Location: Agroecosystem Management Research
2021 Annual Report
Objectives
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.
Objective 4: Determine the ability of innovative fertilizer technology to improve nutrient use efficiency of applied fertilizer for crop production and decrease nutrient loss to the environment.
Subobjective 4A. Determine the effects of long-term variable fertilizer inputs and crop rotations on nutrient-transforming and antibiotic resistance within the soil microbial community
Subobjective 4B. Evaluate seasonal changes in root-associated and bulk soil microbial communities in response to drip irrigation/fertigation or other precision fertilizer application methods that may include Enhanced Efficiency Fertilizers (EEFs), bio-stimulants, manure, or biochar.
Approach
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 and the fate of fertilizer inputs.
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). The effects of novel fertilization methods to limit environmental nutrient losses may impact microbial communities. These impacts will be assessed to evaluate sustainability (Objective 4). 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 the final report for this project which terminated in July 2021 and will be replaced by project, 3042-12630-003-00D, “Managing Manure as a Soil Resource for Improved Biosecurity, Nutrient Availability, and Soil Sustainability.” Significant progress was made on all objectives through continued collaborative partnerships at the ARS location, with other ARS research locations, and researchers at multiple universities working in similar research areas. In a series of collaborative studies, robust, cross-validated methods to measure antibiotic resistance (Objective 1) were developed through a multi-location partnership to assess potential transport issues after manure application and in manure-impacted environments across the nation. Field and laboratory experiments evaluated factors affecting manure nutrient, pathogen, antibiotic, and antibiotic resistant bacteria (ARB) transport in runoff and nitrate leaching past the root zone into shallow ground water (Objective 2 & 3). Finally, soil’s capacity to mitigate specific manure concerns including pathogen persistence, specifically the porcine epidemic diarrhea virus, and determining antibiotic effects on soil microbial processes was explored in laboratory and field studies to better understand environmental risks for manure application (Objectives 2 & 3). Information from these studies 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).
Ongoing efforts related to Objective 1 include the evaluation of a newly developed biomulch and manure-based topdressings in an organic spinach production system, conducted in partnership with a university collaborator. Additionally, progress has been made on a laboratory-based collaboration that was started in 2020, with partners at the University of Texas at Dallas and Agri-Food Canada. The project goal is to evaluate whether the natural bacterial immune system of enterococci in manure and manure-impacted soils and water, impede the dissemination of antibiotic resistance in these environments. To date, 150 field isolates have been screened for the present of two genes, and over 1,400 genomes from publicly available sequences have been evaluated for bacterial immune system and antimicrobial resistance genes. Ongoing work will continue typing field isolates and begin microcosm studies testing the efficacy of the natural bacterial immune system as a blocker of antibiotic resistance plasmid transfer in manure.
Building on the work of multiple soil column experiments that found entrenching carbon-rich ag bioproduct (wheat straw and ash or cedar tree wood chips) beneath the crop root zone in sandy soil reduced nitrate leaching by greater than 90%, field trials in collaboration with University of Nebraska researchers are now underway utilizing mixed wood chips to limit nitrate leaching. New funding to the project to evaluate enhanced efficiency fertilizers have led to the establishment of two new field sites associated with novel fertilizer management. Initial soil samples have been collected and are being analyzed in conjunction with university collaborators for multiple soil attributes related to fertilizer management to establish baseline conditions. These collaborations at this site will be the foundation for larger, multi-year field evaluations.
Accomplishments
1. Setback distance requirements were established for land manure application areas. Setbacks, where manure is not applied but crops continue to be grown, can be an arbitrary decision. Rainfall simulation tests were conducted by ARS scientists in Lincoln, Nebraska, to measure the effects of different setback distances on selected pollutants in runoff following land application of beef cattle or swine manure to cropland areas. After an initial set of tests were completed to identify background constituents, manure was applied, and additional rainfall simulation tests were performed. A setback distance of 12.2 m reduced selected pollutants to background (no manure) runoff values. Analysis showed that dilution was the principal mechanism reducing pollutant transport in setback areas. Producers, conservationists, and land managers can use this information to determine appropriate site-specific setbacks.
2. Baseline levels of antibiotic resistance in agricultural systems were defined. Although there is broad consensus that agricultural antibiotic resistance should be reduced, it is unclear what an appropriate target level for reduction should be, or how to measure if progress is being made. Research at Lincoln, Nebraska, addressed both questions by tracking and quantifying antibiotic resistance in soils from natural settings and organic farming operations, as well as developing, validating, and sharing tools to track and quantify antibiotic resistance in the environment. Data from projects measuring baseline levels of antibiotic resistance in natural prairie soils and organic farming systems was used to inform USDA Office of Chief Scientist, the Presidential Advisory Council on Combating Antimicrobial Resistance, The National Academies of Science and Engineering, The Wellcome Trust, and the Centers for Disease Control and Prevention, as well as support U.S. policy positions for international trade negotiations around antibiotic resistance in U.S. agricultural products. The molecular surveillance tools and quality control measures are now broadly used for tracking antibiotic resistance farm-to-fork.
3. Entrenching wood chips or wheat straw reduces nitrate leaching losses by 90%. Nitrate leaching below the crop root zone has led to widespread nitrate contamination in many shallow aquifers in rural areas. Multiple laboratory studies were conducted by ARS scientists in Lincoln, Nebraska, evaluating how waste byproducts high in cellulose, like wood chips and wheat straw, could be used to foster the growth of bacteria that can transform nitrate leaching out of crop fields. These studies showed that nitrate leaching could be reduced by 90% over a simulated 3-year span. Working with University of Nebraska collaborators and representatives from natural resource districts affected by high nitrate groundwater contamination, a field study is currently underway to test how effectively waste woodchips can be injected deep below crop fields, their impact on nitrate leaching, and potential to affect crop production.
Review Publications
Miller, D.N., Jurgens, M., Durso, L.M., Schmidt, A. 2020. Simulated winter incubation of soil with swine manure differentially affects multiple antimicrobial resistance elements. Frontiers in Microbiology. (11):3235. https://doi.org/10.3389/fmicb.2020.611912.
Durso, L.M., Gilley, J.E., Meyers, M.A., Miller, D.N., Li, X., Schmidt, A.M. 2020. Impact of setback distances on transport and antibiotic resistance profiles of fecal indicators from manure-amended fields. Agrosystems, Geosciences & Environment. 3:e220081. https://doi.org/10.1002/agg2.20081.
Gilley, J.E., Marx, D.B. 2020. Accumulation and release of nutrients by immersed stalks collected on selected dates following harvest. Water, Air, and Soil Pollution. 231:384. https://doi.org/10.1007/s11270-020-04765-x.
Waldrip, H., Parker, D.B., Miller, S., Miller, D.N., Casey, K.D., Todd, R.W., Min, B., Spiehs, M.J., Woodbury, B.L. 2020. Nitrous oxide from beef cattle manure: effects of temperature, water addition and manure properties on denitrification and nitrification. Atmosphere. 11:1056-1078. https://doi.org/10.3390/atmos11101056.
Durso, L.M., Miller, D.N., Gilley, J.E. 2021. Differential survival of non-O157 Shiga-toxigenic Escherichia coli serotypes in manure-impacted water. Foodborne Pathogens and Disease. 2021. https://doi.org/10.1089/fpd.2021.0024.
Wind, L., Briganti, J., Brown, A.M., Neher, T.P., Davis, M.F., Durso, L.M., Spicer, T., Lansing, S. 2021. Finding what is inaccessible: Antimicrobial resistance language use among the One Health domains. Antibiotics. 10:385. https://doi.org/10.3390/antibiotics10040385.
