure you must manage. Swine production systems fall into three broad categories: slatted floor barns with liquid manure handling, bedded systems with solid manure handling, and pasture systems where manure is deposited directly on the land.

Slatted Floor Systems

Slatted floor barns are the most common system for commercial swine production. Manure falls through the slats into a pit below. The pit may be shallow with frequent flushing or deep with storage for several months. The USDA Agricultural Research Service conducts research on animal production systems including manure handling technologies that reduce environmental impact while maintaining productivity.

Deep pit systems store manure under the barn for up to six months or longer. The manure remains mostly liquid with total solids content typically between 2 and 8 percent. The nutrient concentration depends on how much water enters the pit from spillage, washing, and precipitation if the pit is open. Deep pits conserve nitrogen because the manure is not exposed to moving air. However, they concentrate ammonia and hydrogen sulfide in the headspace above the manure, which creates a serious worker safety hazard during agitation and pumping.

Flushing systems use recycled lagoon effluent or fresh water to move manure from shallow pits to a central collection point. A study in the Journal of Environmental Quality compared deep pit systems to flushing systems and found that diluting manure with lagoon effluent reduced odor by lowering the concentration of odor-causing compounds. The study showed that reducing total solids by 90 percent reduced branched chain fatty acids, ammonia, phenols, and indoles in the air by equal amounts. Carbon dioxide was the main carbon gas evolved, averaging over 90 percent of carbon losses, and methane increased with dilution in a quadratic pattern.

Bedded Systems

Bedded systems use straw, wood shavings, or other absorbent materials to keep pigs dry and capture manure in a solid form. The manure and bedding mixture is removed periodically and can be composted or applied directly to land. Solid manure systems conserve phosphorus well but lose more nitrogen to ammonia volatilization than liquid systems unless the manure is incorporated into soil quickly after application.

Pasture Systems

Pasture systems allow pigs to deposit manure directly on the land. Nutrient distribution is uneven because pigs concentrate manure near feeders, waterers, and shade. This creates hotspots of phosphorus and nitrogen that can exceed crop needs and increase the risk of nutrient runoff. Pasture systems require careful stocking rate management and regular soil testing to prevent nutrient buildup.

Manure Storage Systems Compared

The storage system you choose affects nutrient retention, gas emissions, odor, and the logistics of land application. Each system has a different profile of tradeoffs.

Deep Pits

Deep pits store manure under the barn for extended periods. The Journal of Environmental Quality identifies deep pits, anaerobic lagoons, and slurry storages as the common swine manure storage types in the United States. Deep pits retain nitrogen well because the manure surface is protected from wind. However, the same study notes that the nutrient and carbon partitioning depends heavily on what treatment technologies you use in line with the storage.

Deep pits require careful management during agitation. When you stir the pit to suspend solids before pumping, you release large amounts of hydrogen sulfide and ammonia. This gas release can be fatal to workers and pigs. Agitation should only be done with barn ventilation running at maximum capacity and with no people or animals in the building.

Anaerobic Lagoons

Anaerobic lagoons are large earthen basins that store and partially treat manure through natural biological processes. Bacteria break down organic matter in the absence of oxygen, producing methane and carbon dioxide. The liquid fraction is typically irrigated onto cropland. Lagoons are common in warm climates where biological activity continues year round.

The Journal of Environmental Quality synthesis of manure treatment technologies notes that anaerobic digestion converts organic matter into biogas, and for most mesophilic digesters, 56 to 66 percent of the carbon remained in the effluent. This means a significant portion of the carbon in manure stays in the liquid even after digestion. The same study found that the mass of carbon retained in the sludge is underreported in most studies, which means the true carbon balance of lagoon systems is not fully understood.

Lagoons lose most of their nitrogen to the atmosphere as ammonia. A system analysis in Environmental Science and Technology found that changing from liquid systems to solid-liquid separation systems, coupled with mitigation measures, could simultaneously reduce greenhouse gas emissions by 65 percent and ammonia emissions by 78 percent. This finding shows that the choice of storage system has a large effect on both climate and air quality outcomes.

Slurry Storages

Slurry storages are tanks or earthen basins that hold manure without the biological treatment that occurs in lagoons. They are typically smaller than lagoons and are emptied one or more times per year. Slurry storages retain more nitrogen than lagoons because there is less surface area for ammonia volatilization and no continuous biological activity consuming nitrogen.

Covered Storages

Covering a slurry storage or lagoon with a permeable or impermeable cover reduces ammonia emissions and odor. Impermeable covers can capture biogas for energy production. The World Organisation for Animal Health provides international standards for animal welfare and environmental stewardship that are relevant when considering how storage design affects both animals and surrounding communities.

Treatment Technologies

Treatment technologies can be used in line with storage systems to change nutrient partitioning, reduce gas emissions, or produce energy. The Journal of Environmental Quality synthesis examined four mature technologies: acidification, aeration, solid-liquid separation, and anaerobic digestion. The study found that acidification papers suggested significant reductions in gaseous losses, but the available data did not document realistic nitrogen partitioning. Among solid-liquid separation systems, urine-feces segregation retained the most solids in the solid fraction, while filtration retained the least. In aeration studies, the partitioning of nitrogen into different nitrogen gases depended on the amount of aeration.

Solid-Liquid Separation

Solid-liquid separation divides manure into a solid fraction rich in phosphorus and organic matter and a liquid fraction rich in soluble nitrogen and potassium. The solid fraction can be composted, exported off farm, or used as bedding after treatment. The liquid fraction is easier to pump and irrigate than whole manure.

The Environmental Science and Technology system analysis found that solid-liquid separation coupled with mitigation measures could reduce greenhouse gas emissions by 65 percent and ammonia emissions by 78 percent compared to liquid systems. This makes separation one of the most effective single changes you can make to reduce the environmental impact of manure management.

Anaerobic Digestion

Anaerobic digestion uses bacteria to break down organic matter in the absence of oxygen, producing biogas that is roughly 60 percent methane and 40 percent carbon dioxide. The biogas can be burned to generate electricity or heat, or upgraded to renewable natural gas. The digested effluent retains most of the nitrogen and phosphorus, so the nutrient value is preserved.

The Journal of Environmental Quality synthesis found that for most mesophilic digesters, 56 to 66 percent of the carbon remained in the effluent. This means digestion does not remove all carbon from the manure. The remaining carbon can still contribute to odor and methane emissions after digestion unless the effluent is managed carefully.

Research in The Science of the Total Environment explored adding dewatered swine manure-derived biochar to anaerobic digestion of swine wastewater. With 20 grams per liter of biochar assistance, the methanogenic lag time was shortened by 17.4 to 21.1 percent, and the maximum methane production rate increased from 40.8 milliliters per day to 48.3 to 50.5 milliliters per day. Biochar prepared at 300 degrees Celsius performed better than biochar prepared at 500 or 700 degrees Celsius. The same study found that biochar preparation by pyrolysis dramatically reduced antibiotic resistance gene abundance by almost 4 logs, and adding biochar to anaerobic digestion mitigated 74.8 percent of the mobile gene elements abundance.

Composting

Composting is an aerobic process that converts manure and bedding into a stable, humus-like material. The process requires oxygen, moisture, and a carbon to nitrogen ratio in the right range. Composting reduces manure volume, kills pathogens and weed seeds through heat, and produces a product that is easier to handle and apply than raw manure.

Temperature is the key indicator of compost quality. A study in Toxics found that the maximum composting temperature and the duration of high temperature are key indicators of compost quality. The study showed that adjusting the thermophilic stage by prolonging its duration or raising the maximum temperature slightly promoted the absolute abundance of total antibiotic resistance genes by 0.72 to 0.99 logs, but their relative abundance was notably reduced by 49.7 to 64.1 percent. Some antibiotic resistance genes could be effectively removed by composting, while others enriched horizontal gene transfer and diversified potential bacterial hosts. The study also found that organic carbon content was strongly related to several antibiotic resistance genes, implying that organic nutrients shape antibiotic resistance gene distribution by influencing bacterial community succession.

Nitrogen retention is a major challenge in composting. A study in Microorganisms tested adding a thermotolerant nitrifying bacterium, Bacillus subtilis F2, to pig manure composting. The inoculation markedly raised the germination index, nitrate content, and total nitrogen in the final compost, resulting in reduced nitrogen loss. The inoculation led to a distinct succession of bacterial communities and increased amoA gene levels while decreasing nirK abundance during the cooling and maturation phases. The study recommends adding F2 for bolstering nitrogen retention in composting.

Another approach to nitrogen conservation uses microbial inoculants from black soldier fly larvae. A study in Bioresource Technology evaluated two ammonia-mitigating Klebsiella strains isolated from the gut of black soldier fly larvae. Both inoculated treatments entered the thermophilic phase more rapidly and reached higher peak temperatures of 69.15 and 67.08 degrees Celsius compared to 66.03 degrees Celsius in the uninoculated control. Inoculation reduced late-stage volatile organic compound emissions, lowered final ammonium nitrogen accumulation, enhanced nitrate formation, and improved total nitrogen retention. Nitrogen loss decreased from 17.3 percent in the control to 11.6 and 8.6 percent in the two inoculated treatments.

External additives can also improve compost quality and reduce gas emissions. A study in Environmental Science tested basalt and diorite tailings as additives in pig manure composting. Compost products with 10 percent basalt and diorite tailings met organic fertilizer standards for heap temperature, pH, organic matter, and total nutrient content. In the basalt treatment, organic matter loss rate decreased from 15.6 to 2.6 percent compared to the control, and total nutrient accumulation increased from 101 to 114.6 percent. Carbon dioxide and methane cumulative emissions from composting were reduced by 23.5 and 24.4 percent respectively, and the humification coefficient of the compost product increased by 56.3 percent.

Copper is a common additive in swine feed and accumulates in manure. A study in Science of the Total Environment investigated the effect of green synthesized iron nanoparticles on copper transformations during thermophilic aerobic composting. Addition of the nanoparticles increased passivation of active copper forms, including exchangeable, carbonate-bound, and iron and manganese oxide-bound copper by 66.8, 47.5, and 15.4 percent respectively. The fraction of copper bound to organic matter increased with composting and was influenced by the nanoparticle dose. Addition of 500 milliliters per kilogram increased organic matter bound copper to 52.9 percent.

Microplastics are an emerging concern in manure composting. A study in Environmental Pollution tested walnut shell biochar combined with montmorillonite clay during pig manure composting. The addition of biochar dramatically arranged the bacterial community at different stages of composting. Under the intervention of high temperature composting and biochar, the carbon content of microplastics was reduced by up to 20.25 percent. Fourier transform infrared spectrum analysis indicated that the abundance of carbon-carbon, carbon-oxygen, carbon-hydrogen, and carboxyl groups in microplastics sharply reduced with 10 and 12 percent biochar addition, indicating that biochar and composting made microplastics biodegradable.

Antibiotic resistance genes are a concern in manure composting because they can spread to environmental bacteria. A study in Environmental Pollution evaluated the potential risk of horizontal gene transfer during co-composting of chicken manure and pig manure. The abundance of sulfonamide antibiotic resistance genes and integrase genes was higher during pig manure composting than during chicken manure composting. Adding pig manure also increased resistance gene abundance during chicken manure composting. The study concluded that the potential horizontal gene transfer risk was greater during pig manure composting and that the bacterial community of pig manure was more competitive and adaptable than that of chicken manure.

Hydrothermal Carbonization

Hydrothermal carbonization is an emerging technology that converts wet manure into a solid carbonaceous material called hydrochar without pre-drying. A study in Environmental Research compared batch and continuous processes for hydrothermal carbonization of swine manure. The continuous process at low temperature of 180 degrees Celsius resulted in a hydrochar with a lower degree of carbonization compared to the batch process, but similar characteristics were found in both hydrochars at higher operating temperatures of 230 to 250 degrees Celsius. The hydrochars had carbon content of about 52 weight percent, fixed carbon of about 24 weight percent, and higher calorific value of 21 megajoules per kilogram. Thermogravimetric and combustion analyses showed that the hydrochars exhibited characteristics suitable as solid biofuels for industrial use.

The process water from hydrothermal carbonization contains high organic matter. A companion study in Environmental Research examined two approaches for managing this process water. Process water from conventional hydrothermal carbonization at 180 degrees Celsius showed high biodegradability with 55 percent chemical oxygen demand removal and methane production of about 290 milliliters of methane per gram of chemical oxygen demand added. Treatment in an upflow anaerobic sludge blanket reactor allowed obtaining a high methane production yield of 1.3 liters of methane per liter per day and chemical oxygen demand removal of about 70 percent. Acid-assisted hydrothermal carbonization proved viable for nutrient recovery, with migration of 83 percent of the phosphorus to the process water. Chemical precipitation with magnesium hydroxide and magnesium chloride produced solid salts with NPK values of 4/4/0.4 and 8/17/0.5 respectively, with negligible heavy metal content.

Biodiesel Production

Swine manure contains lipids that can be converted to biodiesel. A study in Bioresource Technology demonstrated that biodiesel from swine manure could be a promising way for large scale generation of biofuel. Transesterification of lipid contents extracted from collected swine manure had low biodiesel yield of 14.2 weight percent using sulfuric acid catalyst due to high acid value and impurities. However, thermo-chemical non-catalytic transesterification with a porous material showed 94.7 weight percent yield of biodiesel from the lipid in swine manure. The study estimated that swine manure derived biodiesel could cover 19.7 and 46.8 weight percent of biodiesel currently produced in Korea and the United States respectively.

Odor Management

Odor is often the most visible community impact of swine manure management. Odor compounds are produced by bacteria breaking down organic matter in manure. The main odor groups are volatile fatty acids, branched chain fatty acids, phenols, indoles, and ammonia.

The Journal of Environmental Management study on pit recharge systems found that the initial microbial community structure was controlled by dilution ratio and manure barn source material. Firmicutes and Proteobacteria were the dominant microbial phyla in manure and lagoon effluent respectively, and significantly decreased or increased with dilution. Key microbial species were Clostridium saudiense in manure and Pseudomonas caeni in lagoon effluent. Percentages of these species declined by 8.9 percent or increased by 17.6 percent respectively with each unit of dilution. The study found that environmental factors including solids and pH explained over 75 percent of the variance in odor profiles. This means monitoring solids and pH in recharge waters will significantly impact odor control in pit recharge systems.

The Journal of Environmental Quality study on manure dilution found that solids in the manure were positively correlated to total nitrogen, total carbon, straight chain fatty acids, branched chain fatty acids, total phenols, and total indoles. Solids were also positively correlated to odor activity values for straight chain fatty acids, branched chain fatty acids, ammonia, total phenols, and total indoles. Reducing total solids by 90 percent reduced branched chain fatty acids, ammonia, phenols, and indoles by equal amounts in air. The study concluded that reducing solids in manure by dilution had the biggest impact on reducing odor and increasing organic carbon degradation.

Land Application and Nutrient Management

Land application is the final step in most manure management systems. The goal is to apply manure at rates that meet crop nutrient needs without exceeding them. This requires knowing the nutrient content of the manure, the nutrient needs of the crop, and the nutrient content of the soil.

Nutrient Testing

Manure nutrient content varies widely depending on the storage system, the diet of the pigs, and the amount of water that enters the system. You cannot assume the nutrient content of your manure is the same as a book value. Regular testing is essential for accurate application rates.

The Journal of Animal Science review emphasizes that integrated nutrient management through precision nitrogen, phosphorus, and potassium application combined with manure reuse can significantly reduce nitrogen losses, improve soil organic carbon sequestration, and mitigate nitrous oxide emissions. The review also highlights that emerging manure treatment technologies such as composting, anaerobic digestion, and biochar production offer co-benefits of nutrient recovery and energy generation.

Application Methods

The method of manure application has a large effect on nitrogen retention. Injection and incorporation into soil reduce ammonia volatilization compared to surface application. The USDA Agricultural Research Service conducts research on application methods that reduce nutrient losses and improve crop utilization.

Controlled Drainage

Controlled drainage is a water management practice that can reduce nitrogen losses from fields receiving manure. A study in Agricultural Water Management investigated the effect of controlled drainage on nitrogen fate and transport for a subsurface drained grass field receiving liquid swine lagoon effluent. The four-year field experiment was conducted on a naturally poorly drained pasture in eastern North Carolina. Controlled drainage significantly reduced drainage flow and total nitrogen loading via subsurface drain lines by an average of 397 millimeters per year, a 93 percent reduction, and 34.5 kilograms of nitrogen per hectare per year, a 94 percent reduction. The nitrogen that did not drain from the field in response to controlled drainage was lost via enhanced denitrification, 67 percent, and lateral seepage to adjacent fields, 33 percent.

Constructed Wetlands

Constructed wetlands can remove nitrogen from lagoon pretreated swine wastewater. A study in Bioresource Technology used a series of three stage pilot scale surface flow constructed wetlands planted with Myriophyllum aquaticum fed with three strengths of lagoon pretreated swine wastewater. The wetlands had mean removal efficiency of 87.7 to 97.9 percent for ammonium nitrogen and 85.4 to 96.1 percent for total nitrogen. The recovered total nitrogen mass via multiple harvests of Myriophyllum aquaticum was greatest at 120 to 222 grams of nitrogen per square meter per year when total nitrogen concentrations were 21.8 to 282 milligrams per liter. Based on mass balance estimation, plant uptake, sediment storage, and microbial removal accounted for 13.0 to 55.0 percent, 4.9 to 8.0 percent, and 33.0 to 67.5 percent of total nitrogen loading mass respectively.

Records and Measurements

Accurate records are the foundation of good manure management. You need to know what you produced, where you applied it, and what the nutrient balance was. The USDA National Agricultural Library provides access to research and extension materials on animal health and welfare, including manure management records and best practices.

Manure Production Records

Track the volume of manure removed from each storage structure. For liquid systems, record the depth of manure in the pit or lagoon before and after pumping. For solid systems, record the number of loads removed and the estimated weight per load. Record the date of each removal and the destination of the manure.

Nutrient Analysis Records

Test manure for nitrogen, phosphorus, potassium, and dry matter at least once per year, and more often if you change diets or water management. Keep the laboratory reports with your application records. Use the test results to calculate application rates for each field.

Application Records

For each field application, record the date, the field name or number, the application method, the rate applied, and the weather conditions. Record the crop to be grown and the expected nutrient need. Keep soil test results for each field and track changes in soil phosphorus and potassium over time.

Gas Emission Monitoring

If you are implementing gas mitigation measures, track the relevant parameters. For composting, record temperatures daily during the active phase and track the duration of thermophilic temperatures. For anaerobic digestion, record biogas production and methane content. For lagoons, monitor depth and visual appearance.

Common Failure Patterns

Manure management systems fail in predictable ways. Recognizing these patterns early can prevent environmental violations, worker injuries, and crop damage.

Pit Agitation Accidents

The most dangerous failure in deep pit systems is gas release during agitation. Hydrogen sulfide is heavier than air and accumulates in low areas. It paralyzes the sense of smell at low concentrations and is fatal at higher concentrations. Never enter a pit or barn during agitation without proper respiratory protection and a second person present. The U.S. Food and Drug Administration provides resources on animal veterinary topics including worker safety around animal waste.

Lagoon Overtopping

Lagoons fail when they receive more water than they can store. This happens during periods of heavy rainfall or when the lagoon is not pumped down enough before the wet season. Monitor lagoon depth regularly and maintain a freeboard of at least one foot. If the lagoon approaches capacity, pump down immediately even if the crop does not need the nutrients.

Compost Pile Odor

Compost piles that smell like ammonia or rotten eggs are not composting properly. Ammonia odor indicates too much nitrogen relative to carbon. Rotten egg odor indicates anaerobic conditions from too much moisture or insufficient aeration. Correct the carbon to nitrogen ratio by adding high carbon materials such as straw or wood shavings. Turn the pile to restore oxygen.

Nutrient Imbalance in Soil

Applying manure based on nitrogen needs can build up phosphorus in soil over time. This happens because the nitrogen to phosphorus ratio in manure is often lower than the ratio crops need. Monitor soil phosphorus levels and switch to phosphorus based application rates when soil phosphorus reaches high levels. Export manure or compost to farms with low soil phosphorus if you have excess.

Antibiotic Resistance Gene Spread

Manure can carry antibiotic resistance genes that spread to environmental bacteria. A study in Toxics found that composting can reduce the relative abundance of some antibiotic resistance genes but may enrich others. The study identified sulI, sulII, aadA, and tetL as genes that enriched horizontal gene transfer and diversified potential bacterial hosts. Three potential opportunistic pathogens, Mycobacterium, Bordetella, and Bacillus, exhibited positive correlations with enriched antibiotic resistance genes. This highlights the potential risks of the dissemination of antibiotic resistant bacteria through manure application.

Environmental Compliance and Sustainability

Manure management is regulated at multiple levels. Federal, state, and local regulations may apply depending on the size of your operation and where you are located. The World Organisation for Animal Health provides international standards for animal health and welfare that include environmental stewardship principles.

Regulatory Context

Large concentrated animal feeding operations are typically required to have a nutrient management plan that documents manure production, storage capacity, and application rates. The plan must be updated regularly and records must be kept for inspection. The U.S. Food and Drug Administration regulates animal feed and veterinary drugs, which affects the nutrient and contaminant content of manure.

Sustainability Transitions

The dominant manure management system in some regions is under pressure to change. A case study in Frontiers in Sustainable Food Systems examined the lagoon and sprayfield system in North Carolina, where nearly half of the commercial swine operations are located in two eastern counties. The study notes that lagoon and sprayfield is an efficient and cost-effective method of waste management but has negatively impacted the environment and local communities from both discrete events such as breaches and flooding and ongoing issues such as odor and disease vectors. The study used a multilevel perspective theory with a farm level added to represent the user perspective of regime technology in complex agricultural systems.

Life Cycle Assessment

Life cycle assessment evaluates the environmental impacts of swine production across the entire production chain, from crop cultivation to manure handling. The Journal of Animal Science review explains that life cycle assessments evaluate these impacts across the production chain. The review emphasizes that coupling nutrient management with innovative manure treatment and emission mitigation technologies is essential for advancing the sustainability of swine production and reducing its environmental impact.

A consequential life cycle assessment in Energies examined swine manure management within a thermal gasification scenario. The study provides a framework for evaluating the environmental consequences of changing from one manure management system to another.

Worker Safety and Biosecurity

Manure handling poses specific risks to workers and to herd health. Understanding these risks and having clear protocols is essential.

Gas Hazards

The main gas hazards in manure management are hydrogen sulfide, ammonia, methane, and carbon dioxide. Hydrogen sulfide is produced during anaerobic decomposition and is released in large amounts during agitation. Ammonia is produced from urea and uric acid in manure and is present in barn air. Methane is explosive at concentrations between 5 and 15 percent in air. Carbon dioxide displaces oxygen in enclosed spaces.

The USDA National Agricultural Library provides resources on animal health and welfare that include worker safety around animal facilities. The World Organisation for Animal Health also provides guidance on biosecurity and worker safety in animal production.

Biosecurity

Manure equipment can spread disease between farms. Shared equipment such as pumps, spreaders, and compost turners should be cleaned and disinfected between farms. Vehicles entering and leaving the farm should follow biosecurity protocols. The U.S. Food and Drug Administration regulates animal health products and provides guidance on disease prevention.

Personal Protective Equipment

Workers handling manure should wear appropriate personal protective equipment. This includes gloves, boots, and eye protection. When working in enclosed spaces or during agitation, use a self-contained breathing apparatus or a supplied air respirator. Never rely on a dust mask or cartridge respirator for protection against hydrogen sulfide.

Professional Escalation Criteria

Some situations require professional help beyond what you can manage on farm. Contact a veterinarian, agricultural engineer, or extension specialist when you encounter any of the following:

• A worker or animal shows signs of gas exposure, including headache, dizziness, nausea, or respiratory distress
• A lagoon or storage structure shows signs of structural failure, including cracks, seepage, or bulging
• Manure application rates exceed crop nutrient needs and you cannot find additional land
• Soil phosphorus levels reach very high levels and you need to develop a phosphorus management plan
• You are considering a major change to your manure management system, such as adding anaerobic digestion or solid-liquid separation
• You receive a notice of violation from a regulatory agency
• You are planning a new or expanded facility and need to design a manure management system

The USDA Agricultural Research Service conducts research on animal production systems that can inform system design decisions. The Food and Agriculture Organization of the United Nations provides international guidance on sustainable animal production.

System Selection and Transition Planning

Choosing a manure management system requires matching the system to your farm conditions. Consider the following factors:

Climate

Anaerobic lagoons work best in warm climates where biological activity continues year round. In cold climates, lagoons freeze and biological activity slows dramatically. Deep pits and slurry storages are more suitable for cold climates because they do not rely on biological treatment.

Land Base

The amount of land you have available for manure application determines how much manure you can manage. If you have limited land, you may need to export manure or compost off farm. Solid-liquid separation can help by concentrating phosphorus in a solid fraction that is easier to transport.

Labor

Different systems require different amounts of labor. Composting requires regular turning and monitoring. Anaerobic digestion requires daily attention to the digester. Lagoon systems require periodic pumping and irrigation management. Consider your labor availability when choosing a system.

Capital

The capital cost of manure management systems varies widely. Deep pits are relatively low cost because they are built into the barn. Lagoons are moderate cost. Anaerobic digestion and hydrothermal carbonization are high cost. The Journal of Cleaner Production presents a modeling method based on analytical target cascading for optimal design of manure management for intensive swine feeding operations.

Nutrient Management Goals

If your goal is to maximize nutrient recovery for crop production, choose a system that retains nitrogen and phosphorus. Deep pits and slurry storages retain nutrients well. Lagoons lose most nitrogen to the atmosphere. Composting concentrates nutrients but loses some nitrogen during the active phase.

Odor Sensitivity

If your farm is near neighbors, odor control is a priority. Flushing systems with lagoon effluent dilution reduce odor. Composting with proper management produces low odor. Covered storages reduce odor emissions.

Frequently Asked Questions

What is the difference between a deep pit and an anaerobic lagoon?

A deep pit stores manure under the barn in a concrete pit that is emptied one or more times per year. The manure remains mostly liquid and retains nitrogen well because it is protected from wind. An anaerobic lagoon is an earthen basin that stores and partially treats manure through biological activity. Lagoons lose most nitrogen to the atmosphere as ammonia but produce less odor than deep pits when managed correctly. The Journal of Environmental Quality identifies deep pits, anaerobic lagoons, and slurry storages as the common swine manure storage types in the United States.

How often should I test my manure for nutrient content?

Test manure at least once per year, and more often if you change diets, water management, or storage conditions. Manure nutrient content varies widely depending on the storage system, the diet of the pigs, and the amount of water that enters the system. Regular testing is essential for accurate application rates. The Journal of Animal Science review emphasizes that precision nitrogen, phosphorus, and potassium application combined with manure reuse can significantly reduce nitrogen losses.

What is the safest way to agitate a deep pit before pumping?

Agitate only with barn ventilation running at maximum capacity and with no people or animals in the building. Start agitation slowly and monitor gas levels if possible. Hydrogen sulfide is released in large amounts during agitation and can be fatal. Never enter a pit or barn during agitation without proper respiratory protection and a second person present. The U.S. Food and Drug Administration provides resources on worker safety around animal waste.

Can composting eliminate antibiotic resistance genes from pig manure?

Composting can reduce the relative abundance of some antibiotic resistance genes but may enrich others. A study in Toxics found that adjusting the thermophilic stage slightly promoted the absolute abundance of total antibiotic resistance genes but notably reduced their relative abundance by 49.7 to 64.1 percent. Some genes such as tetW, tetO, tetM, fexA, fexB, ermA, and ermB could be effectively removed by composting, while others such as sulI, sulII, aadA, and tetL enriched horizontal gene transfer.

How does solid-liquid separation reduce greenhouse gas emissions?

Solid-liquid separation divides manure into a solid fraction rich in phosphorus and organic matter and a liquid fraction rich in soluble nitrogen and potassium. A system analysis in Environmental Science and Technology found that changing from liquid systems to solid-liquid separation systems, coupled with mitigation measures, could simultaneously reduce greenhouse gas emissions by 65 percent and ammonia emissions by 78 percent.

What is hydrothermal carbonization and is it practical for my farm?

Hydrothermal carbonization is a technology that converts wet manure into a solid carbonaceous material called hydrochar without pre-drying. A study in Environmental Research found that hydrochars produced at higher operating temperatures of 230 to 250 degrees Celsius had carbon content of about 52 weight percent and higher calor

Related Farming Guides

• Swine Manure Lagoon Management and Safety
• Manure Nutrient Management Planning
• Poultry Manure Composting and Nutrient Stewardship
• Water Buffalo Manure Management and Composting
• Rabbit Manure Management and Composting on Small Farms

References and Further Reading

• FAO Animal Production and Health. Food and Agriculture Organization of the United Nations.
• Animal Health and Welfare. USDA National Agricultural Library.
• Animal and Veterinary Resources. U.S. Food and Drug Administration.
• Animal Health and Welfare. World Organisation for Animal Health.
• Animal Production and Protection. USDA Agricultural Research Service.
• Sustainable swine production: reducing environmental impacts through cropping systems and manure management.. Journal of animal science, 2026.
• Swine manure management by hydrothermal carbonization: Comparative study of batch and continuous operation.. Environmental research, 2024.
• Mitigating Greenhouse Gas and Ammonia Emissions from Swine Manure Management: A System Analysis.. Environmental science & technology, 2017.
• Nutrient and carbon partitioning and performance for swine manure management technologies.. Journal of environmental quality, 2026.
• When dewatered swine manure-derived biochar meets swine wastewater in anaerobic digestion: A win-win scenario towards highly efficient energy recovery and antibiotic resistance genes attenuation for swine manure management.. The Science of the total environment, 2022.
• Swine manure dilution with lagoon effluent impact on odor reduction and manure digestion.. Journal of environmental quality, 2021.
• Biodiesel synthesis from swine manure.. Bioresource technology, 2020.
• Study of two approaches for the process water management from hydrothermal carbonization of swine manure: Anaerobic treatment and nutrient recovery.. Environmental research, 2024.
• Insights into the Mechanisms Driving the Dynamics of Antibiotic Resistance Genes During Pig Manure Composting.. 2026.
• [Impact of Tailings Residue on the Quality and Carbon Transformation in Pig Manure Composting].. 2025.
• Black soldier fly larval gut-derived Klebsiella improves nitrogen retention and reduces ammonia and VOC emissions during pig manure composting.. 2026.
• Enhanced copper passivation in pig manure composting through iron nanoparticle amendment.. 2025.
• Addition of Thermotolerant Nitrifying Bacteria During Pig Manure Composting Enhanced Nitrogen Retention and Modified Microbial Composition.. 2025.
• Addition of Thermotolerant Nitrifying Bacteria During Pig Manure Composting Enhanced Nitrogen Retention and Modified Microbial Composition. 2025.
• Engineered biochar combined clay for microplastic biodegradation during pig manure composting.. 2024.
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