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ARS Home Plains Area Lincoln, Nebraska Agroecosystem Management Research Research





- Miller, Daniel
- Durso, Lisa
- Gilley, John
- 2023
- 2022
- Publications
- Food Safety, (Animal and Plant Products) (108)
- Soil and Air (212)

Research Project: Managing Manure as a Soil Resource for Improved Biosecurity, Nutrient Availability, and Soil Sustainability **Location:
                            Agroecosystem Management Research** 2023 Annual Report **Objectives**
                                

Objective 1: Determine the movement of nitrogen into and out of agroecosystems at critical points and develop practices to ameliorate losses.
Subobjective 1A: Develop a deep carbon injection practice utilizing byproduct cellulose to reduce nitrate leaching in sandy soils.
Subobjective 1B: Coordinate laboratory ammonia measurement to better estimate ammonia deposition impacts from nearby animal feeding operations.
Subobjective 1C: Determine the effects of emerging agricultural contaminants on nutrient transformation and decomposition.

Objective 2: Measure and mitigate pathogens, fecal indicators, and antibiotic resistance in agriculturally impacted environments and determine their interactions with healthy soils to lessen risk from the agricultural environments to natural environments.
Subobjective 2A: Develop and validate methods to detect and quantify AR genes, AR pathogens, and AR commensal organisms in agronomic and environmental matrices with a focus on resistance classes that are a human health priority, and that align with global AR surveillance efforts.
Subobjective 2B: (Deleted Obsolete March 2023)
Subobjective 2C: Evaluate impact of fertilization and crop management strategy on AR in soils.

Objective 3: Improve mathematical representation of hydrologic processes influencing nutrient transport by overland flow on land application areas to reduce uncertainty associated with relevant nutrient applications and nutrient dynamics and to inform and strengthen opportunities for better management strategies.
Subobjective 3A: Quantify surface hydrologic processes influencing nutrient transport by surface runoff on cropland areas where beef and swine manure is applied.
Subobjective 3B: Use previously derived relationships and existing data to identify when and where to apply manure to maximize the use of nutrients and minimize nutrient losses to the environment.

Objective 4: Determine the ability of innovative fertilizer technology and precision fertilizer application to decrease nutrient loss to the environment and affect soil microbial function.
Subobjective 4A: Determine the effects of long-term variable fertilizer inputs and crop rotations on nutrient-transformations and antibiotic resistance within the soil microbial community as related to precision fertilizer application methods that may include Enhanced Efficiency Fertilizers (EEFs), bio-stimulants, manure, or biochar.
Subobjective 4B: Evaluate soil microbial community changes in cool-season grass pastures in response to nitrogen fertilizer management **Approach**
                                

The use of animal manures in farming impacts plant, animal, and human health, providing both benefits and challenges. Nutrient-rich animal manures are a boon to crop production; building soil organic matter, replacing expensive chemical fertilizers and enhancing soil physical and chemical properties. However, manured agronomic soils also present biosecurity risks to both ecosystems and human health, via runoff or leaching of excess nutrients, the impacts of excreted antibiotics and other emerging agricultural contaminants on carbon and nitrogen cycling in the soil, and the potential transfer of biological agents such as zoonotic pathogens and antibiotic resistant microorganisms. The proposed research project will address a number of critical knowledge gaps by i) identifying sources of excess nutrients (e.g., ammonia deposition near cattle feedlots) and the fate of nitrogen leaching into shallow groundwaters; ii) quantifying impacts of conservation practices in reducing nutrient transport and identifying manure management practices that optimize water quality and ecosystem health; iii) developing assays to detect microbes that cause and protect against disease across a continuum of rural-suburban-urban agronomic systems, and methods to support antibiotic resistance risk-assessment efforts; and iv) identifying the effects of manure associated pharmaceuticals on soil and aquatic ecosystem processes (nitrification and denitrification). Quantifying the benefit from sustainable nutrient (re)utilization and its associated positive effects of agronomic impacts to the soils on ecosystem, animal, and human health is a primary goal of this research. Coupled to this, and fully integrated into the larger research enterprise, are the collateral aspects of improving biosecurity and reducing adverse impacts potentially arising from this sustainable nutrient (re)utilization. Both aspects are important individual priorities of this research, but we are seeking to fully integrate these efforts for a more holistic, systematic understanding – one that provides clear systems level solutions to these problems arising from a common resource. **Progress Report**
                                

Progress was made on all objectives and milestones over the past year, and collaborative partnerships continued with other ARS research locations and researchers at multiple universities. 
Subobjective 1A: A collaborative laboratory study was begun with a University of Nebraska collaborator and their student to mimic the conditions where a field study entrenching waste wood chips below the root zone to limit nitrate leaching is being conducted in North Central Nebraska. Although utilizing a much lower woodchip application than in previous studies, nitrate leaching was still substantially reduced. 
Subobjective 1B: The multi-location ARS field project focusing on ammonia deposition near animal production sites and its impact on local native ecosystems and crop production sites at two sites have started collecting meteorological and biogeochemical data. An additional site in Texas is also being instrumented with biogeochemical data collection slated to beginning next year.
Subobjective 1C: In two separate projects (one focused on nanopesticides and the other on microplastics), a series of laboratory incubations were conducted with varying levels of contaminants.  The effects on nutrient transformation and carbon mineralization are limited, but additional analyses need to be made on frozen samples.
Subobjective 2A: Agricultural and environmental antibiotic resistance remains poorly understood in part due to the lack of accessible quantitative methods available for data collection. Progress was made in the validation of a new method that builds on a widely used water quality assay and modifies it to enumerate antibiotic resistant E. coli quickly and easily in agricultural and environmental samples. Limits of detection, sensitivity, and specificity were determined, and protocols were drafted and tested in multiple laboratories. Primary validation was begun on a second assay that works on a similar principle but does not require any specialized equipment.  
Subobjective 2C: It is known that manure application to cropland soils temporarily changes the microbial communities of the soil, commonly increasing the number of antibiotic resistant bacteria, regardless of whether or not the animals contributing the manure have been treated with antibiotics. One hypothesis is that the nutrients in the manure increase the growth of resistant bacteria already living in the soil. Samples were collected and processed from agronomic plots that will allow us to compare the microbial communities from soils at different nutrient levels, and from different nutrient sources.  
Objective 3: Research has been completed identifying the mechanisms influencing nutrient transport resulting from nutrients contained within soil, and from surface application of beef cattle manure. Results from these studies will be presented in oral presentations to be delivered at two annual professional society meetings. 
Objective 4: Two large collaborative studies in Eastern Nebraska involving numerous University of Nebraska collaborators and ARS scientists from Lincoln, Nebraska, are underway to assess the impact of novel fertilizer use in grazing paddocks and in a corn-soybean rotation study. In the grazing paddock study, analysis of fall soil samples showed marked differences in the abundance of nitrogen transformation genes. Two new corn-soybean field sites were also established this year with varying nitrogen application amounts, timing, and forms (including enhanced efficiency fertilizers) in addition to cover crops to better manage nitrogen inputs and losses. This brings to three (out of four planned) operating long-term field sites dedicated to this study. Soils at the rotation site have been collected and evaluated for potential nitrogen transformation activities. Frozen samples await further analysis. **Accomplishments** **Review Publications**
                            *Lindgren, J.K., Messer, T.L., Miller, D.N., Snow, D.D., Franti, T.G. 2022. Neonicotinoid pesticide and nitrate mixture removal and persistence in floating treatment wetlands. Journal of Environmental Quality. https://doi.org/10.1002/jeq2.20411.*
                                *Burch, T.R., Stokdyk, J.P., Firnstahl, A.D., Kieke, B.A., Cook, R.M., Opelt, S.A., Spencer, S.K., Durso, L.M., Borchardt, M.A. 2022. Microbial source tracking and land use associations for antibiotic resistance genes in private wells influenced by human and livestock fecal sources. Journal of Environmental Quality. 52(2):270-286. https://doi.org/10.1002/jeq2.20443.*
                                *Beni, N.N., Karimifard, S., Gilley, J.E., Messer, T., Schmidt, A., Bartelt-Hunt, S. 2023. Higher concentrations of microplastics in runoff from biosolid-amended croplands than manure-amended croplands. Nature Communications. https://doi.org/10.1038/s43247-023-00691-y.*


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