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Research Project: Assessing and Managing Antibiotic Resistance, Nutrients, and Pathogens In Animal-Impacted Agroecosystems

Location: Agroecosystem Management Research

2018 Annual Report

Objective 1: Measure manure pathogens, antibiotic-resistant bacteria, and antibiotic resistance genes (ARB/G) in animal production systems and manure-impacted environments and mitigate their deleterious impacts. Subobjective 1A. Develop and/or validate methods to detect and quantify antibiotic resistant bacteria and genes ARB/G in beef and swine production areas, with a focus on resistance classes that are ecologically relevant to particular agricultural production systems, microbiologically relevant based on carriage of likely pathogens, and clinically relevant based on kinds of drugs used to treat infections in food animals and humans. Subobjective 1B. Measure survival of microbes and persistence of genes in manure-impacted environments. Objective 2: Improve manure land application practices to enhance crop productivity while reducing losses of reactive nitrogen and phosphorus. Subobjective 2A. Utilize rainfall simulation tests to evaluate the potential for reactive manure nitrogen (N) and phosphorus (P) to be transported in runoff from land application areas. Subobjective 2B. Utilize rainfall simulation tests to evaluate the potential for pathogens, fecal indicators, and antibiotic resistance (AR) to be transported in runoff from land application areas. Subobjective 2C. Determine if a reactive subsurface barrier can limit nitrate movement out of surface agricultural soils and into shallow aquifers. Objective 3: Assess the impact and fate of manure-associated pharmaceuticals in agroecosystems. Subobjective 3A. Evaluate how increasing concentrations of common livestock antimicrobials (monensin, lincomycin, and sulfamethazine) effect nitrification, denitrification, and decomposition in crop and pasture soils that have received beef cattle feedlot runoff or manure with crop, pasture, and stream sediments with no history of manure/runoff.

Agronomic use of animal manure to build soil fertility and health has been an economical and sustainable practice for centuries, but it is not without challenges. Manure can be a source of human food pathogens and environmental contaminants including excess nutrients, pathogens, antibiotics, and antibiotic resistant bacteria (ARB). The goal of this project is to address substantial knowledge gaps regarding the movement and fate of the chemical and biological components of manure. In a series of collaborative studies, robust, cross-validated methods to measure antibiotic resistance (Objective 1) will be developed through a multi-location partnership and will assess potential transport issues after manure application and in manure-impacted environments across the nation. Field and laboratory experiments will evaluate setback factors affecting manure nutrient, pathogen, antibiotic, and ARB in runoff and nitrate leaching past the root zone into shallow ground water (Objective 2 & 3). Soil’s capacity to help mitigate specific manure pathogens, including porcine epidemic diarrhea virus, will be explored in laboratory and field studies in addition to determining specific antibiotic thresholds where soil microbial processes are affected to better understand environmental risks for manure application (Objectives 2 & 3). Information from these studies directly contributes to multiple problem areas/components in National Programs 212 and 108. The research objectives within this study plan will provide important information concerning the fate and transport of manure constituents for producers (nutrient loss, safe manure use for crop production), the public (pathogens, antibiotics and ARB), and other government agencies (nutrients and pathogens impacting water quality).

Progress Report
Substantial progress on all objectives and milestones were made over the past year including establishing new collaborative partnerships with other ARS research locations and universities working in similar research areas. Research progress was made to develop technologies that decrease nitrate movement into ground water. Nitrate leaching into tile-drained soils contributes to dead zones in the Gulf of Mexico. Wood chip bioreactors represent recently developed technology used to treat nitrate in tile drains, and a similar technology could be developed to remove nitrate in water leaching into aquifers in sensitive groundwater recharge areas. Modified soil columns were developed to evaluate the potential for reactive woodchip barriers to treat nitrate in water leaching past the root zone. A variety of wood sources and layer thicknesses are being evaluated for nitrate removal efficiency in preparation for future field trials. This research contributes to project Objective 2. Both manure and soils are important reservoirs of antibiotic resistance genes (ARG) and microorganisms capable of infecting humans and animals. A consistent, reliable method for four ARG targets, developed in FY2017 and validated at multiple ARS locations, is now available and has been applied in research studies at several sites (in a longitudinal watershed study in Arkansas, in long-term cropping system soils using various manure and nitrogen application rates, in beef cattle feedlot soils and manures, and in a rainfall simulation study evaluating runoff from manure amended fields). In other projects, antibiotic resistance in soils amended with swine manure and incubated under simulated winter conditions was assessed. These projects yielded important insights into the factors controlling antibiotic resistance, their persistence, and potential background levels in agroecosystems and contributes to project Objective 1.

1. Alkaline stabilization of swine manure controls porcine epidemic diarrhea virus (PEDv). It is estimated that the ongoing outbreak of PEDv costs the pork industry up to $8 billion a year. In a series of laboratory manure incubations, ARS researchers and collaborators in Lincoln, Nebraska showed that hydrated lime addition to PEDv-contaminated swine manure decreased PEDv concentrations rapidly (within an hour) and inhibited the ability of virus in manure to cause disease in pigs. Multiple extension communications, information prepared for commodity organizations, and peer-reviewed papers prepared for veterinary journals have helped publicize this practice which is quickly being adopted to help control PEDv outbreaks.

2. Organic farm soils provide an indication for baseline antibiotic resistance. Antibiotic resistance is ubiquitous in the environment. The use of antibiotics in modern agricultural production is a concern for the public and research community because antibiotic use impacts the development of antibiotic resistance microorganisms which could affect human health. In a recently published study, ARS researchers in Lincoln, Nebraska found that antibiotic resistance was easily detected in thirteen Nebraska organic farming operations. However, when compared to native prairie soils with ‘background’ resistance, most resistance genes were actually more frequently detected in prairie soils. This information indicates that farming practices utilizing manure doesn’t increase long-term resistance in the soil. This research informs and supports U.S. policy positions for international trade negotiations around antibiotic resistance in US agricultural products.

Review Publications
Stevens, E.E., Miller, D.N., Brittenham, B.A., Vitosh-Sillman, S.J., Brodersen, B.W., Jin, V.L., Loy, J.D., Schmidt, A.M. 2018. Alkaline stabilization of manure slurry inactivates porcine epidemic diarrhea virus. Swine Health and Production. 26:95-100.
Durso, L.M., Cook, K.L. 2018. Antibiotic resistance in agroecosystems: A One Health perspective. EcoHealth. 14:1-6.
Topp, E., Larsson, D., Miller, D.N., Van Den Eede, C., Virta, M. 2018. Antimicrobial resistance and the environment: Assessment of advances, gaps and recommendations for agriculture, aquaculture and pharmaceutical manufacturing. FEMS Microbiology Ecology. 94:fix185.
Durso, L.M., Miller, D.N., Henry, C.G. 2018. Impact of vegetative treatment system on multiple measures of antibiotic resistance in agricultural wastewater. International Journal of Environmental Research and Public Health. 15(6):1295.
Cadenas, M., Durso, L.M., Miller, D.N., Waldrip, H., Castleberry, B., Drijber, R.A., Wortman, C. 2018. Tetracycline and sulfonamide antibiotic resistance genes in soils from Nebraska organic farming operations. Frontiers in Microbiology. 9:1283.
Gilley, J.E. 2018. Surface detention on cropland, rangeland, and conservation reserve program areas. Transactions of the ASABE. 61(3):955-966.
Woodbury, B.L., Gilley, J.E., Parker, D.B., Stromer, B.S. 2018. Greenhouse gas emissions from beef feedlot surface materials as affected by diet, moisture, temperature, and time. Transactions of the ASABE. 61(2):571-582.
Gilley, J.E., Bartelt-Hunt, S.L., Eskridge, K.M., Li, X., Schmidt, A.M., Snow, D.D. 2017. Setback distance requirements for removal of swine slurry constituents in runoff. Transactions of the ASABE. Vol. 60(6):1885-1894.