2012 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.
During the second year of this research project we made progress on all objectives and met all milestones. For objective #1, molecular methods were developed to detect and quantify Clostridium species. Assays were validated in runoff from manure amended fields. A feedlot study was also conducted measuring greenhouse gas, ammonia, and hydrogen sulfide emissions. Emissions changed across the surface of the pen and were dependent upon diets fed (ground corn versus distillers byproducts). In a third project involving objective #1, molecular protocols to measure ammonia-oxidizing bacteria in contaminated aquifers were developed targeting both microbial groups involved in nutrient transformation.
For objective #2, a series of cattle feedlot manure application studies on cropland were conducted using small plots and rainfall simulators. These studies were a multi-ARS site collaboration focusing on the fate of manure odor compounds and emission rates overtime and after wetting were collected. Initial results show a small increase in odor compounds after wetting but declined to background levels within 24 hours. In a separate set of laboratory studies, odor compound emissions from swine manure applied to soil columns was followed over several days. The emission of volatile fatty acids decreased rapidly, but aromatic compound emissions decreased slowly.
For objective #3, ongoing 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 results indicate the VTA was able to utilize nutrients and remove microbes applied to the treatment areas. There was minimal movement of manure constituents (pharmaceutical compounds and nutrients) into the soil profile, and pathogens did not persist in the surface soils.
Minimizing impacts of manure application on water quality using narrow grass hedges. Narrow grass hedges placed at selected intervals along a hill slope reduce runoff nutrient loads. Specific information about how manure application and runoff rates affect runoff nutrient transport following land application of swine manure was unknown. ARS scientists at Lincoln, NE determined that runoff loads of ammonium nitrogen increased 40% as swine manure application rate increased by 300%. As runoff rate increased, runoff loads of dissolved phosphorus and total phosphorus increased proportionately. Over-application of manure to meet multi-year requirements increases the risk for nutrient runoff.
Source of pathogenic Escherichia coli O111 at a Colorado prison. Colorado public health officials noticed that inmates at one of their correctional facilities were getting sick with E. coli O111, but they were unable to determine the source of the outbreak. They suspected that it was coming from horses used at the facility. ARS researchers in Lincoln, Nebraska, were called to help track down the source of the outbreak strain. Using ARS methods specifically developed for finding Shiga-toxigenic E. coli O111 from agricultural and environmental sources, the researchers isolated the outbreak strain from cattle that were part of the prison dairy. As a result of knowing the source of E. coli O111, public health officials were able to institute new hygienic measures that prevented any further illness.
Bacterial communities in feces of beef cattle fed diets containing corn and wet distillers grains. There is concern that use of wet distiller’s grains, a byproduct of the ethanol industry, in cattle feed may create a gastrointestinal environment that allows the growth of bacterial pathogens such as Escherichia coli O157:H7 that can impact human health. Since all E. coli must interact with other fecal community members, and compete for resources, ARS researchers in Lincoln, Nebraska looked to see what other kinds of bacteria are present with E. coli in the cattle gut. Results indicate that E. coli experiences fundamentally different microbial communities in animals fed distillers grain compared to animals fed corn. Competition within different communities may reduce O157:H7 in the gut and thus, animal diet would be a legitimate practice to reduce the potential for O157:H7 food contamination.
Swine manure application to soil and effects on water quality. Swine manure is typically applied to fields using broadcast, disc, or injection methods, but the effects of each application method on subsequent water quality were unknown. The effects of manure application method and runoff rate on water quality variables were quantified by ARS scientists at Lincoln, NE. Incorporating swine manure by disking or injection significantly reduced dissolved phosphorus loads in runoff by 45 and 60%, respectively. Each of the measured runoff water quality variables was significantly influenced by runoff rate. Adoption of manure incorporation practices significantly impacts nutrient runoff.
Thayer, C., Gilley, J.E., Durso, L.M., Marx, D. 2012. Runoff nutrient loads as affected by residue cover, manure application rate, and flow rate. Transactions of the ASABE. 55(1): 249-258.
Comstock, N., Towle, M., Warner, A., Reynolds, S., Durso, L.M., Campbell, C., Kiefer, M., Bosch, S.A. 2012. Epidemiologic and occupational investigation of an Escherichia coli O111 outbreak associated with a correctional facility dairy – Colorado, 2010. Morbidity and Mortality Weekly Reports. 61(9).
Gilley, J.E., Eigenberg, R.A., Marx, D.B., Woodbury, B.L. 2012. Nutrient losses in runoff from feedlot surfaces as affected by unconsolidated surface materials. Journal of Soil and Water Conservation. 67(3): 211-217.
Thayer, C.A., Gilley, J.E., Durso, L.M., Marx, D.B. 2012. Wheat strip effects on nutrient loads following variable manure application. Transactions of the ASABE. 55(2):439-449.
Spiehs, M.J., Miller, D.N., Woodbury, B.L., Eigenberg, R.A., Varel, V.H., Parker, D.B. 2012. Effect of feeding wet distillers grains with solubles to beef cattle on air and manure quality. Applied Engineering in Agriculture. 28(3):423-430.
Miller, D.N., Mcghee, R. 2011. Two new designs for manure solids and liquids sampling from tank, pit, and lagoons at various depths. Applied Engineering in Agriculture. 27(5):847-854.
Durso, L.M., Wells, J., Harhay, G.P., Rice, W.C., Kuehn, L.A., Bono, J.L., Shackelford, S.D., Wheeler, T.L., Smith, T.P. 2012. Comparison of bacterial communities in faeces of beef cattle fed diets containing corn and wet distillers grain with solubles. Letters in Applied Microbiology. 55(2):109-14. DOI: 10.1111/J.1472-765X.2012.03265.X.
Bengtsson, J., Hartmann, M., Unterseher, M., Vaishampayan, P.A., Abarenkov, K., Durso, L.M., Bik, E.M., Garey, J.R., Eriksson, K., Nilsson, R. 2012. 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. Research in Microbiology. 163:407-412. DOI: 10.1016J.RESMIC.2012.07.001.