Location: Food Animal Environmental Systems Research
2019 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 such as 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. Evaluated the impact of organic fertilizer as soil amendment on the persistence of microbial and antimicrobial resistant bacterial populations. A longitudinal experiment consisting of poultry litter, commercial fertilizer, and untreated control plots was conducted on a corn field for 172 days post treatment applications, spanning the entire growing season. A total of 576 soil samples were collected on six occasions. Samples were cultured for quantification and detection of generic Escherichia coli, tetracycline resistant E. coli and third generation cephalosporin resistant E. coli, generic enterococci, tetracycline resistant enterococci and macrolide resistant enterococci, extended spectrum beta-lactam resistant bacteria, and carbapenem resistant bacteria. Shotgun sequencing of 72 pooled metagenomic DNA samples were obtained at baseline, one week and one month post treatment was done for microbiome and resistome analysis. Preliminary results of this project were presented at two scientific meetings. Both culture and whole genome sequencing indicated that poultry litter soil amendment temporarily increased microbial and antimicrobial resistant bacterial populations in comparison to commercial fertilizer or untreated control. Although no significant differences were observed between treatment groups beyond 70 days post treatment at the site of application, the risk of dissemination to a wider ecological landscape and water contamination through run off should be considered.
2. Evaluated the impact of continuous in-feed use of tylosin in feedlot cattle on the dynamics of antimicrobial resistance and liver abscess after slaughter. A cohort of weaned calves were randomized at arrival at feedlot to receive tylosin medicated feed (10 calves) or non-medicated feed (10 calves). Animals were followed for about a year during which feces from the rectum, manure from pen-surface and animal feed were collected and cultured for antibiotic resistant Enterococcus species and E. coli. Samples were also analyzed for tylosin concentration, and results were presented at three scientific forums. Metagenomic DNA was extracted from the samples, and quantification of selected genes conferring resistance to macrolide-lincosamides-streptogramin classes of antibiotics, using droplet digital PCR is underway. Meat and liver quality attributes were measured. Subsequent experiments with other cohorts of cattle were discontinued because of abrupt departure of a Western Kentucky University collaborator. Instead, we are studying the dynamics of antimicrobial resistance of enteric bacteria in two cohorts of cow-calf during a peri-weaning period. Fecal samples were collected from both the cows and calves and cultured for antimicrobial resistant bacteria.
3. Research is ongoing to evaluate the effectiveness of using ammonium lactate extractable phosphorus, aluminum, and iron for calculating the degree of phosphorus saturation of arable soils. Most studies to date have used ammonium oxalate extractions but this method is not routinely used, and thus alternative extractions are needed. The degree of phosphorus saturation has been shown to be correlated with water extractable phosphorus and thus is expected to be a good indicator of the soil fertility status as well as the potential for phosphorus being released during runoff and leaching events and thus posing a potential environmental risk. This study is in collaboration with the Swedish University of Agricultural Sciences. Results show relatively mild, yet statistically significant, correlations between lactate ad oxalate extracted aluminum, iron, and phosphorus concentrations. A strong relationship was observed between the degree of phosphorus saturation calculated from both extraction methods and both were strongly correlated with water-extractable phosphorus.
4. Research is ongoing to investigate whether biochar-amended sand filters are an effective management strategy for removing pathogenic and indicator microorganisms from tile-drainage waters. Experiments using a commercially-available biochar have been evaluated at application rates of 0, 5, 10, and 15 (by volume). Three sand sizes have been investigated. Preliminary results indicate that the addition of the commercial biochar reduces the transport of E. coli and Salmonella through laboratory-scale biofilters but that the amount of retention is strongly dependent on biochar application rate. Recent results also show that sand size is a strong determinant on the ability of the biochar to retain bacteria and that this effect varies depending on the type of microorganisms. Specifically, results show that the effect of grain size on the retention of an E. coli isolate is notably different than the effects on the retention of a salmonella isolate. Batch sorption studies have just been completed to help identify whether the bacterial removal rates we observed were a result of physical straining within the column or increased attraction (i.e. sorption) between the bacteria and biochar particles.
5. Two-pilot scale anaerobic digesters/wastewater treatment systems have been operating at the Unit since the summer of 2018. During one trial of the two systems (one exposed to sound at sonic frequencies, one control), the system exposed to sound produced 108% more biogas than did the control system. During the fall, the system was shut down due to cold weather and modified to improve its waste handling capacity. It has recently become operational again, and collaborations have begun with scientists at the ARS location in Florence, SC to add ARS-developed nutrient-removal technologies to the system. This research contributes directly to the project plan’s objectives for developing efficient and safe uses for animal wastes.
6. Continuing field study in monitoring and optimization of methane production from an anaerobic digestion system (15 million gallons) of poultry litter mixed with food wastes 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 mixed poultry litter wastewater to examine the effect of various system parameters on biogas production. Pilot-scale aerobic-anaerobic digestion system utilizing biological pre-treatment of lignocellulosic feedstocks is being evaluated. In addition, pilot-scale sequential filtration-scrubber system (8000 L) to utilize 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.
7. All experiments on nitrogen and sulfur reactions and impacts on temperature and humidity have been finished with some data analyses still ongoing. ARS researchers in collaboration with the University of California, Riverside have at least six publications under development from the research that are anticipated to be submitted over the next 6-8 months.
8. ARS researchers in collaboration with Western Kentucky University continue to analyze many agricultural waste samples. During the first year of this multiyear tylosin study (began in April 2018), 214 cattle samples have been analyzed. ARS scientists in Bowling, Kentucky, are currently analyzing these samples for tylosin resistant genes. Once tylosin resistant gene analysis is complete, data will be statistically analyzed. A manuscript of this work will be completed shortly thereafter.
Accomplishments
1. Tetracycline maintained animal health and avoided the need for critically important antibiotics for human use. Tetracycline is by far the most widely used antibiotic in the U.S. beef cattle production system mainly for the prevention of bovine respiratory disease, an economically significant disease. On the other hand, concerns have been raised that the widespread use of antibiotics in food animals can lead to increased occurrence of antimicrobial resistant infections in humans. ARS scientist in Bowling Green, Kentucky, investigated the impact of tetracycline on the incidence of bovine respiratory disease and its impact on antibiotic resistant bacteria. Calves which did not receive chlortetracycline medicated feed were 28 times more likely to become sick and received the more critically important highest priority antibiotics for human use. Tetracycline resistant bacteria significantly increased 5 days post antibiotic treatment both in the animals and in pen surface; after 1-month there was no difference between the treated and untreated group. This study provides strong evidence that a relatively innocuous application of an older medically-important antibiotic prevents disease with a very short-lived measurable effect on antibiotic resistant bacterial population. In contrast, over 90% of untreated calves had respiratory symptoms and were treated with critically important antibiotics (ceftiofur, enrofloxacin, and macrolides). This data suggests that strategic use of antibiotics can help avoid demand for therapeutic uses of more important antibiotics.
2. Anaerobic digestion does not completely remove antibiotic residues and antibiotic resistance genes from animal manure. Microbial digestion of animal manure in the absence of oxygen provides animal producers an opportunity both for animal waste management and renewable energy. ARS scientists in Bowling Green, Kentucky, investigated its effect on the removal of antibiotic residues and resistance genes under anaerobic digestion of swine manure. Three experiments with varying feeding load were conducted up to 100 days each and the digested liquid and solid products were analyzed for tetracycline residues and tetracycline resistance genes. Results indicate that feeding load has significant impact in reducing the concentrations of resistance genes with high load size significantly reduced resistance genes compared to low or medium feed load. Antibiotic residues and resistance genes were detected in the liquid and solid digested products. Although anaerobic digestion produces a useful energy, the digested byproducts require further treatment before discharge or land applied to protect the environment and public health.
3. Environmental impact of animal production lasts longer. Confined animal feeding operations can facilitate the spread of genes associated with antibiotic resistance. ARS scientist in Bowling Green, Kentucky, investigate the persistence of antibiotic resistance genes in the environment over two years after cattle removal from a backgrounding operation. Soil samples were collected just before cattle were removed, then one year and two years following cattle removal. Bacteria, resistance genes and mobile genetic elements were quantified by PCR. Concentrations of bacteria, the resistance genes and mobile genetic elements, were higher in the feeding area and its immediate vicinity (around the fence and the gate) followed by a gradient decline along the grazing area. Although the concentrations of bacteria, resistance genes and mobile genetic elements in the feeding area significantly decreased two years after cattle removal, their concentrations were still higher than that observed in the grazing area. Higher concentrations over two years in the feeding area when compared to the grazing area suggest a lasting effect of confined beef cattle production system on the persistence of bacteria and resistance elements in the soil.
4. Compilation and publication of a large dataset of field-scale P losses from agricultural fields. Computer models are commonly employed for predicting risks of phosphorus runoff from agricultural fields by enabling simulation of various management practices and climatic scenarios. A complicating factor in developing and evaluating phosphorus loss models is the relative scarcity of available measured field data that adequately capture phosphorus losses before and after implementing management practices in a variety of physiographic settings. As part of a large project that focused on comparing different phosphorus loss models and state phosphorus indices, an ARS scientist from Bowling Green, Kentucky, led a multi-institutional effort to compile data used in these modeling projects into a single database. The database was developed in a machine-readable format and was made available to the public through Ag Data Commons. The database contains phosphorus loadings, land management practices, climatic conditions, and field characterizations measured at multiple research sites throughout the South and Midwest. Collating these data into a single database and making it accessible to the public will allow other researchers to use these data to test their models. This work is in support of the ARS Big Data Initiative and will serve as a source of important phosphorus loss data previously unavailable to the public.
5. Aeration to improve biogas production by recalcitrant feedstock. Previous research has shown that addition to small levels of aeration to otherwise anaerobic digestions can improve biogas production, presumably though hydrolysis of carbohydrate polymers that are normally resistant to degradation. These experiments, however, have been run at very small scale and without provision to retain the supplemental aeration within the wastewater. ARS scientist in Bowling Green, Kentucky, implemented low levels of aeration were provided to poultry litter slurry through a sub-surface manifold that retained air in the sludge. Digestate was supplied at various levels at regular periods throughout the day. Aeration at 200 and 800 mL/day increased biogas production by 14 and 73% compared to anaerobic digestion while aeration at 2000 mL/day decreased biogas production by 19%. This research presents a simple and inexpensive means whereby the efficiency of anaerobic digestion of wastes can be improved.
6. Sound enhances wastewater degradation and improves anaerobic digester performance. The commercial acceptance of anaerobic digestion to produce biofuel has been limited due to inherently low rates of digestion, large infrastructure costs, and sludge disposal costs. ARS scientist in Bowling Green, Kentucky, investigated biogas production and wastewater quality from anaerobic digesters to determine whether sound at audible frequencies (< 20,000 Hz) could enhance their performance. In three separate trials, the performance of control and sound-treated digesters was compared. Anaerobic digesters exposed to sound produced approximately 12% more biogas than did non-exposed digesters, and sound-treated digestate had significantly lower chemical oxygen demand. Sludge at the end of the 100-day digestion averaged 19% less carbon and 18% less nitrogen in sound-treated digesters as compared to sludge from untreated digesters. This research demonstrates that sound can be used to improve biogas production inexpensively, reduce sludge volumes efficiently, and reduce wastewater strength.
7. Extraction of biogenic silica from agricultural residues and its use in livestock air pollution reduction. Gas emissions, including ammonia, methane and other greenhouse gases, sulfides, and other volatile organic carbons from livestock operations are health and environmental concerns. Management of polluted air from confined animal feeding operations (CAFOs) and other livestock facilities is a regulatory concern as well as an economical one. Effective removal of hazardous substances and odor reduction by currently available methods can be unreliable and costly. ARS scientists from Bowling Green, Kentucky, along with researchers from universities in South Korea and Mexico, carried out an extraction of silica nanoparticles (Si NPs) from different agricultural residues such as rice hull and corn stover to be used as potential adsorbent materials for air pollutants. Different extraction parameters such as pH, temperature, and type of agricultural residues determine the yield of Si NPs. The results also show that biogenic silica nanoparticles amended with metallic oxides could reduce certain air pollutants in filtration systems. Therefore, it is feasible to source naturally occurring Si NPs as adsorbent material for air pollution abatement strategy around CAFOs for sustainability and cost effectiveness.
8. Improving biogas production from high lignocellulosic livestock wastes via naturally occurring enzymes. Animal wastes with high lignin and cellulosic contents such as poultry litter can serve as the feedstock for biogas production (mainly methane) that could be used as alternative energy source. However, these high lignin and cellulosic feedstocks are quite recalcitrant to be readily utilized by methanogens to produce beneficial biogas, methane. Therefore, a pre-treatment is necessary to breakdown these lignin and cellulosic materials for better gas production. In this study, ARS scientists from Bowling Green, Kentucky, and a scientist from university in Mexico, carried out an evaluation of various enzymes on methane production from aged animal wastes (poultry litters) and crop residues with high lignin and cellulosic. Aerobic and anaerobic batch reactors containing different mixtures of fungal enzymes and aged poultry litter feedstocks were set up to evaluate methane production. The results showed that more methane production was observed from feedstocks with enzymatic pre-treatment and aged poultry litters, especially the naturally exposed ones. Thus, biological pre-treatment of recalcitrant feedstock helps improve biogas production. This study has shown that pre-treatment of high lignocellulosic biomass such as wheat straw or rice hull/wood chip poultry litter and the aging of poultry litter naturally could help improve the anaerobic digestion of these recalcitrant biomass and increase biogas production for potential bioenergy utilization to be sustainable.
Review Publications
Loughrin, J.H., Lovanh, N.C. 2019. Aeration to improve biogas production by recalcitrant feedstock. Environments. 6(4):44. https://doi.org/10.3390/environments6040044.
Gutema, F.D., Agga, G.E., Abdi, R.D., De Zeutter, L., Duchateau, L., Gabriël, S. 2019. Prevalence and serotype diversity of Salmonella in apparently healthy cattle: Systematic review and meta-analysis of published studies, 2000–2017. Frontiers in Veterinary Science. 6:102. https://doi.org/10.3389/fvets.2019.00102.
Aregawi, W.G., Agga, G.E., Gishe, J., Abdi, R.D. 2018. Seroprevalence and participatory epidemiology of camelpox in Afar region of Ethiopia. Preventive Veterinary Medicine. 161:25-32. https://doi.org/10.1016/j.prevetmed.2018.10.003.
Agga, G.E., Cook, K.L., Netthisinghe, A.M., Gilfillen, R.A., Woosley, P.B., Sistani, K.R. 2019. Persistence of antibiotic resistance genes in beef cattle backgrounding environment over two years after cessation of operation. PLoS One. 12(2):1-19. https://doi.org/10.1371/journal.pone.0212510.
Manikandan, V., Velmurugan, P., Lovanh, N.C., Jayanthi, P., Park, Y., Cho, M., Oh, B. 2018. Removal of reactive dye using novel low cost activated carbon obtained from Prunus x yedoensis leaf by chemical activation. Indian Journal of Chemical Technology. 25(6):583-587.
Agga, G.E., Schmidt, J.W., Arthur, T.M. 2016. Effects of in-feed chlortetracycline prophylaxis of beef cattle on animal health and antimicrobial-resistant Escherichia coli. Applied and Environmental Microbiology. 82(24):7197-7204. doi:10.1128/AEM.01928-16.
Miller, E.W., Vikram, A., Agga, G.E., Arthur, T.M., Schmidt, J.W. 2018. Effects of in-feed Chlortetracycline prophylaxis in beef cattle on antimicrobial resistance genes. Foodborne Pathogens and Disease. 15(1):689-697. https://doi.org/10.1089/fpd.2018.2475.
Couch, M., Agga, G.E., Kasumba, J., Parekh, R.R., Loughrin, J.H., Conte, E.D. 2019. Abundances of tetracycline resistance genes and tetracycline antibiotics during anaerobic digestion of swine waste. Journal of Environmental Quality. 48(1):171-178. https://doi.org/10.2134/jeq2018.09.0331.
Aregawi, W.G., Agga, G.E., Abdi, R.D., Buscher, P. 2019. Systematic review and meta-analysis on the global distribution, host range, and prevalence of Trypanosoma evansi. Parasites & Vectors. 12:67. https://doi.org/10.1186/s13071-019-3311-4.
