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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

2017 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
This is report summarizes milestones, progress, and accomplishments for the first year of a new project (3042-12630-003-00D) approved during FY2016. Substantial research results were obtained through strong collaborative partnerships with other ARS research locations and universities over the past year. Research progress in manure application setbacks contributed to NP 212 Component 2 “Managing Nutrients in Agroecosystems” and Component 3 “Reducing Environmental Risk of Agricultural Operations”. Manure application setbacks are used to ensure applied manure does not runoff to surface and ground water. Because detailed information to help identify proper setback distances is very limited, a study using swine manure slurry applied at agronomic rates was conducted to measure how setback distance affected concentrations and transport rates of specific manure constituents (nutrients, microbes, and pharmaceutical compounds) following land application. Consistent with an earlier study of cattle feedlot manure, setback distances of 12.2 meters effectively reduced all swine manure nutrient concentrations (except nitrate) and transport rates to background levels observed in no-manure control areas indicating that setbacks effectively reduce swine manure pollutants in runoff from swine manure application areas. This research contributes to project objective 2. Research progress in antibiotic resistant bacteria and pathogens contributed to NP 212 Component 3 “Reducing Environmental Risk of Agricultural Operations”. Both manure and soils are important reservoirs of antibiotic resistance genes (ARG) and microorganisms (bacteria and virus) capable of infecting humans and animals. Consistent reliable methods are prerequisite for assessing sources and fates of resistance genes in the environment. Assays for four ARG targets and a 16S control were validated this year, including completion of all level 1 (Research level) & level 2 (Expert level) validation criteria. This included test method definition and documentation of devices, reagents, organisms, and experimental conditions. It also included determination of intra-laboratory performance methods such as trueness, precision, calibration, sensitivity, and limits of detection. Assays were assessed for repeatability between operators and machines within the host laboratory, and between laboratories and operators at remote locations. Additionally, ARG assays from three additional ARS laboratories have been identified for inclusion in the cross-laboratory validation effort. In other projects, pathogens (multiple Shigatoxin producing E. coli strains and porcine epidemic diarrhea virus) were monitored for survival in simulated wastewater runoff and manure pits treated with quicklime. Both projects yielded important insights into the factors controlling pathogen persistence and potential control in agroecosystems and contributes to project objective 1. Additional projects are ongoing to better define control measures.


Review Publications
Durso, L.M., Miller, D.N., Snow, D.D., Santin, M., Henry, C.G., Woodbury, B.L. 2016. Evaluation of fecal indicators and pathogens in a beef cattle feedlot vegetative treatment system. Journal of Environmental Quality. 46(1):169-176.
Gilley, J.E., Sindelar, A.J., Woodbury, B.L. 2016. Cropland filter strip removal of cattle manure constituents in runoff. Transactions of the ASABE. 59(6)/1681-1693.
Schuster, N.R., Bartelt-Hunt, S., Durso, L.M., Gilley, J.E., Li, X., Marx, D.B., Schmidt, A.M., Snow, D.D. 2017. Runoff nutrient and microbial transport following swine slurry application. Transactions of the ASABE. 60(1)/53-66. doi: 10.13031/trans.11370.
Miller, D.N., Spiehs, M.J., Varel, V.H., Woodbury, B.L., Wells, J., Berry, E.D. 2016. Distillers by-product cattle diets enhance reduced sulfur gas fluxes from feedlot soils and manures. Journal of Environmental Quality. 45:1161-1168.
Segal, L.M., Miller, D.N., McGhee, R., Loecke, T.D., Cook, K.L., Shapiro, C.A., Drijber, R.A. 2017. Bacterial and archaeal ammonia oxidizers respond differently to long-term tillage and fertilizer management at a continuous maize site. Soil and Tillage Research. 168:110-117.
Spiehs, M.J., Brown-Brandl, T.M., Parker, D.B., Miller, D.N., Berry, E.D., Wells, J.E. 2016. Ammonia, total reduced sulfides, and greenhouse gases of pine chip and corn stover bedding packs. Journal of Environmental Quality. 45:630-637.