2007 Annual Report 1a.Objectives (from AD-416) Increase the current effort to develop and evaluate management practices and treatment technologies that reduce air emissions of ammonia and odor causing compounds from animal production operations, manure storage areas, and field application sites. The overall goal of the research project formulated in a real partnership between ARS and Western Kentucky University (WKU) is to conduct cost effective and problem solving research associated with animal waste management. The research will evaluate management practices and treatment strategies that protect water quality, reduce atmospheric emissions, and control pathogens at the animal production facilities, manure storage areas, and field application sites, particularly for the unique karst topography. This Project is a unique situation in the sense that non-ARS scientists from a university are included in a research project to conduct research under the same National Program. Hence, to achieve the ultimate goal of this project, the integration and coordination of scientific expertise of the scientists from ARS and WKU are required within and across all objectives. The objectives and related specific sub-objectives are organized according to the three major components (Nutrient, Emission, and Pathogen) of the National Program 206, which mostly apply to this project. The specific objectives for the next 5 years are: Nutrient Component Objective 1: Develop management practices and decision tools for long-term use of animal manure as an alternative source of fertilizer for forages and row crops with regard to the following factors: Impacts on crop yield, nutrient loading, availability and uptake, application rate and timing, tillage, methods of application, soil quality, and soil carbon sequestration and greenhouse gas emissions. Objective 2: Determine if nutrient loading from agricultural watersheds in karst terrain is a function of physical watershed characteristics. Emission Component Objective 3: Reduce odiferous emissions by developing innovative molecular-based methods to identify and quantify microorganisms and biological activities responsible for production of odorous compounds in livestock wastes. Objective 4: Develop new analytical approaches to quantify gases (e.g. methane, H2S), volatile odor compounds (e.g. p-cresol, skatole, and other VOCs) and evaluate treatment technologies for odor abatement at animal production facilities and manure-applied fields. Pathogen Component Objective 5: Employ molecular-based methods to improve detection, quantification, and evaluation of transport, and survival of pathogens including Salmonella and E. coli O157:H7 from animal manure. Also, compare survival of these pathogens with indicator organisms through a series of laboratory and watershed studies. 1b.Approach (from AD-416) This research project was conceived as a cooperative/partnership and comprehensive research program between USDA-ARS Animal Waste Management Research Unit (AWMRU) and Western Kentucky University (WKU). The research is designed to utilize the scientific expertise and facilities of both institutions to conduct problem-solving research related to animal waste management in Kentucky and the Southeastern US. The research effort will be multi-disciplinary and multifaceted in support of decision making and systems development. Research focuses will be on all three components (Nutrient, Atmospheric Emission, and Pathogens) of the National Program 206. State-of-the-art laboratories and equipments exist at both AWMRU and WKU, which can be accessed by the scientists. Main instruments include: ICP, GC-MS, Lachat, C/N Analyzer, Real time PCR, etc. 4.Accomplishments 1) Poultry litter application method and runoff initiation effect on nutrient and E. coli losses from pasture field: More than 85% of poultry litter applied in the U.S. is being applied to pasture lands year-round. Many studies have indicated the advantages of manure incorporation into soil in contrast to broadcast application to reduce nutrient losses. However, subsurface application of poultry litter through injection banding into a perennial forage system to reduce nutrients and bacterial losses has not been evaluated. In this study, we used rainfall simulations to examine the effect of broiler litter application method on nutrient and E. coli losses in runoff from tall fescue pasture in the Appalachian Plateau. The results strongly suggest that subsurface banding of broiler litter into perennial grassland significantly reduce nutrient and pathogen losses by runoff events compared to the traditional surface-broadcast practice. Also, litter application timing that increases the time to potential runoff event will greatly reduce nutrient and E. coli losses in runoff. This research supports Problem Areas 3 and 4 of the Nutrient Component of NP 206 – Management Tools for Indexing and Evaluating Nutrient Fate and Transport. 2) Broiler litter as a cotton fertilizer: The same southern and southeastern states that grow most of the U.S. cotton also generate an enormous amount of poultry litter which is applied on land not far from where it is generated, a practice which leads to serious environmental concerns. Applying litter to cotton land away from chicken houses can ease the burden, but very little litter is applied to fertilize cotton, partly because of the scarcity of precise, well-packaged research knowledge. This research has established that (1) the often-recommended litter rate of 2 ton/acre is inadequate for many cotton production situations on a short-term basis and that (2) this rate should be supplemented with about 60 pounds/acre of fertilizer nitrogen when about 3 bales/acre lint yield is expected. The research also showed cotton is an efficient crop in extracting nitrogen supplied by as much litter as 3 tons/acre and, therefore, the risk of litter-derived nitrogen detrimentally affecting the immediate environment is no greater than the risk of fertilizer-derived nitrogen. However, fertilizing cotton with 3 tons/acre or more may lead to gradual accumulation of phosphorus in the soil to detrimental levels. This research expanded research-based knowledge for using poultry litter for cotton production and benefits poultry and cotton producers in the southern and southeastern U.S. The accomplishment addresses Problem Area 4 -- Farming Systems and Practices for Efficient and Balanced Manure Nutrient Management -- of the Nutrient Management Component under NP 206. 3) Comparison of the survival behavior between Campylobacter jejuni and Escherichia coli: Campylobacter jejuni is an important pathogen commonly found in agricultural wastes and is a leading cause of gastroenteritis in the U.S., yet very little is known about this organism’s survival. Research showed that survival of C. jejuni is affected by groundwater nutrient composition and its survival varies in a markedly different manner than that of E. coli. These findings call into question the effectiveness of using Escherichia coli as an indicator of potential groundwater contamination by Campylobacter jejuni. This research supports Problem Area 2a of the Pathogens Component of NP 206 – Inactivation Rates and Transport Characteristics of Pathogens in Animal Agriculture. 4) Limitations to using linearized Langmuir equations: One of the most commonly used models for describing solute sorption to soils is the Langmuir model. Because the Langmuir model is nonlinear, however, many researchers use linearized versions of this model. This research examined the limitations of using linearized Langmuir equations by fitting phosphorus sorption data with four linearized versions of the Langmuir equation and comparing results with those obtained with the nonlinear Langmuir equation. The results clearly demonstrated that the use of linearized Langmuir equations needlessly limits the ability to model sorption data with good accuracy. Therefore, to encourage the use of the nonlinear Langmuir equation, an easy-to-use Microsoft Excel spreadsheet was developed, capable of performing nonlinear regression and providing best-fit parameters and statistics of fit. The spreadsheet is now available to the public via the World Wide Web. This research supports Problem Area 3 of the Nutrient Component of NP 206 – Management Tools for Indexing and Evaluating Nutrient Fate and Transport. 5) Detection of the causative agent of Johne’s disease in agricultural environments: Detection of Johne’s disease, an enteric infection of cattle caused by Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis), has been impeded by the lack of rapid, reliable detection methods. In this research, molecular biological methods were optimized to detect M. paratuberculosis in agricultural environments. Data from this study showed that the Johne’s disease agent could remain in pasture soil for more than 200 days after the removal of a clinically infected dairy cow. Methods developed in these studies will be used by Johne’s disease researchers to identify environmental sources of the organism. Studies are underway to evaluate survival of the organism in biofilms of concrete, plastic, stainless or galvanized steel trough materials. This data has been published and presented at 3 different meetings and a collaborative effort is underway with scientists at the Miner Institute in New York to evaluate the survival of the causative agent of Johne's disease over the course of the ensiling process. This research addresses Problem Area 1 (Methods Assessment and Development) of the Pathogens and Pharmaceutically Active Compounds (PACs) Component of NP 206. . 6)Identification of odor producing microorganisms in swine wastes: Skatole is one of the most malodorous compounds produced from anaerobic degradation of animal waste. Little is known of the biochemistry involved in skatole production, the phylogeny of skatole-producing microorganisms or the conditions that favor their growth. Research conducted in this lab showed that skatole production in swine lagoon slurries is greatly enhanced by the addition of indole acetic acid, an intermediate of tryptophan degradation. Molecular biological methods showed population shifts in skatole-producing microbial communities were linked to increases in the occurrence of Bacteroides sp. and acetogenic microorganisms. These studies provided valuable new information about the identity of organisms associated with odor production in swine lagoon slurries. These data have been published and presented at national and international meetings. Studies are on-going to characterize how odor-producing microbial populations change on a spatial and temporal scale. This research addresses Problem Area 1 (Understanding the Biological, Chemical, and Physical Mechanisms Affecting Emissions) of NP 206. 7) Development of equilibrium sampling techniques for the quantification of malodors from waste lagoons: The factors that are most important in controlling the emission of malodorous compounds from wastewater lagoons are largely unknown. One of the main reasons for this is that these compounds, while extremely offensive in odor, often occur in amounts that are below the limit of quantification of techniques currently available for their capture. Our research entailed development of an equilibrium sampler that was able to measure malodorous compounds at very low levels in wastewater and air samples from a swine wastewater lagoon. We have established changes in the wastewater concentrations of malodors due to management practice and season and studies are underway to also determine relative air flux of malodors. This research has been published and presented at a national meeting and collaborative research is being conducted with scientists at Western Kentucky University to determine the relationship of emissions with meteorological conditions at the lagoon. This research supports Problem Area 1 (Understanding the Biological, Chemical, and Physical Mechanisms Affecting Emissions) of NP 206. 8) Understanding of spatial shifts in microbial population structure within poultry litter as affected by environmental conditions: Microbial diversity in poultry litter plays an important role in shaping the quality of the poultry litter as a fertilizer and as a nutritional feedstock, and influences malodor production and potential health risks. It is, therefore, essential to understand how the structure of microbial populations within poultry litter is influenced by the physical environment of the poultry house. This knowledge, in turn, could aid in the development of management practices that would reduce microbial populations responsible for toxic air emissions (especially ammonia emissions) and pathogen incidence. Understanding the contributing factors affecting microbial community structure may provide a rational basis for improving the design and optimizing the remedial options for toxic air and pathogenic reduction, whether these involve microscale biological treatment such as enzyme inhibition or physicochemical treatment such as adding chemicals to reduce emissions. We found that there appear to be differences in the types of microorganisms over the length of a poultry house, which correspond to the differences in the environmental conditions of the poultry litter. This research supports Problem Area 1 (Understanding the Biological, Chemical, and Physical Mechanisms Affecting Emissions) of NP 206. 6.Technology Transfer Number of web sites managed 1 Number of non-peer reviewed presentations and proceedings 11 Number of newspaper articles and other presentations for non-science audiences 5 Review Publications Tewolde, H., Sistani, K.R., Rowe, D.E., Adeli, A. 2007. Nitrogen Extraction by Cotton Fertilized with Broiler Litter. Crop Science. 47:1131-1142. Tewolde, H., Sistani, K.R., Rowe, D.E., Adeli, A., Johnson, J.R. 2007. Lint yield and fiber quality of cotton fertilized with broiler litter. Agronomy Journal. 99:184-194. Tewolde, H., Sistani, K.R., Rowe, D.E., Adeli, A. 2007 Phosphorus Extraction by Cotton Fertilized with Broiler Litter. Agron J. 99:999-1008 Cook, K.L., Rothrock Jr, M.J., Loughrin, J.H., Doerner, K. Characterization of skatole-producing microbial populations in enriched swine lagoon slurry.Federation of European Microbiological Societies Microbiology Letters. 60:329-340 Loughrin, J.H., Way, T.R. An equilibrium sampler for malodors in wastewater. Transactions of the ASABE. Vol. 49(4):1167-1172. Loughrin, J.H. 2006. A comparison of solid phase microextraction and stir bar sorbtive extraction for the quantification of malodors in wastewater. Journal of Agricultural and Food Chemistry. Cook, K.L., Bolster, C.H. Survival of Campylobacter Jejuni and Escherichia Coli in Groundwater During Prolonged Starvation at Low Temperatures. Journal of Applied Microbiology. 103 (2007) 573-583 Lovanh, N.C., Cook, K.L., Rothrock Jr, M.J., Miles, D.M., Sistani, K.R. 2007. Spatial Shifts in Microbial Population Structure Within Poultry Litter Associated with Physicochemical Properties. Poultry Science. Vol 86 pages 1840-1849 Cook, K.L., Britt, J. 2006. Optimization of Methods for Obtaining, Extracting and Detecting Mycobacterium avium subsp. paratuberculosis in Environmental Samples using Quantitative, Real-Time PCR. Journal of Microbiological Methods. V29:154-160 Sistani, K.R., Mays, D.A., Dawkins, R.A. Tall fescue fertilized with alum-treated and untreated broiler litter: runoff, soil, and plant nutrient content. Journal of Sustainable Agriculture. Vol 28(3):109-119