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 Environmentally Integrated Dairy Management Research: Madison, WI
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ARS Home Midwest Area Madison, Wisconsin U.S. Dairy Forage Research Center Environmentally Integrated Dairy Management Research Research





- Burch, Tucker
- Young, Eric
- Heffron, Joseph
- 2023
- 2022
- Publications
- Food Animal Production (101)
- Soil and Air (212)
- Sustainable Agricultural Systems Research (216)

Research Project: Managing Nutrients and Assessing Pathogen Emission Risks for Sustainable Dairy Production Systems **Location:
                            Environmentally Integrated Dairy Management Research** 2023 Annual Report **Objectives**
                                

Objective 1: Quantify the ability of innovative dairy nutrient management practices to improve soil nutrient distribution and runoff water quality. 
1A: Evaluate the association between Runoff Risk Advisory Forecast (RRAF) forecasts and microbial contamination of private household wells in the dairy region of northeastern Wisconsin.
1B: Develop a prediction tool that expands upon the RRAF, incorporating groundwater-related factors, to be able to predict and avoid manure runoff contamination of private household wells.
1C: Quantify pasture management effects on surface runoff water quality, soil nutrient distribution, and soil health measures.
1D: Determine the impacts of using high-resolution soil mapping on crop nutrient recommendations and loss indices at the UW-Marshfield Agricultural Research Station.
1E: Characterize soil properties and evaluate nutrient attenuation in soils and shallow subsurface runoff flows of select riparian buffers adjoining forage crop fields at UW-MARS and the U.S. Dairy Forage Research Center (USDFRC) Prairie du Sac Research Farm using field sampling and modeling approaches. 

Objective 2: Evaluate the ability of novel dairy manure management practices to improve on-farm nutrient use efficiency.  
2A: Evaluate the impact of separated dairy manure solids and heifer manure on corn yield, soil biological indicators, and nitrate leaching over multiple growing seasons. 

Objective 3: Develop and apply improved quantitative microbial risk assessment (QMRA) methods to assess the public health impacts of alternative dairy production practices.  
3A: Develop a screening-level exposure and risk assessment model for waterborne gastrointestinal pathogens in private wells contaminated by human and/or bovine fecal material. 
3B: Develop an updated, outbreak-based Cryptosporidium dose-response model.  
3C: Conduct a state-wide QMRA for transmission of antibiotic resistant bacteria (ARB) via private wells in Wisconsin. **Approach**
                                

Dairy production has intensified over the past 30 years, shifting from many small farms to fewer large farms. Driven by goals of efficiency and economic productivity, this change has benefited producers and consumers alike. However, it has also altered the environmental impacts of dairy production because larger farms tend to concentrate livestock manure in smaller geographic regions and require more intense manure applications compared to less concentrated production systems, placing increased pressure on soil health and water quality as a result. At the same time, the pressures facing modern dairy operations, including high input costs, uncertain milk and commodity prices, and increasing regulatory demands and public scrutiny, have led to renewed interest in less intensive production practices (e.g., grazing-based systems). Technical recommendations for co-optimizing production and environmental impacts in these systems is limited. The proposed research will focus on impacts of dairy management practices on soil health, nutrient loss in water runoff and leaching, and public health risks of antimicrobial resistance and pathogen exposures. The approach is collaborative, including major contributions from the University of Wisconsin-Marshfield Agricultural Research Station (UW-MARS), UW-Madison, UW-Extension, the National Cooperative Soil Survey, and the U.S. Geological Survey Upper Midwest Water Science Center, among others. The approach also consists of observational and experimental field work along with complementary mathematical modeling efforts. Observational field work is based on randomized sampling of private wells in northeast Wisconsin and multivariate predictive statistical modeling. Field work is based on continued use and development of our long-standing field facilities at UW-MARS. And additional mathematical modeling is largely grounded in the quantitative microbial risk assessment (QMRA) approach. This work impacts dairy and forage production systems in the upper Midwest and elsewhere. Products and outcomes consist of best management practices for nutrients, zoonotic pathogens, and antimicrobial resistance; fundamental knowledge about soil health and function; and improved tools for QMRAs. Stakeholders include dairy producers, the dairy industry, environmental and public health agencies, and rural residents. **Progress Report**
                                

Objective 1, Sub-objectives 1A and 1B: We established a new outgoing agreement with the United States Geological Survey collaborators in August of 2022, which allowed us to catch up on missed milestones from fiscal year 2022. We have now conducted 4 of 6 planned sampling events from 30 private wells in northeast Wisconsin. The fifth event is currently planned for July of this year, after which we will schedule the final event for late summer or early fall of this year. Samples from the first sampling event have been analyzed in the lab; samples from the other three completed sampling events have been processed and archived for analysis later in the year. Following the retirement of its previous incumbent in May of 2022, our unit’s vacant Research Microbiologist position was filled in January of 2023, and we are in the process of getting this new scientist integrated into the project. In the meantime, we have increased the scope of sampling and lab analyses for Sub-objective 1A to include nitrate in groundwater, which will allow extension of this work beyond the microbial analyses originally planned. We have also amended the agreement with our United States Geological Survey collaborators to increase the scope of their role on the project, adding characterization of the relationship between runoff forecasts and groundwater recharge in the study area. Results of this newly planned work will inform Sub-objective 1A by providing additional insights on the relationship between the Wisconsin Runoff Risk Advisory Forecast system and private well contamination. 

Objective 1, Sub-objective 1C: The four experimental watersheds for this sub-objective are currently managed as grazed pasture during the present calibration phase of the study design. Dairy heifers are rotated through each pasture in sequence during the growing season. Four new flumes were installed during 2022 and watersheds were sampled intensively in spring 2023 to characterize carbon and nutrient distribution. A manuscript is currently being written summarizing results from the most recent grazing phase trial data. We also began collecting samples for microbial analyses for this project in spring of 2022 and have archived 48 such samples so far. Forty of these samples have been analyzed as of May.

Objective 1, Sub-objective 1D: We have a cooperative agreement in place with the University of Wisconsin-Madison and USDA’s Natural Resource Conservation Service to assist in digital soil mapping and sampling aspects of this sub-objective. A postdoctoral associate will be hired through University of Wisconsin-Madison. Acquisition of soils and associated electronic covariate data for digital mapping will begin after the postdoc is in place during late summer or early fall of this year. Sampling for soil carbon and nutrient stocks will be performed during the fall of 2023 and 2024 growing season, with data analysis following data acquisition in 2024.    

Objective 1, Sub-objective 1E: This sub-objective is behind schedule due to a delay in finding an appropriate site and finding a contractor to install groundwater wells. A contractor will be hired in June of 2023 to install groundwater wells in transects across a riparian zone at the Marshfield Agricultural Research Station. Lysimeters will also be installed to monitor nutrients in soil water. This buffer area receives surface and subsurface runoff from surrounding crop production fields. Soil porewater and groundwater quality will be characterized seasonally and after larger recharge events. Soils will also be sampled and characterized for nutrient availability in 2023. Differences between upland and riparian sampling locations will be used to quantify nutrient attenuation by the buffer.

Objective 2, Sub-objective 2A: After the first round of manure application, a lack of treatment effects was noted with respect to corn yields, soil nutrients, and greenhouse gas fluxes. Low nitrogen concentrations were also measured in soil leachate, implying minimal nitrogen leaching potential in this heavy silt loam. For this reason and other logistical constraints, we are now evaluating nitrogen leaching by traditional agronomic soil sampling and nitrogen analysis in the laboratory. After corn is harvested in October of 2023, separated dairy manure solids and composted heifer manure will be applied at high agronomic rates and incorporated with vertical tillage followed by continued monitoring of yields, soil nutrient status, nitrogen leaching, and greenhouse gas fluxes.

Objective 3, Sub-objectives 3A and 3C: Comprehensive literature reviews for these two sub-objectives have been completed. Literature review for sub-objective 3A focused on E. coli and gastrointestinal pathogens in dairy manure and human sewage, whereas literature review for sub-objective 3C focused on E. coli and antibiotic-resistant pathogens. Data obtained for sub-objective 3A are sufficient to carry out remaining milestones, and work on initial point estimates of risk will begin next fiscal year. Data obtained for sub-objective 3C are more limited than expected, so the goals of this work will have to be re-formulated. Currently, the most feasible option is increasing the sub-objective’s scope to consider risk of exposure to antibiotic resistance genes. The requisite data for conducting these analyses are readily available, including from several of our own studies, and this outcome can be used to achieve the sub-objective’s milestones as originally planned.

Objective 3, Sub-objective 3B: Initial no-pooling assessments for Cryptosporidium dose-response have been completed based on available outbreak data, and preliminary results illustrate variation across outbreaks and within Cryptosporidium species. The next phase of analysis, planned for fiscal year 2024, will attempt to explain and control for these sources of variation. **Accomplishments**
                                

1. Chisel plow use after land application of dairy manure reduces greenhouse gas emissions. Land application of dairy manure provides nutrients to crops and contributes to global greenhouse gas emissions. Tilling manure into soil after application reduces nutrient loss from crop fields, but the impacts of different tillage types on greenhouse gas emissions are not well known. ARS researchers in Marshfield, Wisconsin, investigated conventional and low-disturbance tillage effects on gas emissions from fields following dairy manure application. Ammonia, nitrous oxide, methane, and carbon dioxide emissions in fields, along with corn silage yields were measured. Fields with manure incorporated by low-disturbance vertical tillage or by conventional chisel plow tillage were compared to control fields (no manure, or manure with no tilling). Corn silage yields in chisel-plowed fields were greater than or equal to both controls, and ammonia emissions for vertical and chisel plow tillage were lower than broadcast application. Chisel plowing also produced lower carbon dioxide fluxes than vertical tillage, while vertical tillage produced lower nitrous oxide emissions. Results indicate that chisel plow tilling is effective in reducing greenhouse gases after spreading manure. 2. Dramatic decrease in runoff water quality following dairy manure application on top of snow in the upper Midwest. Manure is an important source of crop fertility in dairy systems, and careful management is needed to reduce the loss of nitrogen and phosphorus in surface runoff from fields where manure is applied. Runoff during the non-growing season represents a large fraction of annual runoff flows in cold climates, particularly from snowmelt events. Runoff water quality may be more impacted by manure applied on top of snow compared to applying manure before snow when soils are not frozen. ARS researchers in Marshfield, Wisconsin, conducted trials at three Upper Midwest sites to assess snowmelt runoff water quality after dairy manure application. Manure drastically increased loads of nutrients and manure solids compared to no-manure controls. Our research indicates that liquid dairy manure applied on top of snow resulted in high nitrogen and phosphorus losses and presented an elevated water quality risk with respect to manure nutrient loss in runoff compared to not applying manure during wintertime. 3. Antimicrobial resistance genes associated with human and livestock fecal contamination in rural Wisconsin private wells. Antimicrobial resistance is a global public health problem, contributing to more than two million infections per year in the United States. It is believed to be driven by a combination of factors related to humans, livestock, and the natural environment. However, few studies on antimicrobial resistance capture all three simultaneously. ARS researchers in Marshfield, Wisconsin, measured antimicrobial resistance genes (ARGs) as indicators for resistant bacteria in groundwater from a rural region of northeast Wisconsin where contamination by human and livestock sources occurs. ARGs were found in groundwater obtained from residential private wells, and their frequency of occurrence was related to land use factors like presence of septic systems or presence of agricultural fields nearby, rainfall, hydrogeological conditions, and well construction factors like well depth and casing depth. The most common land use factor associated with ARGs was the presence of residential septic systems within 3,000 feet or less of a given well. However, ARGs were also associated with genetic markers that were specific to human and bovine fecal contamination. Thus, this study found that both sources contributed to contamination of groundwater by ARGs in this setting. 4. Benefits of manure injection prior to planting and after crops are growing. Manure provides essential crop nutrients but may contribute to agricultural greenhouse gas emissions. ARS scientists from Marshfield, Wisconsin, compared ammonia and greenhouse gases (nitrous oxide, carbon dioxide, and methane) emitted from corn silage plots after liquid dairy manure was either injected or surface applied in the spring before planting or later in the spring when corn was at the five-leaf growth stage. Injecting manure during both time periods significantly reduced ammonia emissions compared to surface applications, while nitrous oxide release was greater for injected treatments. Treatments had little impact on methane or carbon dioxide emissions. Results showed that injection reduced ammonia emissions by 95% compared to surface application but increased cumulative nitrous oxide emission by 66%. **Review Publications**
                            *Young, E.O., Wilson, M., Sherman, J.F., Vadas, P.A., Arriaga, F., Feyereisen, G.W. 2022. Nitrogen, phosphorus, and snowmelt runoff losses after application of dairy manure with variable solids content. Water: A Multidiscplinary Research Journal. 14(22). Article 3745. https://doi.org/10.3390/w14223745.*
                                *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.*
                                *Sherman, J.F., Young, E.O. 2022. Greenhouse gas emissions with low disturbance liquid dairy manure incorporation into a live winter cereal cover crop-corn system. Agronomy. 12(12). Article 2978. https://doi.org/10.3390/agronomy12122978.*
                                *Sherman, J.F., Young, E.O., Jokela, W.E., Kieke, B. 2022. Manure application timing and incorporation effects on ammonia and greenhouse gas emissions in corn. Agronomy. 12(11). Article 1952. https://doi.org/10.3390/agriculture12111952.*
                                *Burch, T.R., Newton, R.J., Kimbell, L.K., LaMartina, E.L., O'Malley, K., Thomson, S., Marshall, C., McNamara, P.J. 2022. Targeting current and future threats: Recent methodological trends in environmental antimicrobial resistance research and their relationship to risk assessment. Environmental Science: Water Research & Technology. 8:1787-1802. https://doi.org/10.1039/D2EW00087C.*


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