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United States Department of Agriculture

Agricultural Research Service

Research Project: Safe Management and Use of Manure, Biosolids, and Industrial Byproducts

Location: Genetics and Sustainable Agriculture Research

2011 Annual Report

1a. Objectives (from AD-416)
Develop improved manure (swine lagoon effluent and poultry litter) application and management practices that reduce nutrient losses to the environment, increases utilization by crop plants, increase recycling of nutrients, and enhance soil quality. Determine and reduce bacterial pathogen levels in manured fields and assess impacts on soil fungal and bacterial ecology, including antibiotic resistance. Determine ammonia and greenhouse gas emissions from broiler houses and manured fields and develop management practices to reduce them. Evaluate the benefits and potential risks from possible new uses of manure and industrial byproducts (e.g. FGD gypsum).

1b. Approach (from AD-416)
Multidisciplinary approach will be utilized in converting “wastes” into valuable inputs for energy, forage, fiber, and grain crops. Presence, prevalence, and fate of nutrients, gaseous emissions, bacterial approaches, antibiotic resistance, and soil fungi associated with swine and poultry manure, municipal biosolids, and waste-impacted soils, plants, air, and water will be addressed. New uses of manure will be investigated, including swine manure for bioenergy crops, poultry litter for plant disease biocontrol, and litter with gypsum for remediation of degraded soil. Experiments employ a combination of traditional methods and state-of-the-art techniques and equipment. Work will be done in cooperator rearing houses and manure storage areas on confined animal feeding operations and in crop fields of manure end users. Contamination of soil, water, air, and plants from land application of manure and biosolids will be assessed and off-site transport of nutrients, pathogens, and antibiotic resistance will be determined. Information will be developed into best management practices to protect the environment and human and animal health by maximizing crop nutrient utilization, minimizing bacterial contamination and antibiotic resistance, reducing ammonia and greenhouse gas emissions, and exploiting biocontrol potential.

3. Progress Report
Renovation of coal strip-mined soils: A chronological sequence of research on soil quality is evaluating poultry litter and industrial by-products on soil productivity and biomass. A litter nutrient runoff test was completed. Broiler litter and industrial by-products are being evaluated for corn, soybean, and cotton production. Effects of residual fertilizer value from litter applied to cotton on subsequent crops of soybean are being tested. In-house poultry litter composting was done and molecular tests of bacterial clone libraries and 16 ribosomal subunits (16S) counts begun. Field and cultural tests were done in a swine mortality compost study. A litter bacteria runoff test was done and quantitative polymerase chain reaction (PCR) and endotoxin tests begun. Survival of pathogens in manure and biosolids was tested and 16S clone libraries and quantitative PCR begun. Manure and biosolids treatments were set up to test pathogen survival in the field, and soil was tested for fecal indicators, pathogens, and antibiotic-resistant bacteria. Bacterial pathogen decay time was tested on inoculated plants in growth chambers. A broiler house study of seeding new litter with old looks at Salmonella. Bacterial and nutrient levels were tested in a newly decommissioned swine manure lagoon. Germination and winter survival of Mercheron, a varaiety of napiergrass, were less than 50% when seeded in October. Concentration of nutrients and ash in napiergrass fertilized with swine-lagoon effluent will be determined periodically during the summer of 2011. Growth of napiergrass under simulated-summer temperatures tended to increase the biomass and concentration of fermentable sugars in leaves. Bermudagrass Potassium (K) nutrition is related to a naturally occurring disease epidemic. Intensive, year-round harvesting of forage grasses is useful for amelioration of high soil Phosphorus (P), but will probably require close attention to Nitrogen (N) and K nutrition. Research of a naturally-occurring disease epidemic identified 6 species of "Helminthosporium-type" fungi in bermudagrass, and disease severity was related to plant and soil K concentration. Evaluation of the effects of K fertilization and thatch removal by field burning on disease occurrence and severity has begun. We completed the 3rd year of a 3-factor study showing the advantages of a cover crop when poultry litter is applied to cotton by subsurface banding in the fall. Soil samples were collected in the first year of a sustainable land application study. Incubation of raw poultry litter with selected byproducts for 45 days altered soil pH.

4. Accomplishments
1. Poultry manure application time impact. Although spring-applied litter has the best agronomic response, this is often not practical because of weather in the southeast, thus, forcing producers to apply broiler litter in the fall. However, fall application of broiler litter over a winter fallow results in substantial leaching losses of Nitrogen (N) and reduces the potential fertilizer value of the manure. ARS scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, studied the impacts of a cover crop of winter rye on fall application of litter. Overseeding a cover crop to fall-applied broiler litter synchronized available N with crop needs, maximized N use efficiency, and minimized the risks of leaching losses of N. This practice helps fill critical gaps in understanding whether detrimental effect of fall-applied broiler litter can be mitigated by a combination of cover cropping strategies. The management practice positively impacts the agronomic and economic aspects to the farmers and is currently being implemented in some areas in the region. A module based on this work was selected and written into a Continued Education (CEU) article for Crops & Soils magazine and went out to approximately 14,000 certified crop advisers and soil scientists. Url is:

2. Shallow incorporation of poultry litter in no-till production system decreases nutrient runoff. Use of broiler litter to fertilize no-till crops exposes the litter and its nutrients to risk of loss in runoff, lowers litter effectiveness as a nutrient source, and degrades the quality of surface waters. ARS scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, evaluated the impact of broiler litter management practices on surface runoff quality from an upland soil under a no-till system. They found that either shallow incorporation of broiler litter into the top inch of soil surface or precision application of subsurface banding of poultry litter in shallow trenches reduced total Nitrogen (N) and total Phosphorus (P) in runoff by 82 and 88%. Litter associated bacteria in the runoff also decreased by two orders of magnitude when compared to surface broadcast of litter. In addition, soil fertility and cotton yields were improved. Subsurface banding of litter to row crops, under no-till systems, could be a very effective management practice to help prevent poultry litter applications from degrading the quality of surface waters.

3. Microbial risk analysis: manure vs. biosolids. The presence of microbial pathogens in manure and biosolids has long been recognized as a drawback to use of these waste residuals in settings where the public could be exposed to the pathogens. Regulations and recommendations in place for 20 years have minimized exposures, but recent national and foreign outbreaks of enteric illness call into question our understanding of pathogen inactivation and risk. ARS scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, conducted an in depth quantitative microbial risk analysis using current (local), historical, and national data sets for various manures and municipal Class B biosolids. Risks were analyzed for a number of situations, including occupational and public exposures (raw vegetable consumption, aerosol exposure, etc.). Using empirical data and exposure modeling, the scientists determined that specific microbial risks differed for the respective waste residuals; bacterial risks are greater for manure, while viral risks are greater for biosolids. Using these models, the scientists estimated that for public risks to approach significant levels, a “regrowth” step must occur that increases pathogen loads to detectable outbreak levels after residuals are applied in the environment; so applying residuals as field crop fertilizer under conditions that preclude or minimize pathogen regrowth poses minimal public risk. This research provided a first of its kind comparison of the two residual types and highlighted the need for more microbial incidence data.

4. Poultry litter management practice affects pathogens. In-house composting of used broiler litter between flocks is a recently introduced management practice thought to reduce levels of food-borne and nuisance pathogens that cost the industry millions of dollars in lost revenue. The practice, however, may promote faster pathogen recolonization, as levels of other beneficial bacteria are reduced, thus limiting their ability to compete against harmful bacteria. ARS scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, compared recolonization rates after in-house composting and normal decaking practices. They simulated a normal flock cycle in controlled environmental chambers by regularly adding pathogen-inoculated fresh poultry fecal matter to litter microcosms. They found that in-house composting increased the rate that pathogens, including Salmonella, recolonized the litter, but by the end of the flock cycle, levels in composted and non-composted litter were the same. This study demonstrated that although in-house composting has a neutral effect on pathogen levels in spent litter intended for land application as crop fertilizer, faster pathogen recolonization may expose broilers to higher pathogen levels earlier and longer in the flock cycle.

5. Pathogen survival after land application of manure. Enteric pathogens on soils and plants fertilized with manure can pose risks to grazing animals and humans if the pathogens survive or grow in the soil or plant environments. ARS scientists at the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, studied the survival of naturally occurring bacterial pathogens and fecal indicator bacteria in swine manure lagoon effluent during and immediately following land application in a commercial farming operation. Bacteria were monitored in aerosols, soil, and on grass leaves. Survival of most indicator bacteria and pathogens was intermittent and most bacteria were either inactivated within 72 hours of land application or were diluted in the application process to levels below cultural detection limits in the soil and grass environments. Aerosolized pathogens were rarely detected and then only within the immediate (less than 10 miles) downwind vicinity. This study established that bacterial pathogens known to be present in swine manure were rarely detected in environmental samples after land application of lagoon effluent, suggesting that: 1) land application of lagoon effluents dilutes bacterial pathogens and mitigates potential risks; and 2) efforts to track pathogens, such as from an outbreak of enteric illness, back to manure-contaminated plants or soil will require development of more sensitive detection techniques than those currently available.

6. Choice of bedding material in broiler houses can reduce ammonia generation. Ammonia release to the atmosphere is an environmental concern with possible negative effects on air quality (particulate formation), terrestrial life (decreased ecosystem diversity), and water resources (nutrient enrichment). ARS scientists in the Genetics and Precision Agriculture Research unit at Mississippi State, MS, showed that ammonia generation is reduced when organic materials (wood shavings and rice hulls) rather than inorganic materials (sand and vermiculite) are used for bedding. Increasing moisture content caused more ammonia generation in all materials. A conservative estimate for limiting in-house ammonia in only 10% of U.S. poultry houses equates to more than $26 million in additional grower revenues due to increased broiler production efficiency. This identification of optimal bedding materials provides producers with research information allowing them to minimize ammonia generation. This information is also of value to poultry companies for optimizing management strategies that limit unnecessary bedding moisture.

7. Poultry litter provides biological control of spores of plant pathogenic fungi in soil. Species of Bipolaris, Curvularia, and Exserohilum are plant disease-causing fungi that attack leaves and stems of many turfgrasses and cereal crops and also invade soil where they can infect roots and kill plants. The potential of poultry litter to provide biological control of spores (microscopic structures that germinate and initiate disease) of four species of these fungi in soil was evaluated for the first time. ARS scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, placed spores into porous nylon membranes, incubated them in moist soil for two weeks with and without poultry litter added at 4% and 8% by weight, retrieved spores, and evaluated their ability to germinate. In repeated experiments, spores of all species incubated in soil without litter germinated at frequencies of 70-87% following their retrieval. When spores were incubated in soil containing 4% litter, germination was reduced to 2-42% among the four fungi, and with 8% litter, it was further reduced to 1-17% with many spores visibly fragmented or disintegrated. These results indicate that poultry litter may provide significant biological control of spores of four species of plant pathogenic fungi when incorporated into soil, but its effectiveness as a biological control material differs among the species.

8. Nitrogen fertilization of ryegrass increases removal of soil Phosphorus (P). Some manure-impacted soils represent a risk for nutrient loss that may damage water quality. ARS scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, determined Nitrogen (N) effects on ryegrass-bermudagrass uptake of P and soil test P following the cessation of poultry manure applications. Maximum uptake of 61 kilogram P per hectare was obtained by applying 112 kilogram N per hectare in March and 56 kilogram N per hectare in May. Ryegrass P uptake was greater with 168 than 112 kilogram N per hectare. Harvest and removal of ryegrass-bermudagrass hay for two years resulted in a 38-44% reduction in soil test P. Knowledge of soil test P allows a producer to be proactive about when and where to resume manure applications.

9. Residual productivity of no-till cotton soil after application of poultry litter. Farmers often ask if manures improve the productivity of soil after ceasing application. ARS scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, found that a no-till field that received six years of suboptimal rates of 2 or 3 tons per acre of poultry litter produced up to 30% more cotton yield when the field was returned to commercial nitrogen fertilization in the 7th and 8th years. This showed that continuous application of poultry manure improves the productivity of no-till soil for at least 2 years after ceasing manure application. Poultry litter application of 3 tons per acre or the full commercial nitrogen fertilization of 120 pounds per acre to a severely nitrogen depleted soil due to continuous cotton without fertilization for six years failed to restore the productivity of the soil in the first 2 years of application. This suggests a severely depleted soil may require several years of repeated applications of adequate poultry litter or inorganic fertilization to restore its productivity. These results provide research-based information for row crop farmers on the relative long-term value of repeated application of suboptimal rates of poultry litter in the southeastern U.S.

10. Liming marginal acidic soils may be unnecessary if using poultry litter for cotton fertilization. Soils with borderline acidity have to be limed to correct the low pH before planting cotton or other row crops. But liming may not be necessary if using poultry manure in place of conventional synthetic nitrogen fertilizers. ARS scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, studied the productivity of cotton fertilized with manure versus a commercial nitrogen fertilizer in an upland soil with marginal soil acidity. Their results showed fertilizing with ammonium nitrate, an inorganic nitrogen fertilizer, further acidified the soil, elevated leaf manganese concentration to potentially toxic levels, and reduced lint yield. Poultry manure, unlike ammonium nitrate, maintained or reduced acidity of the soil, prevented the elevation of tissue manganese concentration, and improved lint yield. Fertilizing with poultry litter makes liming unnecessary for profitable cotton production in soils with marginal soil acidity and productivity.

Review Publications
McLaughlin, M.R., Brooks, J.P., Adeli, A., Read, J.J. 2010. Comparison of selected nutrients and bacteria from common contiguous soils inside and outside swine lagoon effluent spray fields after long-term use. Journal of Environmental Quality. 39:1829-1840.

Miles, D.M., Brooks, J.P., Sistani, K.R. 2011. Spatial contrasts of seasonal and intraflock broiler litter trace gas emissions, physical and chemical properties. Journal of Environmental Quality. 40:176-187.

Tewolde, H., Adeli, A., Rowe, D.E., Sistani, K.R. 2011. Cotton lint yield improvement attributed to residual effect of repeated poultry litter application. Agronomy Journal. 103:107-112.

Adeli, A., Tewolde, H., Jenkins, J.N., Rowe, D.E. 2011. Cover crop use for managing broiler litter applied to cotton in the fall. Agronomy Journal. 103:200-210.

Read, J.J., Aiken, G.E., Lang, D.E. 2010. Herbage nutritive value of tall fescue fertilized with broiler litter and inorganic fertilizer. Forage and Grazinglands. Available:

Tewolde, H., Adeli, A., Sistani, K.R., Rowe, D.E. 2010. Potassium and magnesium nutrition of cotton fertilized with broiler litter. Journal of Cotton Science. 14:1-12.

Adeli, A., Shankle, M.W., Tewolde, H., Brooks, J.P., Sistani, K.R., McLaughlin, M.R., Rowe, D.E. 2011. Effect of surface incorporation of broiler litter applied to no-till cotton on runoff quality. Journal of Environmental Quality. 40:566-574.

Miles, D.M., Rowe, D.E., Cathcart, T.C. 2011. Litter ammonia generation: moisture content and organic versus inorganic bedding materials. Poultry Science. 90:1162-1169.

Zerzghi, H., Gerba, C.P., Brooks, J.P., Pepper, I.L. 2010. Long-term effects of land application of Class B biosolids on the soil microbial populations, pathogens, and activity. Journal of Environmental Quality. 39:402-408.

Pepper, I.L., Brooks, J.P., Sinclair, R.G., Gurian, P.L., Gerba, C.P. 2010. Pathogens and indicators in United States Class B biosolids: national and historic distributions. Journal of Environmental Quality. 39:2185-2190.

Zerzghi, H., Brooks, J.P., Gerba, C.P., Pepper, I.L. 2010. Influence of long-term land application of class B biosolids on soil bacterial diversity. Journal of Applied Microbiology. 109:698-706.

Brooks, J.P., McLaughlin, M.R., Scheffler, B.E., Miles, D.M. 2010. Microbial and antibiotic resistant constituents associated with biological aerosols and poultry litter within a commercial poultry house. Science of the Total Environment. 408:4770-4777.

Miles, D.M., Rowe, D.E., Cathcart, T.C. 2011. High litter moisture content suppresses litter ammonia volatilization. Poultry Science. 90:1397-1405.

McLaughlin, M.R., Brooks, J.P., Adeli, A., Tewolde, H. 2011. Nutrients and bacteria in common contiguous Mississippi soils with and without broiler litter fertilization. Journal of Environmental Quality. 40:1322-1331.

Last Modified: 06/28/2017
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