Progress 07/13/16 to 07/12/21
Outputs
PROGRESS REPORT Objectives (from AD-416): 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 (from AD-416): 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). 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. Record of Any Impact of Maximized Teleworking Requirement: Restrictions on in person laboratory hours has impacted multiple projects related to the project objectives. Although project milestones were met, planned work with collaborators was delayed or cancelled. ACCOMPLISHMENTS 01 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. 02 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. 03 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.
Impacts
(N/A)
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.
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Progress 10/01/19 to 09/30/20
Outputs
Progress Report Objectives (from AD-416): 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. Approach (from AD-416): 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). 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. Accomplishments 01 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. 02 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.
Impacts
(N/A)
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.
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Progress 10/01/18 to 09/30/19
Outputs
Progress Report Objectives (from AD-416): 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. Approach (from AD-416): 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). 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. Accomplishments 01 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.
Impacts
(N/A)
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.
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Progress 10/01/17 to 09/30/18
Outputs
Progress Report Objectives (from AD-416): 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. Approach (from AD-416): 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). 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. Accomplishments 01 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. 02 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.
Impacts
(N/A)
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.
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Progress 10/01/16 to 09/30/17
Outputs
Progress Report Objectives (from AD-416): 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. Approach (from AD-416): 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). 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.
Impacts
(N/A)
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.
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