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United States Department of Agriculture

Agricultural Research Service


Location: Agroecosystem Management Research

2013 Annual Report

1a. Objectives (from AD-416):
Objective 1: Spatially characterize conditions within manure-impacted environments that lead to pathogen persistence, nutrient losses, and gaseous emission hot spots. Sub objective 1A: Develop, evaluate, and validate high-throughput methods for the detection, quantification and identification of microbial pathogens and fecal indicator organisms from environmental sources such as feedlot runoff, and ground and surface water samples. Sub objective 1B: Identify areas within cattle feedlot pens prone to gas emissions (odors, nutrients, and greenhouse gases) and evaluate the relationship between those areas and the spatial distribution of pathogens and fecal indicator microorganisms. Sub objective 1C: Determine the spatial distribution of contaminants, nitrogen-transforming activities, and microorganisms responsible for nitrogen transformation in a contamination plume originating from a cattle feedlot runoff holding pond. Objective 2: Develop land application practices that incorporate the use of manure as a nutrient source for crop production while minimizing potential adverse environmental impacts. Sub objective 2A: Utilize rainfall simulations tests to evaluate the potential for pathogen and nutrient runoff from manure applied to cropland. Sub objective 2B: Utilize laboratory soil columns to evaluate odor compound emissions after manure application to cropland. Objective 3: Develop manure management practices (e.g. vegetative treatment systems) to control gaseous emissions, nutrients, and microorganisms (e.g. E. coli O157:H7). Sub objective 3A: Determine the movement and persistence of nutrients, pathogens, and fecal indicator organisms within the vegetative treatment system (VTS) during standard and non-standard VTS operation. Sub objective 3B: Evaluate the antibiotic resistant phenotypes and genotypes of bacteria isolated directly from manure, and compare to bacteria from the corresponding feedlot runoff, and the agricultural fields to which the manure has been applied.

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. New high-throughput methods for the detection of specific fecal microorganisms and antibiotic resistance genes will be developed and applied towards this goal. In field studies, specific areas within manure-impacted environments (beef cattle feedlot pens, vegetative treatment areas for feedlot runoff treatment, a cattle feedlot holding pond groundwater contamination plume, and crop fields utilizing manure as fertilizer) will be identified that disproportionately emit gases (odor compounds, ammonia, and greenhouse gases) or have a large potential for nutrient or pathogen transport through the use of flux chambers and gas chromatography, by the use of artificial rainfall simulators, and by microbiological methods. In laboratory studies, molecular techniques will be used to assess microbial communities in order to understand the relationships between microbes and environmental processes affecting nutrients, emissions, and pathogen fate.

3. Progress Report:
During the third year of this research project we made progress on all objectives and substantially or fully met all milestones. For objective #1, limited financial resources impacted the field validation of molecular methods to detect and quantify Cryptosporidium species. Assays were validated in Cryptosporidium spiked manures and soils but were not validated in naturally contaminated soils. The results of lab-based studies are very encouraging and we anticipate applying these methods to future studies. Data analysis of greenhouse gas, ammonia, and hydrogen sulfide emissions from feedlot #1 are nearly complete and results have been presented at scientific meetings. Finally, a collaborative project was established with ARS scientists in Bowling Green, KY to refine molecular protocols to quantify bacteria involved in nitrogen transformations. For objective #2, data analysis of research results from a series of cattle feedlot manure application studies on cropland using small plots and rainfall simulators was completed and a manuscript was submitted. These studies were a multi-ARS site collaboration focusing on the fate of manure odor compounds and their emission rates as a function of wetting and diet. For objective #3, a second year of field work at the vegetative treatment area (VTA) was conducted examining pharmaceutically active compounds, pathogens, and nutrient dynamics when cattle feedlot runoff was applied. Initial water and soil analyses indicate the VTA was able to utilize nutrients and remove microbes applied to the treatment areas. There was also minimal movement of manure constituents (pharmaceutical compounds and nutrients) into the soil profile, and pathogens did not persist in the surface soils. Presentations on initial data from the site have been made at multiple local, national, and international meetings.

4. Accomplishments
1. Antibiotic resistance genes are a natural component of the environment. It is widely assumed that antibiotic resistant bacteria are found only in agricultural animals and feedlots. A recent analysis of environmental genetic material from many locations around the world demonstrated that antibiotic resistance genes can be found almost anywhere, including remote and pristine places such as Antarctic lakes and the Sargasso Sea. Discussions about the use of antibiotics in animal agriculture and how antibiotic resistant bacteria may affect human health need to include the naturally occurring resistance in these managed environments. All animals, including cattle and humans, have a large community of bacteria that live naturally in their lower intestines that are introduced into the environment via feces. ARS scientists in Lincoln, NE are using new tools to track the antibiotic resistance genes found in cattle feces. By quantifying which genes and which bacteria, present in cattle feces are most likely to survive in the environment we can target management to reduce negative impacts to the environment and human health.

2. Analysis of environmental genetic material show that tracking pathogenic E. coli in food production is not just a fecal issue. Some E. coli are human pathogens and can contaminate meat and vegetables making people sick. ARS scientists in Lincoln, NE are using new genetic techniques to take a census of bacteria in cattle feces and feedlot pen soil to see which bacteria are associated with pathogenic E. coli and which bacteria might be important competitors. New environmental genetic tools allow specific identifications of the sources. This analysis has shown that pathogenic E. coli are associated not only with feces but also with soil. A better understanding of sources of contamination will lead to reduced incidence of food borne illnesses.

Review Publications
Durso, L.M., Miller, D.N., Wienhold, B.J. 2012. Distribution and quantification of antibiotic resistance genes and bacteria across agricultural and non-agricultural metagenomes. PLoS One [online]. Available:

Durso, L.M. 2013. Mining metagenomic datasets for antibiotic resistance genes. In: Nelson, K. editor. Encyclopedia of Metagenomics: SpringerReference ( Berlin/Heidelberg, Germany: Springer-Verlag. DOI:10.1007/SpringerReference_332403 2013-01-23 22:12:18 UTC.

Escarcha, J.F., Callaway, T.R., Byrd II, J.A., Miller, D.N., Edrington, T.S., Anderson, R.C., Nisbet, D.J. 2012. Effects of dietary alfalfa inclusion on Salmonella Typhimurium populations in growing layer chicks. Foodborne Pathogens and Disease. 9:945-951.

Broadway, P.R., Callaway, T.R., Carroll, J.A., Donaldson, J.R., Rathmann, R.J., Johnson, B.J., Cribbs, J.T., Durso, L.M., Nisbet, D.J., Schmidt, T.B. 2012. Evaluation of the ruminal bacterial diversity of cattle fed diets containing citrus pulp pellets. Agriculture, Food and Analytical Bacteriology. 2:297-308.

Durso, L.M., Wells, J., Kim, M.S. 2013. Diversity of microbiomes in beef cattle. In: Nelson, K., editor. Encyclopedia of Metagenomics. Springer Reference ( Berlin/Heidelberg, Germany: Springer-Verlag. Available:

Eun, J., Davis, T.Z., Vera, J., Miller, D.N., Panter, K.E., Zobell, D. 2013. Addition of high concentration of inorganic selenium in orchardgrass (Dactylis glomerata L.) hay diet does not interfere with microbial fermentation in mixed ruminal microorganisms in continuous cultures. Professional Animal Scientist. 29(1): 39-45.

Parker, D.B., Gilley, J.E., Woodbury, B.L., Kim, K., Galvin, G., Bartelt-Hunt, S.L., Li, X., Snow, D.D. 2013. Odorous VOC emissions following land application of swine manure slurry. Atmospheric Environment. 66:91-100. DOI:10.1016/j.atmosenv.2012.01.001.

Gilley, J.E., Boone, G.D., Marx, D.B. 2013. Hydraulic conditions required to not move unconsolidated surface materials located within feedlots. Transactions of the ASABE. 56(3): 911-918.

Spiehs, M.J., Brown Brandl, T.M., Parker, D.B., Miller, D.N., Berry, E.D., Wells, J.E. 2013. Effect of bedding materials on concentration of odorous compounds and Escherichia coli in beef cattle bedded manure packs. Journal of Environmental Quality. 42(1):65-75.

Last Modified: 05/26/2017
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