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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 Precision Agriculture Research

2012 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:
Broiler litter (BL) and swine mortality compost +/- flue gas desulfurization (FGD) gypsum were tested with standard treatments for reclaiming coal strip mine soil by comparing biomass, nutrient leaching, and soil quality. The impact of BL +/- FGD gypsum on biomass, grain production, and soil carbon (C) sequestration was tested in a corn-winter cover crop-soybean rotation in an historically low organic matter soil. BL +/- FGD gypsum was tested as fertilizer for corn; NH3, greenhouse gas (GHG: CO2, N2O, CH4) emissions, nitrogen (N) mineralization, and yield were measured. Changes in chemical properties over time were measured in lab tests of BL +/- byproducts. A simulated grazing study estimated N loss in pasture soil fertilized with BL. Pelletized BL applied in precision bands +/- FGD gypsum was evaluated for effects on cotton yield and soil quality in irrigated and dry land systems. Pelletized and non-pelletized BL were compared in a forage system measuring forage yield and runoff water quality. A field study of cotton fertilized with pelletized BL was continued; plant reflectance and tissue N status were measured at different growth stages. Residual effects of BL fertilization of cotton and corn were evaluated on a subsequent soybean crop. Year 2 of a sustainable land application study of a cotton-corn rotation was completed. Instrumentation was secured and a new on-farm study begun on variable rate BL applied to row crops. Studies continued in no-till cotton on the efficacy of two ARS-patented subsurface BL banding applicators. Emissions of NH3 and GHG were measured in commercial broiler houses and precisely controlled lab experiments to provide baseline data and suggest mitigation strategies for confined animal feeding operations, fertilizer applications, and generation of value-added products from animal wastes. BL and amendments were tested for pathogen runoff and runoff control. Cultural and molecular tests were done. Clone library and quantitative polymerase chain reaction (qPCR) analyses were completed for chronosequence and treatment-based studies of reclaimed coal strip mine soils. Environmental factors, gas emissions, and microbial levels were measured in a swine mortality compost study. Pathogen survival, microbial ecology, and antibiotic resistance (AR) patterns were determined in soils receiving manure and biosolids. AR testing was conducted on Salmonella isolates from a litter-seeded broiler house. New microbial risk pathogen inactivation models were tested and newly derived empirical pathogen environmental inactivation rates determined. Empirical relationships were developed to reconcile disparate microbial population estimates from cultural and qPCR methods. A study of swine-effluent fertilization for bioenergy crop production in a center pivot irrigation spray field compared ‘Merkeron’ napier grass and hybrid bermudagrass for tissue nutrient levels and biomass yield, and soils for C sequestration. All napier grass vegetative propogules (billets) planted in late-August grew, but lack of cold tolerance reduced winter survival.


4.Accomplishments
1. Flue gas desulfurization (FGD) gypsum and poultry manure application. Poultry manure derived-nutrients placed in the soil surface from manure application are vulnerable to loss through emission and runoff and reduces the fertilizer value of this by-product. A mechanism to help protect nutrients from loss and enhance their potential uses is needed for sustained productivity. ARS scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, evaluated the impact of combining FGD gypsum, a low cost coal combustion by-product, with poultry manure applied to no-till corn and cotton, and results indicated that co-application of broiler litter with FGD gypsum improved soil carbon (C) storage, protected nutrient from loss, enhanced crop nutrient utilization potential, and improved yield, particularly in soils low in organic matter. FGD gypsum can be an agriculturally important resource and its co-application with poultry manure could be recommended as a best management practice if the growers become aware of its beneficial and potential uses.

2. Subsurface banding of broiler litter better method for corn fertilization. The fertilizer value of broiler litter has been recognized by the farmer and applied to row crops under both tillage and no-till systems. However, application of poultry litter to the row crops under no-till soil management concentrates litter derived-nutrients at the soil surface, enhances volatilization of nitrogen (N) and greatly increases nutrient losses in runoff water. Losses of applied nutrients can cost farmers substantial income and degrade air and water quality. ARS scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, studied the impacts of broiler litter placement on corn yield and N utilization under the no-till system and found that subsurface banding of broiler litter substantially increased corn N use efficiency by 56%, and grain yield by 16% when compared to surface broadcast litter. This indicates that subsurface banding of broiler litter could be considered as an effective management practice for no-till corn and other row crop production and would become a method of choice for applying solid manures, if the technology can be developed and commercialized as a practical option for the producers.

3. Winter cover crop increases effectiveness of fall-applied broiler litter as cotton fertilizer. Applying broiler litter and other manures in the fall to fertilize spring-planted crops carries great risk of losing the nutrient benefits. ARS scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, in cooperation with researchers at other ARS locations, and Mississippi State University found that planting wheat cover crop as a conservation practice soon after applying poultry litter in the fall in shallow subsurface bands increases the effectiveness of the litter as cotton fertilizer for spring-planted crops. The same research also showed cover crop was much more beneficial for cotton that received no fertilizers in the fall or spring suggesting that the winter-planted wheat conserved nutrients from loss during the fall or winter months before planting cotton in the spring. These results are expected to contribute to the sustainability and environmental acceptability of poultry litter use as a fertilizer for cotton and other row crops in the southern and southeastern United States.

4. Cotton fertilized with poultry litter accumulates more mineral elements in the seed. Accumulation of excess nutrients in the soil is a concern when poultry litter is used to fertilize crops for several years. ARS scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, in cooperation with researchers at other ARS locations and Mississippi State University demonstrated that cotton reduces the risk of excess nutrient buildup in litter-fertilized soils by absorbing and accumulating many of the nutrient elements into the seed. Seeds of cotton fertilized with litter accumulated more copper, zinc, phosphorus, magnesium, and boron than cotton fertilized with commercial inorganic fertilizers. These elements are thus removed from the field at harvest and their buildup in the soil minimized. These results are expected to help farmers and extension experts in managing excess nutrient buildup in the soil in the southern and southeastern U.S. where both cotton and poultry production are major enterprises.

5. Nutrients and fecal bacteria in pasture soils. In Mississippi, broiler litter is often used to fertilize bermudagrass pastures and approximately 57% of the total land area is utilized for grazing by livestock. Due to the potential for excess loading of nitrogen (N) and fecal bacteria in pasture-based systems, ARS scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, determined if the combination of broiler litter and cattle feces (dung) increases the N load and concentration of bacteria in surface-water runoff, as compared to litter alone. In greenhouse studies on runoff water quality from a Marrieta soil, total N loads of 64, 366, and 378 milligrams were observed in the ‘control’, poultry litter and litter + cattle dung treatments, respectively. Therefore, grazing by cattle appeared to pose little additional risk of N loss in pasture soil fertilized with poultry litter. Based on total N applied, these N loads correspond to N-leaching losses of 9.3% for troughs with litter and 9.5% for troughs with litter + dung. Fecal bacteria measured in cattle dung were not observed in the runoff water using cultural or molecular methods. Results provide information to producers and policy makers on managing bermudagrass, broiler litter, and livestock to minimize watershed runoff losses of N.

6. Ammonia loss from poultry litter is amplified by higher air flow rates. ARS scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, quantified ammonia generation from litter while increasing air flow rates per volume of litter. Ammonia release to the atmosphere is an environmental concern with potential negative effects for air quality (particulate formation), terrestrial life (decreased ecosystem diversity), and water resources (eutrophication). For emerging mitigation technologies where ammonia is captured, the results indicate a need to combine forced ventilation with other parameters (like temperature) that maximize ammonia generation from litter. Growers can reduce ammonia on the farm by covering litter stockpiles to reduce wind flow over them or, within broiler houses, couple intense ventilation between flocks with an ammonia scrubber.

7. Recommendations for litter moisture and ammonia control in broiler houses is conveyed to growers. ARS scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, discovered the critical litter moisture content where ammonia generation is maximized. Simple techniques were communicated, via factsheet, showing growers how to measure litter moisture and barn ammonia concentration to improve litter management. In addition, broiler house management solutions to optimize water inputs to litter were provided. Growers and integrators can use this information to produce healthier birds, reduce environmental concerns due to ammonia release, and to improve profits.

8. Pathogen survival in organic waste is related to organic matter content. The presence of foodborne pathogens in soils used for food crop production can be influenced by many factors, including the level and type of organic matter (OM) in the organic fertilizer. Traditionally, quantitative risk analyses have relied on “one size fits all” pathogen inactivation rates when predicting pathogen survival. ARS scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, have demonstrated the influence of high OM content of the organic fertilizer on pathogen survival in a series of studies. Experiments using culture and molecular analyses demonstrated that high OM matrices, such as biosolids and cattle manure, protected Salmonella and E. coli O157 better than low OM liquid matrices. Pathogen inactivation rates were substantially affected by OM levels, and demonstrated that traditional inactivation rates for biosolids and cattle manure, need to be revised. In addition, the exclusive use of molecular data can yield more conservative results than culture only; future risk analyses need to take this into account. This research is the first of its kind to produce and compare cultural and molecular data in risk analyses. These results provide further light on foodborne outbreaks potentially linked to manure.

9. Seasonal changes in nutrient and bacterial levels affect lagoon water quality. Confined animal feeding operations (CAFOs) using anaerobic lagoons for manure treatment often use the lagoon water for crop irrigation following farm-specific nutrient management plans (NMPs). Implementation of stricter U.S. environmental regulations in 2013 will set soil phosphorus (P) limits, impacting land applications of manure, and requiring revision of NMPs. More precise knowledge of lagoon water quality was needed to support NMP requirements and to also improve understanding of nitrogen (N) and carbon (C) losses in lagoon ammonia and greenhouse gas emissions, and environmental contamination risks by fecal bacteria, including zoonotic pathogens. ARS scientists of the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, determined year-round levels of nutrients and bacteria from swine CAFO lagoon water. Temporal and spatial differences in levels of fertilizer nutrients (e.g. N, P, and potassium (K)), heavy metals (i.e. copper (Cu) and zinc (Zn)) and bacteria, including fecal indicators (i.e. enterococci and staphyolococci) and zoonotic pathogens (i.e. Campylobacter, Clostridium, E. coli, Listeria, and Salmonella) were described, analyzed, and correlated with environmental factors (e.g. temperature). These results enable decision makers to develop improved NMPs and environmental risk assessments.

10. Remotely controlled manure lagoon water column sampler designed, built, and tested. Conventional water column samplers used in manure lagoon studies were limited to shallow samples collected near shore or required a manned boat, prompting ARS scientists of the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, to design a new unmanned sampler capable of remotely simultaneously collecting multiple samples from different depths in the water column. The new sampler was tested in a study of lagoon water quality, which showed that pH, electrical conductivity, nutrient concentrations, and bacterial levels did not differ significantly between samples collected at 0.04, 0.47, and 1.0 m depths, but differences between samples collected in winter and those collected in early spring were significant for five of ten nutrients and four of seven bacterial groups. Results demonstrated the utility of the new sampler in collection of samples from multiple depths, showed no stratification of nutrients or bacteria between 0.04 and 1.0 m depths, and suggested that a more extensive study of nutrients and bacteria could omit collections from 0.47 m, but should include a greater range of dates and seasons. This technology enables safer and more precise collection of stratified water samples from manure lagoons and other water bodies.

11. Pathogen presence in broiler houses is dependent on flock age. Targeting foodborne (e.g. Salmonella) and nuisance (e.g. Clostridium) pathogens in broiler houses could reduce broiler house microbial treatment costs. According to two recent studies by ARS scientists of the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, pathogen presence in broiler house litter is not necessarily based on intra-house specific site variations. These studies showed and confirmed that foodborne and nuisance pathogens were linked to flock age. In-house pathogen variability was associated with the ‘brood end’ of the house, but not with high moisture or high traffic locations. Pathogen presence appeared to be cyclical, and to be reintroduced with baby chicks in successive flocks, suggesting egg and chick production as the probable source. Inter-house traffic and management operations likely contributed to transfer of pathogens from contaminated to uncontaminated sites within and between houses.


Review Publications
Read, J.J. 2012. Spring nitrogen fertilization of ryegrass-bermudagrass for phytoremediation of phosphorus-enriched soils. Agronomy Journal. 104:908-916.

Read, J.J., Brink, G.E., McLaughlin, M.R., Sistani, K.R. 2011. Nitrogen and winter cover crop effects on spring and summer nutrient uptake. Grass and Forage Science. 66:381-390.

Tewolde, H., Adeli, A., Sistani, K.R., Rowe, D.E. 2011. Mineral nutrition of cotton fertilized with poultry litter versus ammonium nitrate. Agronomy Journal. 103:1704-1711.

Adeli, A., Tewolde, H., Jenkins, J.N. 2012. Broiler litter type and placement effects on corn growth, nitrogen utilization and residual soil nitrate-nitrogen in a no-till field. Agronomy Journal. 104:43-48.

Adeli, A., Tewolde, H., Rowe, D.E., Sistani, K.R. 2011. Continuous and residual effects of broiler litter application to cotton on soil properties. Soil Science. 176:668-675.

Last Modified: 7/25/2014
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