Location: Food Animal Environmental Systems Research
2018 Annual Report
Objectives
Obj 1: Enhance the benefits of using animal manure as means of improving soil productivity for longterm production systems. 1.1 Improve soil health/quality through a longterm mngmnt practice involving animal manure, cover crop, & crop rotation. 1.2 Determine if poultry litter application timing (fall/spring) & cover crop (cover crop/no cover crop) affects on corn N use efficiency & yield. 1.3 Develop improved models for describing phosphorus cycling in soils amended with animal manure. 1.4 Develop an energy-efficient & cost-effective method of capturing ammonia from animal facilities & subsequent usage as fertilizer. 1.5 Evaluate poultry litter application on the incidence of Clostridium botulinum in haylage forage harvest systems & stand persistence. 1.6 Improve sustainability through a management strategy using cover crop grazing & animal manure to improve soil quality & fertility while increasing grain & livestock production. 1.7 Combining a multi-proxy investigation of agricultural contaminant transport in Karst groundwater systems & informal education to improve stewardship & best management practices.
Obj 2: Develop strategies for managing the survival & transport of antibiotics, pathogens & indicator species through agroecosystems. 2.1 Determine whether biochar-amended sand filters are an effective management practice for removing pathogenic & indicator microorganisms from tile drainage waters. 2.2 Characterize persistence and transmission of antibiotics, antibiotic resistance (AR) genes, AR mobile genetic elements and AR bacteria through agro-ecosystems. 2.3 Determine factors controlling adhesion & survival of manure-borne pathogens in manured soils & on crops & identify mitigation strategies. 2.4 Develop of methods for measuring antibiotics in agricultural samples & the correlation of the presence of antibiotic resistant bacteria. 2.5 Develop a strategy for rapid detection & deletion of antibiotic resistance genes using DNA-binding domain based nucleases.
Obj 3: Assess gaseous & particulate matter emissions resulting from animal prod. facil. & manure application sites. 3.1 Develop methods for the determination of VOC that contribute to malodorous emissions from field applied manures & use these methods to compare emissions from different manure application methods to field crops. 3.2 Obtain field measurements of the temporal variability of gas & particulate matter emissions. 3.3 Determine the fate of atmospheric N and sulfur emissions from agricultural systems. 3.4 Measure & model the fates of VOCs, PM, & GHGs from agricultural systems. 3.5 Model the chemical partitioning of N compounds between gas & particulate phase.
Obj 4: Improve production efficiency & emissions management of renewable bioenergy production systems using technologies such as anaerobic digesters. 4.1 Investigate biogas production and substrate utilization of poultry litter & use microaeration to improve biogas production. 4.2 Optimize anaerobic digestion of poultry wastes to reduce emissions & obtain bioenergy for sustainability. 4.3 Develop novel & cost-effective composite alginate filter materials to capture ammonia, GHG, odors from livestock prod. facil.
Approach
This project was conceived as a cooperative/partnership and comprehensive research program between ARS and Cooperator. The project 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 U.S. Through a series of innovative, cooperative research experiments at the animal production facilities and manure application sites, we will investigate manure microbial and nutrient losses as gas and through runoff water and odorous compounds from land and animal production sites. We will also determine levels of these compounds/contaminants in manure, application sites, and loading rates in agroecosystems. We will also investigate and find solutions to the environmental and agronomic problems such as nutrients, pathogens, greenhouse gases (GHGs), ammonia, odor-causing VOCs, particulates, dust, and sediment associated with animal production facilities and manure application lands. This will be accomplished based on new knowledge gained through the multidisciplinary approaches and the expertise of the scientists at this location through basic and applied research in the laboratory and in real farming sites and animal production environments. We will use the research results and develop best management practices (BMPs) for crop production on land receiving animal manure with regard to manure application timing, rate, nutrient, and loss of hazardous compounds within the agroecosystem of the unique “karst topography” common to this region. The research effort will be multi-disciplinary and multifaceted in support of decision making and systems development. Information generated from this research will be integrated into regional and national databases and statistical models to contribute towards improved environmental quality, sustainability, and economic viability of farms.
Progress Report
The research conducted under the objectives/sub-objectives of the project plan addresses environmental and agronomic problems related to the use of animal manure and other agricultural waste including nutrients, pathogens, greenhouse gases (GHGs), odor causing volatile organic compounds, dust and sediment associated with animal production facilities and manure application sites. The research also determines best management practices (BMPs) for crop production on land receiving animal manure and agricultural waste with regard to crop management and soil types particularly in unique “karst topography”. Following are research related activities and progress for the past year:
1. Research activities (soil, plant, and manure sampling and analyses, planting, harvesting, etc.) continued two field plot experiments under Objective 1 (Enhance the benefits of using animal manure as means of improving soil productivity for long term production systems). The crop rotation (corn, beans, and wheat), cover crops, and timing of manure application are being studied to investigate how maximizing the five principles of soil health management practices (no-till, organic matter, live roots, plant diversity and animal manure) can improve soil’s physical, biological, and chemical properties. Fertilizer treatments, i.e., poultry litter, chemical fertilizer, and control (no fertilizer or litter applied), were assigned to field plots and planted with soybeans for the current growing season. Cover crops were rolled down or killed by chemical application prior to the planting of the next rotation crop. A field plot site was prepared for the fall vs. spring manure application study.
2. Compilation of a large dataset of field-scale P losses from agricultural fields is ongoing. This data set included data collected from multiple researchers in multiple states which were recently used in a series of publications evaluating the accuracy of commonly used P loss models and state P indices. This work is in support of the ARS Big Data Initiative and will serve as a source of important P loss data previously unavailable to the public.
3. Research is being conducted to determine whether biochar-amended sand filters are an effective management strategy for removing pathogenic and indicator microorganisms from tile-drainage waters (sub-objective 2.1). Experiments using a commercially available biochar have been evaluated at application rates of 0, 5, 10, 15 and 30% (by volume). Three sand sizes have been investigated. Preliminary results indicate that the addition of the commercial biochar greatly reduces the transport of E. coli and Salmonella through laboratory-scale biofilters but the amount of retention is strongly dependent on biochar application rate.
4. Evaluated the impact of poultry litter as soil amendment on the persistence of bacteria and their resistant strains under field conditions. Experimental plots were followed for 172 days post treatment applications, during which a total of 552 soil samples were collected on six occasions. Four samples were collected per subplot. Soil samples are being cultured for both generic and bacteria resistant to selected medically important antibiotics. DNA was extracted from the soil samples collected before treatment, at 1 week and 1-month post treatment application. A total of 72 pooled DNA samples (pooled by subplot and sampling day) were sequenced by shotgun metagenomic sequencing and bioinformatics analysis for microbiome and resistome diversity is underway.
5. ARS scientists collaborated on a project with Western Kentucky University scientists evaluating the impact of continuous tylosin use in feedlot cattle on antibiotic resistance and quality of liver at the slaughter. Upon arrival at the feedlot, 10 calves were randomized to receive either tylosin medicated feed or non-medicated feed. Animals were followed for almost a year during which fecal samples were rectally collected and cultured for antibiotic resistant Enterococcus species and E. coli. Animals are being harvested for beef production and meat and liver quality attributes are measured. Another set of feedlot cattle were identified to begin the second experiment as soon as the slaughtering process of the cattle from the first experiment is completed.
6. ARS researchers are analyzing data from the environmental chamber experiments at the University of California, Riverside. Gas emissions common to agriculture and containing nitrogen and sulfur were exposed in the chamber to photochemical oxidation conditions typical to the ambient atmosphere to examine for products, especially particulate matter. The inorganic nitrogen (ammonia) and inorganic sulfur (hydrogen sulfide) experiments show minimal reactions and practically no product formation resulting in particulate matter. Organic nitrogen (amine) and organic sulfur (thiol/disulfide) experiments are completed. The organic compound reactions result in significant particulate matter formation with different compounds producing different yields and products. We have started looking at year three goals by examining humidity effects on chemical reactions. Also, we obtained gas and particulate data with our suite of analytical methods at the cooperating poultry house with sampling sessions covering three seasons (spring, summer, fall) so far. These studies complement the smog chamber experiments by monitoring gaseous emissions and particulate matter formation in the real-environment near agriculture facilities. Data is being analyzed in-house.
7. Continuing field study in monitoring and optimization of methane production from a complete-mixed anaerobic digestion system (300K gallons) of poultry litter and evaluation of different lignocellulosic enzymes on biogas production from recalcitrant livestock waste feedstocks. Just completed, lab-scale systems (200 L) of anaerobic digestion of poultry rendering wastewater to examine the effect of various system parameters on biogas production. A pilot-scale aerobic-anaerobic digestion system utilizing biological pre-treatment of lignocellulosic feedstocks will be evaluated. In addition, pilot-scale sequential filtration-scrubber system (8000 L) utilizing nanoparticles and nanofibers from agricultural residues for agricultural air pollution mitigation is in progress. Evaluation of nanotechnology in antimicrobial and odors reduction in livestock production is ongoing.
8. Experiments were completed on anaerobic digesters fed poultry litter, a feedstock recalcitrant to degradation under anaerobic conditions. Two digesters were operated under strictly anaerobic conditions and with supplemental low levels of aeration supplied to the sludge layers. With two additional digesters, sound was applied to an anaerobic and aerated digester to see if this could enhance the production of biogas. The sound treatment enhanced biogas production by 19 percent in the anaerobic treatment but decreased biogas production by seven percent when supplemental aeration was used. Biogas quality was best in the strictly anaerobic treatments. Sludge production was lower in the anaerobic treatments than when supplemental aeration was used and lowest in the sound treated anaerobic treatment, most likely due to enhanced suspension of solids in the digesters. This experiment was conducted over a 15-month period clearly demonstrating that the technology has the potential to be both reliable and produce significant gains in biogas production.
9. After completion of two pilot-scale anaerobic digester/sequencing batch reactor wastewater treatment systems in 2017, feeding of the systems was commenced in the spring, and the systems have been operating for four months. Initial gas production was low due to problems associated with over feeding and resultant low levels of alkalinity in the systems. This was overcome by adding waste from a commercial digester to the systems. Since then, the system exposed to underwater sound has produced 24 percent more biogas than the control system. Both systems consist of anaerobic digesters and nitrification-denitrification tanks to produce biogas and effect improvements in wastewater quality. Both systems have reduced Enterococci by about 80 percent and chemical oxygen demand by approximately 90 percent. Little improvement has been seen in the populations of E. coli and total coliforms.
Accomplishments
1. Impact of raised without antibiotics beef cattle production system on antibiotic resistance. There is an increasing concern that antibiotic use in food animals leads to antibiotic resistant foodborne bacteria. ARS scientists from Clay Center, Nebraska and Bowling Green, Kentucky, in collaboration with Colorado State University researchers investigated the impact of raising beef cattle without antibiotics on antibiotic resistance. Each month fecal samples were collected from 30 raised without antibiotics cattle, and 30 conventional raised cattle over one year at a commercial slaughterhouse. Levels of third generation cephalosporin resistant E. coli, erythromycin resistant Enterococcus species, and erythromycin and tetracycline resistance genes were significantly lower in raised without antibiotics cattle. Resistance to most of the remaining antibiotics, and the levels of bacteria such as Salmonella were not different. Macrolides and tetracyclines, to which higher levels of resistances were observed, are the most commonly used antibiotics for disease prevention in conventional beef cattle production. This study indicates optimized use and antibiotic stewardship can reduce the burden of antibiotic resistance associated with food animal production systems. Results of this study can be used for quantitative risk assessment to quantify the impact of raising beef cattle without antibiotics in reducing human infections because of this intervention.
2. Antimicrobial resistant Staphylococcus aureus in dairy cattle production. Large amount of antibiotics is used in dairy cattle production to prevent and treat diseases in cows. Staphylococcus aureus bacterium is a significant pathogen as a cause of udder infection in dairy cows. Methicillin resistant Staphylococcus aureus is an important human pathogen causing skin infections, pneumonia and bloodstream infections. The organism can be excreted through milk and humans can get the infection by drinking unpasteurized milk from infected cows. ARS scientists in Bowling Green, Kentucky collaborated with researchers at the University of Tennessee in which, a banked collection of Staphylococcus aureus isolates from milk samples were tested against 10 antibiotics from 2004 to 2016. Over a third of the isolates tested were resistant to at least one antibiotic, and sulfonamide resistance was the highest. Antibiotic resistant Staphylococcus aureus was detected in more than a quarter of the farms. Even though resistance to most of the medically important antibiotics was low, the widespread distribution of the resistant strains is a cause for concern. Periodic monitoring of antibiotic resistance in dairy cattle production system is necessary for future interventions to reduce the economic, environmental and public health impacts of the pathogen.
3. Understanding the effects of biochemical factors from mixed animal wastes feedstock in biogas production for renewable energy. Animal wastes can serve as the feedstock for biogas production (mainly methane) that could be used as an alternative energy source. The green energy derived from animal wastes is carbon neutral and offsets those generated from fossil fuels. ARS scientists from Bowling Green, Kentucky and a university in Mexico quantified methane production from animal wastes with different nitrogen, potential inhibitors, and carbon sources. The results showed that methane productions increased as the solid concentrations, temperature, and total carbon increased. However, biogas production decreased substantially when ammonia concentrations in the feedstock were high. The addition of more carbon source, mainly animal waste, to the feedstock provided a better substrate for methane production during anaerobic digestion. In addition, methane productions were the greatest when additional seed (source of acclimated microbes) was used. Therefore, the additional carbon source as well as acclimated seed are necessary to increase methane production from animal waste anaerobic digesters. Inhibitors such as ammonia appears to hinder the biomethanation in the anaerobic digestion of animal wastes for optimum methane production. This research indicated that production of biogas from animal waste is a sustainable on farm energy source for livestock producers.
4. Improving the synthesis of nanoparticles from agro-industrial residues for sustainability and anti-microbial agents against pathogens. To increase profit margin along with productivity, concentrated animal farming operations commonly administer low doses of antibiotics and other antimicrobials to food animal species for growth promotion or weight gain. This conflict between the need to maintain the effectiveness of antibiotics and their use to promote livestock weight gain continues to raise major concerns regarding escalating antibiotic-resistance pathogens in our food supplies. Thus, it is necessary to find a simple and environmental friendly way to counter or reduce the proliferation of these pathogens in the environment by utilizing naturally occurring antimicrobial agents. Naturally occurring nanoparticles with antimicrobial properties hold great promise in this arena. ARS scientists from Bowling Green, Kentucky, and a university in South Korea carried out a study on nontoxic and eco-friendly methods for the synthesis of nanoparticles using agricultural residues along with the study on the antimicrobial properties of nanoparticles obtained from plants. The results show that some of these nanoparticles had activity against pathogens. Therefore, the present study provides a potential eco-friendly and sustainable way to improve the synthesis of antimicrobial nanoparticles and their potency against pathogens in agricultural settings.
5. Investigating biochar and poultry litter impact on corn production. Biochar holds great promise as a soil amendment to sequester carbon, improve soil fertility, adsorb organic pollutants, stimulate soil microbial activities, conserve plant nutrients, and improve crop yield. Scientists from ARS lab in Bowling Green, Kentucky, conducted field research to investigate the impact of utilizing a hardwood biochar as a soil amendment in central Kentucky, USA to assess its impact on corn grain, biomass yields, and greenhouse gas emission. Biochar was initially applied to research plots with or without addition of fertilizer and poultry litter (PL). Biochar alone did not increase corn dry matter biomass, grain yield, and N, P, K uptake; however, these parameters were increased when biochar was combined with PL or chemical fertilizer. Poultry litter treatment produced significantly greater N2O and CO2 emissions, but the emissions decreased significantly when PL was combined with biochar. Overall, this hardwood biochar did not possess chemical characteristics capable of improving corn productivity within the experimental timeframe, but it can have a positive impact when combined with PL or chemical fertilizer.
6. Comparing two methods for calculating the P sorption capacity parameter in soils. Phosphorus cycling in soils is an important process affecting P movement through the landscape. An important parameter controlling P cycling is the P sorption capacity parameter (PSP). This parameter is used to partition P among three different pools: active, labile, and stable. ARS researchers at Bowling Green, Kentucky in collaboration with ARS colleagues in Madison, Wisconsin, focused on comparing two commonly used methods for estimating PSP. Results show a very poor correlation in PSP between these two methods suggesting they are not estimating the same soil parameter. The value of PSP determines the predicted size of each P pool thus, significantly different values of PSP can result in significant differences in predicted P concentrations for each pool. Because the amount of P available for plant uptake as well as the amount of P vulnerable to loss during runoff events is determined by the concentrations of P in each pool, these results indicate that significant differences in estimates of P loss risk from agricultural fields may be obtained for the same model depending on how PSP is estimated. Therefore, different management strategies may be prescribed depending on how PSP is estimated.
7. Laboratory evaluation of relative ionization efficiencies in an aerosol mass spectrometer. Mass concentrations of chemical species calculated from the aerosol mass spectrometer depend on two factors: particle collection efficiency and relative ionization efficiency. Previous studies have characterized collection efficiency but not relative ionization efficiency, especially for organic species. For this study, ARS researchers and collaborators developed a new ionization efficiency calibration protocol to better account for particle size and mass and directly measure collection efficiency. The relative ionization efficiency value for organic aerosol was consistent within the margin of error of the value of 1.4 currently used by researchers and provides better confidence in the data that has been acquired using this method.
8. A method for the quantification of dissolved gases and bicarbonate in water and wastewater. Determining the concentration of carbon dioxide in water is important due to its importance in many biological processes including wastewater treatment. Carbon dioxide dissolved in water exists in different forms such as dissolved carbon dioxide, carbonic acid, and bicarbonate. The determination of dissolved carbon dioxide is usually done by neutralization of its alkaline form, bicarbonate, with an acid. A rapid method for the determination of the concentrations of dissolved carbon dioxide in water and its assortment into its solvated and bicarbonate forms was developed. Small water samples were collected in the field and injected into vials partially filled with dilute hydrochloric acid. A portion of the gas sample in the vials was injected onto a gas chromatograph instrument to measure the carbon dioxide and using the measured pH of the sample and well-known equations, the concentrations of carbon dioxide and its various forms could be calculated. Natural water samples as well as wastewater from a sewage treatment plant and a swine rearing operation were analyzed by this method and the results compared favorably to those obtained by titration. The method allows for more rapid throughput of samples, and can be used to measure other dissolved gases such as methane and nitrous oxide.
Review Publications
Ramirez-Avila, J.J., Osmond, D., Radcliffe, D., Bolster, C.H., Ortega-Achury, S.L., Forsberg, A., Sharpley, A.N., Oldham, L. 2017. Evaluation of the APEX model to simulate runoff quality from agricultural fields in the southern region of the United States. Journal of Environmental Quality. 46:1357-1364. https://doi.org/10.2134/jeq2017.07.0258.
Lee, J., Velmurugan, P., Park, J., Murugan, K., Lovanh, N.C., Park, Y., Oh, B., Venkatachalam, P., Benelli, G. 2018. A novel photo-biological engineering method for Salvia miltiorrhiza-mediated fabrication of silver nanoparticles using LED lights sources and its effectiveness against Aedes aegypti mosquito larvae and microbial pathogens. Physiological and Molecular Plant Pathology. 101:178-186. https://doi.org/10.1016/j.pmpp.2017.03.010.
Bolster, C.H., Vadas, P.A. 2018. Comparison of two methods for calculating the P sorption capacity parameter in soils. Soil Science Society of America Journal. 82(2):493-501. https://doi.org/10.2136/sssaj2017.09.0317.
Loughrin, J.H., Antle, S.W., Polk, J. 2017. A gas chromatographic method for the determination of bicarbonate and dissolved gases. Frontiers in Environmental Science. 5:65. https://doi.org/10.3389/fenvs.2017.00065.
Hiko, A., Tasisa, K., Agga, G.E. 2018. Helminthiasis and gram negative enteric bacteria in freshwater fish from selected lakes of Haramaya District, Ethiopia. Journal of fisheries and Aquaculture. 9(2):242. doi: 10.4172/2150-3508.1000242.
Bolster, C.H., Brooks, J.P., Cook, K.L. 2018. Effect of manure application rate and rainfall timing on the leaching of antibiotic-resistant bacteria and their associated genes. Water, Air, and Soil Pollution. https://doi.org/10.1007/s11270-018-3781-6.
Xu, W., Lambe, A., Silva, P.J., Hu, W., Onash, T., Williams, L., Croteau, P., Zhang, X., Renbaum-Wolff, L., Fortner, E., Jimenez, J.L., Jayne, J.T., Worsnop, D., Canagaratna, M. 2018. Laboratory evaluation of species-dependent relative ionization efficiencies in the Aerodyne Aerosol Mass Spectrometer. Aerosol Science and Technology. 52(6):626-641. https://doi.org/10.1080/02786826.2018.1439570.
Abdi, R.D., Gillespie, B.E., Vaughn, J., Merrill, C., Headrick, S.I., Ensermu, D.B., D'Souza, D.H., Agga, G.E., Almeida, R.A., Oliver, S.P., Kerro, D.O. 2018. Antimicrobial resistance of Staphylococcus aureus isolates from dairy cows and genetic diversity of resistant isolates. Foodborne Pathogens and Disease. https://doi.org/10.1089/fpd.2017.2362.
Vikram, A., Rovira, P., Agga, G.E., Arthur, T.M., Bosilevac, J.M., Wheeler, T.L., Morley, P., Belk, K., Schmidt, J.W. 2017. Impact of "raised without antibiotics" beef cattle production practices on occurrences of antimicrobial resistance. Applied and Environmental Microbiology. 83:e01682-17. https://doi.org/10.1128/AEM.01682-17.
Hiko, A., Ibrahim, H., Agga, G.E. 2018. Abattoir based survey of bovine cystic echinococcosis in selected commercial abattoir in Ethiopia. Journal of Veterinary Science and Technology. 9(2):527. doi: 10.4172/2157-7579.1000527.
