Food Safety Research Information Office
Title:Environmentally Sound Manure Management for Reduction of Gas Emissions, Nutrients, and Pathogens
Objective: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.

More Info:
Approach: 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.
Funding Source:United States Department of Agriculture (USDA), Agricultural Research Service (ARS)
Start Date:2010
End Date:2015
Project Number:5440-12630-001-00
Accession Number:420589
Institutions:USDA/ARS - Northern Plains Area
Investigators:Durso, Lisa
Gilley, John
Miller, Daniel
Wienhold, Brian
Project Reports:2011 Annual Report
Published Journal
Articles USDA
ARS (NP 108):
Primary isolation of shiga toxigenic Escherichia coli from environmental sources
Durso LM.
J Environ Qual. 2013 Sep 10;42(5):1295-307.
Hydraulic conditions required to not move unconsolidated surface material located within feedlots
Gilley JE, Boone GD, Marx DB.
Transactions of the ASABE. 2013;56(3):911-8.
Fate and transport of antimicrobial and antimicrobial resistance genes in soil and runoff following land application of swine slurry
Joy SR, Bartelt-Hunt S, Snow D, Gilley JE, Woodbury B, Parker D, Marx DB, Li X.
Environ Sci Technol. 2013;47(21):12081–8.
Runoff nutrient transport as affected by land application method, swine growth stage, and runoff rate
Gilley JE, Bartelt-Hunt SL, Lamb SJ, Li X, Marx DB, Snow DD, Parker DB, Woodbury BL .
T ASABE. 2013;56(6):1295-303.
Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non-agricultural metagenomes
Durso LM, Miller DN, Wienhold BJ.
PLoS One. 2012 Nov 2;7(11):e48325.
Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets
Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson RH.
Res Microbiol. 2012 Jul;163(6):407-12.
Comparison of bacterial communities in faeces of beef cattle fed diets containing corn and wet distillers' grain with solubles
Durso LM, Wells JE, Harhay GP, Rice WC, Kuehn L, Bono JL, Shackelford S, Wheeler T, Smith TP.
Lett Appl Microbiol. 2012 Jun 13;55(2):109-14.
Outbreak of Shiga toxin-producing Escherichia coli O111 infections associated with a correctional facility dairy - Colorado, 2010
Centers for Disease Control and Prevention (CDC).
MMWR Morb Mortal Wkly Rep. 2012 Mar 9;61(9):149-52.
Wheat strip effects on nutrient loads following variable manure applications
Thayer CA, Gilley JE, Durso LM, Marx DB.
Transactions of the ASABE. 2012;55(2):439-49.
Runoff nutrient loads as affected by residue cover, manure application rate, and flow rate
Thayer CA, Gilley JE, Durso LM, Marx DB.
Transactions of the ASABE. 2012;55(1):249-58.
Effects of animal diet, manure application rate, and tillage on transport of microorganisms from manure-amended fields
Durso LM, Gilley JE, Marx DB, Woodbury BL.
Appl Environ Microbiol. 2011 Sep;77(18):6715-7.
Non-Journal Publications:
Temporal characterization of bacteria in hayrings serving as stable fly larval development sites - (Abstract Only)
Accepted Publication (07-Jun-13)
Pathogen survival in fields irrigated with livestock-contaminated irrigation water - (Abstract Only)
Accepted Publication (19-Apr-13)
Diversity of microbiomes in beef cattle - (Book / Chapter)
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:
Effect of feeding distiller’s grains on reduced sulfur emissions - (Proceedings)
Miller, D.N., Spiehs, M.J., Woodbury, B.L. 2013. Effect of feeding distiller’s grains on reduced sulfur emissions. In: Waste to Worth: Spreading Science and Solutions, April 1-5, 2013, Denver, Colorado. Available:
Mining metagenomic datasets for antibiotic resistance genes - (Book / Chapter)
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.
Assessment of antibiotic resistance in runoff from cattle feedlots - (Abstract Only)
Accepted Publication (12-Sep-12)
Antibiotic resistance in agricultural and non-agricultural settings - (Abstract Only)
Accepted Publication (28-Jun-12)
Evaluation of a vegetative treatment system to reduce fecal microorganisms and antibiotic resistant bacteria in beef cattle feedlot runoff - (Abstract Only)
Miller, D.N., Durso, L.M., Henry, C.G. 2012. Evaluation of a vegetative treatment system to reduce fecal microorganisms and antibiotic resistant bacteria in beef cattle feedlot runoff. Microbial Ecology International Symposium. Section PS22 Microbial Disease Ecology. Poster 391A.
Linking microbial community structure and function to characterize antibiotic resistant bacteria and antibiotic resistant genes from cattle feces - (Abstract Only)
Durso, L.M. 2011. Linking microbial community structure and function to characterize antibiotic resistant bacteria and antibiotic resistant genes from cattle feces [abstract]. ASA-CSSA-SSSA Annual Meeting Abstracts. Poster No. 355-4(135). Available:
Nitrifier activity and diversity in swine lagoon covers - (Abstract Only)
Miller, D.N. 2011. Nitrifier activity and diversity in swine lagoon covers [abstract]. ASA-CSSA-SSSA Annual Meeting Abstracts. Paper No. 355-6. Available:
Assessing the performance of a vegetative treatment system to reduce pathogens in feedlot runoff - (Abstract Only)
Accepted Publication (31-Mar-11)
Microbiological quality of runoff from manure-amended fields as affected by perennial grass buffer strip - (Abstract Only)
Durso, L.M., Gilley, J.E., Woodbury, B.L., Marx, D.B. 2011. Microbiological quality of runoff from manure-amended fields as affected by perennial grass buffer strip. American Society for Microbiology 111th General Meeting, New Orleans, Louisiana. 2011 CDROM: ASM Abstracts. Poster Board No. 2803.
Seasonal differences in odor compound content and emission from pit, slurry tank, and lagoon storage structures - (Proceedings)
Accepted Publication (14-Jan-11)
Food Safety Categories:On-Farm Food Safety
Contaminants and Contamination
Farm-to-Table Categories:On-farm food production
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