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ARS Home » Plains Area » Lincoln, Nebraska » Agroecosystem Management Research » Research » Research Project #431160

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

Location: Agroecosystem Management Research

2020 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
Continued progress was made on all objectives and milestones over the past year, and new collaborative partnerships with other ARS research locations and researchers at universities working in similar research areas were established. Research progress was made in multiple projects investigating antibiotic resistance in manure and soils using methods developed in previous years. A four-target quantitative antibiotic resistance gene (ARG) assay validated in previous years was deployed in multiple states and has been used to collect data on a targeted high-priority set of environmental ARG targets in manure, water, soil, and gastrointestinal samples for five other studies. Validation began on an improved probe-based assay for the same targets, with final analysis scheduled for 2021. These projects will yield important insights into the factors controlling antibiotic resistance, their persistence, and potential background levels in agroecosystems and contributes to project Objective 1. For Objective 2, data analysis and presentation of rainfall simulation studies conducted in previous years continued including the fate of multiple resistance genes in soils and runoff to better predict how resistance genes could transport away from manure application sites. Also, within Objective 2, multiple trials using soil columns showed that subsurface incorporation of wood pulp reduces nitrate leaching by 90%. Reducing nitrate leaching impacts local water quality and could reduce nutrient loss in tile-drained soils which contribute to Gulf of Mexico dead zones. At 10-tons per acre, ground wood chips worked well for nitrate removal. Ongoing soil column trials are evaluating low-cost carbon biomass sources (red cedar, ash, and wheat straw) at the 10-ton per acre treatment level. Field trials in north-central Nebraska are expected to begin in fiscal year 2021. Work in Objective 3 is ongoing. Soil was collected at four additional animal-impacted sites (total of seven sites ranging in animal impact), stabilized, and prepared for multiple laboratory incubations. Incubations however were unfortunately delayed due to COVID-19. However, prior to the implementation of maximum telework, progress was made on denitrification methods including molecular biological methods to analyze important microbial groups involved in soil nutrient transformation.

1. Tetracycline resistance higher in prairie vs organic farm soils. Tetracycline resistance higher in prairie vs organic farm soils. Soil is a natural reservoir for antibiotic resistance. Farming changes many soil properties over time, and there is a concern that some practices may enhance the potential for antibiotic resistance to jump from soils into animals and humans. Researchers at Lincoln, Nebraska, conducted a survey of tetracycline antibiotic resistance in soils collected at organic-certified farm operations, which was compared to an earlier survey at nearby prairie sites. Particular resistance genes were found in the prairie site cores more often, and the number of different genes (diversity) were higher in prairie soils. The act of farming does not adversely impact tetracycline resistance in soils.

2. Bringing an agricultural perspective to inform global antibiotic resistance policy. Bringing an agricultural perspective to inform global antibiotic resistance policy. Antibiotic resistance is one of the greatest health threats of our age, with the specter of losing these important drugs impacting everything from routine infections, to lifesaving heart surgeries, and elective procedures such as joint replacements. Global antibiotic resistance control efforts have adopted a One Health approach for health, policy, and trade relevant outcomes by working to integrate human public health, animal health, and environmental health research. However, data from environmental and agricultural systems remains severely under-represented. ARS researchers in Lincoln, Nebraska, have identified this gap and have been analyzing, interpreting, and integrating their research in agricultural and natural systems in a way that makes it accessible to the One Health community. ARS antibiotic resistance research has not only developed tools and quality control measures that are now broadly used for tracking antibiotic resistance farm-to-fork, but also collected and interpreted data that has been instrumental in bringing an agricultural perspective to national and international policy and trade efforts.

Review Publications
Gilley, J.E., Bartelt-Hunt, S.L., Eskridge, K.M., Li, X., Schmidt, A.M., Snow, D.D. 2020. Retention of swine slurry constituents in soil and crop residue. Transactions of the ASABE. 231:322.
D'Alessio, M., Durso, L.M., Williams, C.F., Olson, C.A., Ray, C., Paparozzi, E.T. 2020. Applied injected air into subsurface drip irrigation: plant uptake of pharmaceuticals and soil microbial communities. Journal of Environmental Engineering. 146(2).
Durso, L.M., Gilley, J.E., Marx, D.B., Thayer, C.A., Woodbury, B.L. 2019. Microbial transport as affected by residue cover and manure application rate. Transactions of the ASABE. 62(3):687-694.
Meyers, M.A., Durso, L.M., Gilley, J.E., Waldrip, H., Castleberry, B., Millmier, S.A. 2020. Selected soil antibiotic resistance gene profile changes following manure application and rainfall. Environmental Quality. 49(3):754–761.
Levine, R.E., Zhang, Y., Leng, Y., Snow, D.D., Dassada, D., Durso, L.M., Li, X. 2019. Microbial transformation of sulfonamide antibiotics under various background nutrient conditions. Bulletin of Environmental Contamination and Toxicology. 103:808–813.
Yang, Y., Ashworth, A.J., Debruyn, J.M., Willett, C., Durso, L.M., Cook, K.L., Moore Jr, P.A., Owens, P.R. 2019. Soil bacterial biodiversity is driven by long-term pasture management, poultry litter, and cattle manure inputs. PeerJ. 7:e7839.
Duerschner, J., Bartelt-Hunt, S.L., Eskridge, K.M., Gilley, J.E., Li, X., Schmidt, A.M. 2020. Swine slurry characteristics as affected by selected additives and disinfectants. Environmental Pollution. 260:114058.
Barrios, R.E., Bartelt-Hunt, S.L., Gilley, J.E., Schmidt, A.M., Snow, D.D., Li, X. 2020. Fate and transport of antibiotics and antibiotic resistance genes in runoff and soil as affected by timing of swine slurry application. Environmental Pollution. 712(10):136505.
Gilley, J.E., Bartelt-Hunt, S.L., Snow, D.D., Schmidt, A.M., Eskridge, K.M., Li, X. 2020. Influence of setback distance on antibiotics and antibiotic resistance genes in runoff and soil following the land application of swine manure slurry. Journal of Environmental Science and Technology. 54(8):4800-4809.