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United States Department of Agriculture

Agricultural Research Service

2009 Annual Report

1a.Objectives (from AD-416)
1. Define the critical environmental and biological factors such as temperature, moisture content, organic matter content/composition, and nutrient content affecting emissions of odor compounds, greenhouse gases, and ammonia from beef cattle feedlot surfaces. 2. Measure the effects of critical environmental and biological factors identified in Objective 1 on nutrient transport of N, P, and indicator microorganisms from beef cattle feedlot surfaces. 3. Determine the potential for emissions of pathogenic, fecal indicator microorganisms, nutrient and odor compounds in wastewater, soil and air during and after spray wastewater application. 4. Evaluate alternative treatment technologies such as constructed wetlands, cattle feedlot runoff systems, and water treatment technologies to reduce or eliminate the occurrence, transmission, or persistence of manure-borne pathogens and excessive nutrients (N and P) and other constituents (biological oxygen demand, pH, and total suspended solids).

1b.Approach (from AD-416)
Experiments will be conducted in the field and in the laboratory to evaluate gas emissions, nutrient transport, and microbial transport and fate associated with specific types of confined animal feeding operations and wastewater treatment processes. Specific areas within beef cattle feedlot pens will be identified that disproportionately emit gases (odor compounds, ammonia, and greenhouse gases) or have a large potential for nutrient runoff through the use of flux chambers and gas chromatography and by the use of artificial rainfall simulators. Flux chambers, mass losses from soil, and bioaerosol sampling will be used to determine the loss of nutrients, odor compounds, and the potential to disseminate manure-borne microorganisms in multi-year studies at field sites where swine wastewater is center pivot applied to agricultural fields. Standard microbiological techniques will be used to determine the prevalence of manure-borne microorganisms after alternative treatments have been used to treat wastewater.

3.Progress Report
Multiple field studies were conducted in cattle feedlots examining emissions and nutrient and pathogen run off from beef cattle feedlot pens where cattle were fed varying levels of distiller’s byproducts. A wide variation in hydrogen sulfide and run off constituents was observed in differing regions (i.e., central mound versus edges) in beef cattle feedlot pens. These studies confirmed that spatially, nutrients, pathogens, organic matter, and gaseous fluxes were quite variable and likely dependent upon numerous environmental factors, most notably moisture and manure content. Initial results also indicate that hydrogen sulfide emissions decrease with time after animals are removed, prior to pen cleaning. Multiple oral presentations describing enhance hydrogen sulfide emissions have been made during the past year with a larger follow-up feedlot study planned for the coming year. An ongoing field study this summer is following the manure from feedlot pen to field application of manure as fertilizer to evaluate the potential for nutrient and pathogen run off from field plots.

1. Cattle feces and cattle feedlot surface material contain distinct microbial communities. Cattle manure is a vehicle for transmission of a number of health-related microorganisms, including Shiga-toxigenic Escherichia coli O157:H7, yet little is known about what bacteria interact and compete with these pathogens in manure. ARS scientists in Lincoln, NE have thoroughly characterized the bacterial communities in the cattle lower gastrointestinal tract (feces) and in beef cattle feedlot surface material. Although much of the mass of the feedlot surface is composed of deposited manure, the microbial communities of feces and feedlot surface material are distinct. These results help define the ecology of pathogens in manure.

2. Unique fecal microbial communities are found in genetically related cattle. There are a number of health-related microorganisms that are associated with cattle feces. In addition to these pathogens, there are many other bacteria that also live in the gastrointestinal tracts of cattle. ARS scientists in Lincoln, NE characterized these bacterial communities from six genetically related cattle and found that there were significant differences in the communities of the six animals. Although some bacteria were shared by all six animals, many bacteria were found only in a single animal. Factors such as diet, age, weight, and gender were all controlled, and were the same for all six animals. This research helps us understand what bacteria are present in cattle feces, and how the pathogens interact with these other bacteria. This research is part of a program to understand the ecology of pathogens in manure so that effective control measures can be developed.

6.Technology Transfer

Number of the New/Active MTAs (providing only)1
Number of Other Technology Transfer5

Review Publications
Clawson, M.L., Keen, J.E., Smith, T.P., Durso, L.M., Mcdaneld, T.G., Mandrell, R.E., Davis, M.A., Bono, J.L. 2009. Phylogenetic Classification of Escherichia coli O157:H7 Strains of Human and Bovine Origin Using a Novel Set of Nucleotide Polymorphisms. Genome Biology [serial online]. 10:R56. Available:

Jacobsen, L., Durso, L.M., Conway, T., Nickerson, K.W. 2009. Escherichia coli O157:H7 and Other E. coli Strains Share Physiological Properties Associated with Intestinal Colonization. Applied and Environmental Microbiology. 75(13):4633-4635.

Goode, B., O'Reilly, C., Dunn, J., Fullerton, K., Smith, S., Ghneim, G., Keen, J., Durso, L.M., Davies, M., Montgomery, S. 2009. Outbreak of Escherichia coli O157:H7 Infections After Petting Zoo Visits, North Carolina State Fair, October-November 2004. Archives of Pediatrics and Adolescent Medicine. 163(1):42-48.

Kim, M., Gilley, J.E. 2008. Artificial neural network estimation of soil erosion and nutrient concentrations in runoff from land application areas. Computers and Electronics in Agriculture. 64(2):268-275.

Gilley, J.E., Sabatka, W.F., Eghball, B., Marx, D.B. 2008. Nutrient transport as affected by rate of overland flow. Transactions of the ASABE. 51(4):1287-1293.

Varel, V.H., Wells, J., Berry, E.D., Spiehs, M.J., Miller, D.N., Ferrell, C.L., Shackelford, S.D., Koohmaraie, M. 2008. Odorant production and persistence of Escherichia coli in manure slurries from cattle fed zero, twenty, forty, or sixty percent wet distillers grains with solubles. Journal of Animal Science 86:3617-3627.

Miller, D.N., Smith, R.L. 2009. Microbial Characterization of Nitrification in a Shallow, Nitrogen-Contaminated Aquifer, Cape Cod, Massachusetts and Detection of a Novel Cluster Associated with Nitrifying Betaproteobacteria. Journal of Contaminant Hydrology. 103(3-4):182-193.

Last Modified: 7/2/2015
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