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

Location: Agroecosystem Management Research

2019 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. Additionally, 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 FY2017 and FY2018. One antibiotic resistance assay validated in FY 2018 was deployed in multiple states and is being used to collect data on a small but consistent set of antibiotic resistant genes (ARG) targets in manure, water, soil, and gastrointestinal samples. Data collection is expected to continue through 2020, with final analysis scheduled for 2021. Work on a second study, evaluating the environmental persistence of seven Shiga toxigenic E. coli serotypes and the persistence of their genes in simulated runoff, continues on schedule, and all data collection has been completed this year. 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, the results of rainfall simulation studies conducted in previous years was compiled and additional analyses were conducted including measuring eighteen resistance genes in soils and runoff to better understand how resistance genes could transport away from manure application sites. Also, within Objective 2, multiple runs on modified soil columns developed in previous years demonstrated that subsurface incorporation of wood pulp can eliminate nitrate leaching—an important nutrient loss in tile-drained soils that contributes to dead zones in the Gulf of Mexico and adversely impacts rural communities that rely on shallow aquifers for drinking water. At 10-tons per acre, ground wood chips worked well for nitrate removal. In the next course of runs, low-cost wood chip sources will be evaluated with the aim of implementing subsurface woodchip treatment at a larger field site in north-central Nebraska next year. Work in Objective 3 was unfortunately delayed due to a very wet spring and early summer that did not allow field access for soil collection. We anticipate soils will be collected soon and will be used for multiple laboratory incubations over the next year. During the delay, an initial study was conducted using other older soils that helped refine the incubation conditions to better measure antibiotic effects on nitrification. The extra time also allowed the team to better refine equipment used for denitrification measurements.

1. Manure borne nutrients and microbes respond differently to agronomic practices. Producers have many considerations to balance when land applying manures, including preventing contamination of surface waters with both nutrients and microbes. Filter strips of annual or perennial vegetation or crop residues consistently reduce the transport of manure nutrients in runoff from land application areas by slowing the flow of runoff and allowing nutrient rich particles to settle out, but they have not been thoroughly investigated for reduction of fecal indicators or pathogens. In a series of large-scale simulated rainfall experiments where manure was added at rates required to meet the nitrogen requirements for corn, ARS scientists in Lincoln, Nebraska, found that perennial narrow grass hedges, annual wheat strips, and crop residue cover reduced total counts E. coli and enterococci. However, the relative effectiveness was less than that for nutrients, as the microbes tended to remain suspended in runoff. In addition to agronomic measures to limit runoff of nutrients from land-applied manure, agricultural best management practices for producers will need to consider the unique way that manure-borne microbes move following rainfall.

Review Publications
Ziara, R.M., Miller, D.N., Subbiah, J., Dvorak, B.I. 2018. Lactate wastewater dark fermentation: The effect of temperature and initial pH on biohydrogen production and microbial community. International Journal of Hydrogen Energy. 44(2):661-673.
Durso, L.M., Gilley, J.E., Marx, D.B., Woodbury, B.L. 2019. Narrow grass hedge effects on microbial transport following variable applications of beef cattle manure. Transactions of the ASABE. 62(1):149-156.
Greene, S.L., Khoury, C.K., Williams, K.A. 2018. Wild plant genetic resources in North America: an overview. In: Greene, S.L., Williams, K.A., Khoury, C.K., Kantar, M.B., Marek, L.F., editors. North American Crop Wild Relatives. Volume 1: Conservation Strategies. New York, NY: Springer, Cham. p. 3-32.