Skip to main content
ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Environmentally Integrated Dairy Management Research » Research » Research Project #431196

Research Project: Improving Nutrient Use Efficiency and Mitigating Nutrient and Pathogen Losses from Dairy Production Systems

Location: Environmentally Integrated Dairy Management Research

2020 Annual Report

Objective 1: Develop land and manure management practices to improve crop and forage productivity, quality, and nutrient use efficiency; and reduce pathogens and losses of nutrients. Sub-objective 1.A. Conduct multi-scale experiments to investigate biochemical and physical processes controlling snowmelt, snowmelt infiltration and runoff, and nutrient losses from soil and manure. Sub-objective 1.B. Evaluate nutrient cycling, nitrous oxide and ammonia emissions, and nutrient and pathogen runoff losses with conventional and improved liquid dairy manure management practices for alfalfa production and in a silage corn-rye cover crop system. Sub-objective 1.C. Determine manure/crop management effects on N, P, and pathogens in runoff from dairy cropping systems. Sub-objective 1.D. Evaluate effects of alternative manure application methods on alfalfa-grass yield, quality, and silage fermentation characteristics. Sub-objective 1.E. Determine potential of fall-grown oat to capture nutrients from summer manure or fertilizer applications and produce a late-fall, energy-dense forage crop. Determine potential of spring wheat and barley for fall-forage yield, quality, and nutrient capture from mid-summer manure or fertilizer applications. Evaluate oat mixtures with wheat, triticale or cereal rye (1 planting) for total fall and spring forage yield (2 harvests), as well as nutrient capture. Objective 2. Develop, improve, calibrate, and validate model routines for nutrient management to assess environmental impacts, nutrient use efficiency, and economics at the farm scale. Objective 3: Characterize soil biodiversity and manure pathogen dynamics and interactions. Sub-objective 3.A. Conduct laboratory microcosm experiments to manipulate soil biodiversity and measure die-off rates of dairy manure-borne pathogens. Sub-objective 3.B. Conduct field studies relating agricultural cultivation practices to soil biodiversity and die-off rates of manure-related pathogens. Objective 4. Reduce nutrient losses from replacement dairy heifer production through management strategies that target nutrient use efficiency and growth performance. Sub-objective 4.A. Improve understanding of heifer development and growth, especially effects of genomic testing for residual feed intake (RFI) on nutrient-use efficiency and growth. Sub-objective 4.B. Determine effect of common management strategies (pen stocking rate, limit feeding, ionophores, diet composition, etc.) on nutrient-use efficiency and growth performance of heifers.

Improved management of dairy farms requires successfully managing its nutrient flows, both to maximize nutrient use by animals and crops to optimize profit, and to minimize nutrient loss to the environment. We will investigate most aspects of nutrient cycling throughout the dairy-farm system with a variety of methods and at different scales, including replicated field plots, field-scale paired watersheds, feeding trials with replicated pens of heifers, and computer modeling. We will also examine pathogen transport and viability at different points in the dairy farm system. Some experiments will investigate only one or two nutrient or pathogen pathways, while others will be more comprehensive, including, for example, surface runoff, gaseous emission, and plant removal. Computer modeling will investigate the whole-farm system. Our research team also has a longer-term goal, which is to integrate information across experiments to more completely describe, quantify, model, and manage the entire dairy-farm for improved efficiency and sustainability. Achieving this goal will help ensure the existence of profitable, environmentally acceptable dairy farming for coming decades.

Progress Report
Our experiments comparing conventional and improved dairy manure management practices (with respect to nutrient cycling, nitrous oxide and ammonia emissions, and nutrient runoff losses) were completed and a manuscript was published on alfalfa-grass runoff water quality with low-disturbance manure application (LDMA) compared to broadcast application. A second manuscript was published on the impacts of LDMA on corn silage yield, rye cover crop growth, and nitrogen leaching, and two additional manuscripts are being prepared for publication. One will focus on surface runoff water quality, and the second on greenhouse gas fluxes. For our experiments investigating improved manure management practices in alfalfa-grass systems, baseline (calibration) and treatment phase water quality data have been collected and analyzed. Treatment phase data are still being collected at this time for each of three grazing management treatments, and a manuscript summarizing treatment phase results is being prepared for publication. Our experiments investigating application of dairy slurry to growing alfalfa (with respect to undesirable clostridial silage fermentations) were delayed due to heavy soils and unfavorable weather (particularly flooding) during winter and spring for the past several years. As a result, our alfalfa stands have been damaged, and this experiment will need to be rescheduled when alfalfa monocultures are available. In contrast, our experiments investigating alternative forage crops (fall-grown oat, spring wheat and barley, and mixtures of fall-grown oat with winter wheat, triticale, and rye) have progressed relatively smoothly. All experiments involving fall-grown oat have been completed and published, and a peer-reviewed journal article describing the spring wheat and barley work has been accepted for publication. The experiment involving mixtures of fall-grown oat with other crops was delayed due to seeding failure in fall of 2017, but the last data for this experiment were collected during spring of 2020. Due to unanticipated delays in prior fiscal years, completing our groundwater microbial diversity experiment has taken longer than expected, but we are continuing to collect die-off rates of dairy manure-borne pathogens in our laboratory microcosm experiments. Finally, our experiments examining nutrient losses in dairy replacement heifers have all been completed. One project examining the relationship between genomic indicators in lactating cows and feed efficiency in growing pre-bred heifers has been published, and data from the other experiment in this series has been summarized in preparation for publication. Similarly, all experiments examining the effect of overcrowding on heifer growth performance have been completed and published.

1. Managing manure to optimize nutrient-use efficiency while minimizing environmental and health risks is an important challenge in dairy systems. While manure incorporation mitigates nutrient losses in surface runoff water compared to unincorporated manure, less research has focused on specific types of incorporation or injection methods for optimizing manure benefits in forage and no-tillage systems. In contrast to annual crops and conventional tillage, manure applied in hay-crop forage and no-till systems should cause minimal disturbance, while still reducing nutrient-loss potential. Low disturbance manure application methods are specifically designed to reduce disturbance and nutrient-loss potential. Shallow-disk injection, banding, and aeration with banding are promising low-disturbance methods; however, limited work has been focused on runoff water associated with these methods in hay-crop forages. ARS researchers at Marshfield, Wisconsin, evaluated runoff water quality (with simulated rainfall) from alfalfa-grass field plots after low disturbance application in relation to a no-manure control and a traditional surface-broadcast treatment. Shallow-disk injection had statistically lower mean runoff dissolved reactive Phosphoris (P) (bioavailable P) concentrations than aeration/banding. Shallow-disk injection also resulted in significantly lower cumulative total Nitrogen (N), total P, and dissolved reactive runoff P loading than aeration/banding. Results indicate shallow-disk injection may reduce runoff nutrient-loss potential; however, further characterization of longer-term agronomic, soil, economic, and farm-system impacts are needed. These results can be used to better manage manure application and optimize nutrient-use efficiency while minimizing environmental and health risks in dairy systems.

2. Use of recycled manure products for bedding within freestalls. Currently, multiple management choices exist for the resting surface and bedding type for dairy herds housed in freestalls throughout the United States. Of these, sand bedding is usually considered the bedding of choice within freestalls, but the costs and burdens of handling sand-laden manure may cause dairy producers to seek alternatives. ARS researchers at Marshfield, Wisconsin, compared bedding systems with respect to manure composition, cow welfare and hygiene assessments, measures of milk production and quality, and incidence of mastitis during a three year trial with primarily first-lactation Holstein cows housed in a freestall-barn containing four identical quadrants (pens). Bedding systems evaluated included deep-bedded organic manure solids, shallow-bedded manure solids spread over mattresses, and deep-bedded recycled or new sand. Generally, differences between bedding systems with respect to cow welfare, comfort, hygiene, and milk production favored use of sand-bedding materials; however, responses for most variables were within often-recommended thresholds for good management, regardless of bedding system. The use of organic solids resulted in greater numbers of mammary infections than observed for sand-bedding systems, and many of these were systemic in nature. Further evaluation of preparatory, handling, and usage procedures for organic solids may offer some opportunity to minimize health risks associated with organic solids.

3. Low disturbance manure application (LDMA) conserves nitrogen (N) with minimal crop damage. Manure is an important source of plant-available N and phosphorus (P) on dairy farms, and manure application methods can affect the amount of N and P lost in runoff and atmospheric emissions. However, traditional tillage implements for incorporating manure cause substantial soil disturbance compared to reduced or no-tillage practices. LDMA methods offer benefits of tillage while mitigating erosion and sediment-bound N and P runoff losses, but the impacts of LDMA on corn silage yield, cover crop establishment, and soil properties are not well known. ARS researchers at Marshfield, Wisconsin, determined the effect of several fall-applied LDMA treatments (sweep-injection, strip-till injection, aeration/banding, shallow disk incorporation) on corn silage yield, winter rye establishment, and soil nitrate concentrations in relation to broadcast, broadcast/disk incorporation, spring applied fertilizer N (applied at multiple rates) and a no-manure control. Results showed that corn silage yield was significantly greater for sweep injection compared to other LDMA methods, which did not differ from the high N fertilizer rate corn silage yield. Compared to broadcast-disking, LDMA maintained more crop residue with levels comparable to fertilizer and control plots. Soil nitrate-N at 0-30 and 30-60-cm depths was influenced by LDMA and fertilizer N; however, leaching to 60-90-cm was comparable among treatments. Results indicate LDMA with injection conserved more N than other methods with minimal winter rye damage. These results enable better predictions of agronomic and environmental outcomes based on differing manure management strategies in dairy systems.

4. Groundwater quality in northeastern Wisconsin is affected by both human fecal sources and dairy manure. Previous studies have shown that the region’s Silurian dolomite aquifer is vulnerable to contamination because the dolomite is extensively fractured and many regions have thin soils that do not attenuate contaminants moving from the land surface to the water table. Wastewater from septic systems and livestock manure from farming operations are possible contaminant sources, while environmental conditions and geology (e.g., precipitation, groundwater recharge, and depth to bedrock) can affect the timing and extent of private well contamination. ARS researchers at Marshfield, Wisconsin, assessed private well contamination rates in Kewaunee County based on fecal indicator microorganisms, nitrate-N concentrations, and measurements of pathogens and microbial source-tracking indicators. The contamination rate for wells with detectable coliform bacteria (an indication of fecal contamination) or with nitrate-N concentrations greater than 10 mg/L was 26% in the fall of 2015 and 28% in the summer of 2016. Furthermore, pathogens that cause illness in people were present in private wells, and both human wastewater and cattle manure were identified as sources of fecal contamination in contaminated wells. Finally, forecasts of runoff predicted from the Runoff Risk Advisory Tool appear to be associated with bovine contamination of private wells. Findings from the present study and from previous hydrogeological and water-quality investigations of the Silurian dolomite aquifer provide opportunities for ensuring clean groundwater for the residents of northeastern Wisconsin and other communities surrounding the Great Lakes that share the same or similar geology.

5. Baled silage from perennial grasses and a unique flowering response by orchardgrass. The production of baled silages continues to be a popular form of forage conservation, particularly with small and mid-sized dairy or beef producers. Many manufacturers advertise engineered cutting mechanisms as an advantage of their baling equipment, but the effect of these cutting mechanisms on silage fermentation characteristics is unknown. ARS researchers at Marshfield, Wisconsin, examined large round bales (4 x 4-ft) of orchardgrass, meadow fescue, or tall fescue made with or without engagement of a factory-installed bale-cutting mechanism on the baler. Bale-cutting increased initial wet and dry bale weights by 4.1 and 4.7%, respectively, but had no effect on forage nutritive value, and little effect on silage fermentation. A unique non-flowering (vegetative) growth response by first-cutting orchardgrass forage produced sharply greater fiber digestibility compared to meadow or tall fescue, which could not be explained based on typical detergent analysis of fiber composition. Meadow fescue corroborated a commonly reported advantage over tall fescue with respect to fiber digestibility, but was not comparable to orchardgrass exhibiting the unique non-flowering growth response. Cutting mechanisms have useful purposes, such as easing the mixing of baled silages into blended diets, but can't be justified on the basis of improved silage fermentation. These results can be used by small and mid-size cattle producers to inform purchasing and management decisions when investing in new equipment and/or producing baled silage.

6. Pathogen transport mechanisms identified in Wisconsin groundwater. For groundwater to become contaminated with microorganisms from the land surface, for example from land–applied dairy manure, a microorganism must first move downward through the soil before it reaches the water table. Soil can potentially remove (“filter out”) downward moving microorganisms, but it is unknown if soil types differ in their removal potential. ARS researchers at Marshfield, Wisconsin, investigated soils overlying two important aquifers in Wisconsin, the Central Sands region and the Silurian dolomite in the northeast. Using microscopic plastic microspheres to mimic microorganisms we found the Central Sands soil removed nearly all microspheres over a three-foot distance. Removal was highly effective regardless of microsphere size. In contrast, the soil overlying the Silurian dolomite aquifer was not nearly as effective in microsphere removal. Twenty-three feet of soil was needed to remove virus-sized microspheres to the same level as the Central Sands. With 33 feet of soil, the longest distance investigated, microspheres the same sizes as bacteria and protozoa (e.g., Cryptosporidium) were removed only 99% and 93%, respectively. These findings are consistent with computer models that predict microorganism attachment to soil grains and consistent with the microorganism contamination rates measured in the Central Sands and Silurian dolomite aquifers. These findings are useful for establishing minimum distances between microorganism contamination sources on or near the land surface (e.g., septic system drain fields) and the water table to prevent groundwater contamination.

7. Rainfall and septic systems affect contamination of private wells. Rural homeowners without access to public water systems rely on private wells for their household water needs. Unlike public water systems, private well water quality is not monitored and there are few studies on the extent and sources of contamination of private wells. ARS researchers at Marshfield, Wisconsin, intensively sampled five private wells in rural Pennsylvania to understand the variability in microbial contamination, the role of septic systems as sources of contamination, and the effect of rainfall on well water quality. All five wells were positive for the type of microorganisms only found in human fecal wastes. When we added dye to three of the well owners’ septic systems, the dye appeared in their wells, clearly demonstrating that septic system effluent was reaching the wells. In addition, the greater the amount of rain, the more likely a well would be contaminated with human fecal wastes. These findings further our understanding of private well water quality and highlight the importance of septic systems as a contamination source.

8. Viral, bacterial, and protozoan pathogens are present in groundwater wells supplying public water systems in Minnesota. Groundwater is the source of drinking water for many municipalities and rural public places such as schools, restaurants, and motels that have their own wells. These public water systems test the quality of their water using simple tests for bacteria that are indicative of fecal contamination. The indicators give only a partial picture of water quality as it is a single test and the bacteria identified in the tests typically do not cause illness. To fully characterize groundwater quality in Minnesota, ARS researchers at Marshfield, Wisconsin, took 964 samples from 145 wells supplying public water systems; the samples were analyzed for a variety of waterborne pathogens and microorganisms found in human and livestock fecal wastes. Fecal contamination was found in 58% of samples and 96% of wells. We evaluated performance of the indicators for identifying pathogens in well water and learned the indicators were good at predicting pathogen absence but not presence. Some scientists use relationships between indicator and pathogen concentrations in sewage and extrapolate these to surface water to estimate health risk from activities, such as swimming. However, we showed such an approach would not work for estimating illnesses from drinking fecal-contaminated groundwater. Compared to simple indicator tests, our approach provides a comprehensive picture of groundwater cleanliness; however, it is still difficult to interpret the data in terms of health risk. Overall, our results indicate the extent of contamination by human and zoonotic pathogens (those potentially originating on livestock operations) in public water systems in Minnesota.

9. Waterborne pathogen monitoring in urban India reveals potential infection risks in groundwater supplies. A priority of the United Nations (UN) Sustainable Development Goals list is access to clean drinking water free of fecal contamination. The UN recommends fecal contamination be assessed by measuring E. coli bacteria, but achieving this goal in developing countries is challenging. ARS researchers at Marshfield, Wisconsin, analyzed water samples from the city of Jaipur, India, and showed significant contamination of waterborne pathogens in the municipal water supply, especially in the municipal groundwater wells. Under the World Health Organization (WHO) “Guidelines for Drinking-Water Quality”, the number of samples in with detectable E. coli would warrant a “Fair” rating for Jaipur’s drinking water quality. When samples were positive for waterborne pathogens, E. coli also was present only 33% of the time, highlighting the limitation of relying on E. coli as the sole indicator of fecal contamination. We further learned the most advanced techniques for measuring waterborne pathogens have detection limits still too high to determine whether drinking water meets WHO guidelines for acceptable risk. Other approaches in addition to pathogen and indicator measurements will be needed to ensure the clean drinking water goal is achieved.

10. Effects of sample size on in-vitro determinations of fiber digestibility. Accurate and precise determinations of in-vitro neutral-detergent-fiber digestibility (NDFD) are critical to proper evaluation of forage nutritive value, and essential for proper diet formulation for dairy cows. Currently, NDFD is determined with a variety of methodologies that include traditional incubation of an unrestrained sample within a sealed, dedicated tube or flask (STD), as well as the batch procedures using filter bag technology. ARS scientists at Marshfield, Wisconsin, compared NDFD values obtained from the filter bag system using a variety of sample sizes and incubation times with those determined by STD procedures obtained from a commercial laboratory. Comparisons of the filter bag and STD methodologies suggest that the best agreement for many incubation times occurs when smaller samples are sealed within fiber bags, but these efforts need to be expanded to a broader array of forage species before broad-based recommendations can be made. Results of this study inform scientists on how best to measure NDFD, which is crucial to managing nutrition on dairy operations.

11. Improved dose-response model developed for Giardia. Giardia is a gastrointestinal parasite that infects both humans and animals, and is responsible for 300 million infections per year globally, including one million in the United States. Giardia can be transmitted from livestock to humans in contaminated drinking water and recreational water. Quantitative microbial risk assessment (QMRA) is a mathematical model that can be used to estimate the extent of this transmission and the effectiveness of proposed public health interventions to prevent it. However, the mathematical model used by QMRA to describe interactions between Giardia and human hosts is out of date, because it ignores valuable information about Giardia infectivity that has come to light since the model’s original development. ARS researchers at Marshfield, Wisconsin, have updated this model, and results indicate that the previous model overestimated the certainty with which host-pathogen interactions could be described for Giardia. Furthermore, the current study’s updated model includes a novel ability to incorporate variability in host-pathogen interactions into predictions for Giardia. These improved model predictions will enable more accurate forecasting of Giardia transmission from livestock facilities, as the pressures driving this transmission are likely to shift in the face of land-use change and continuing intensification of livestock agriculture.

Review Publications
Li, L., Akins, M.S., Esser, N.M., Ogden, R.K., Coblentz, W.K. 2019. Comparison of feeding diets diluted with sorghum-sudangrass silage or low-quality grass on nutrient intake and digestibility and growth performance of Holstein dairy heifers. Journal of Dairy Science. 102(11):9932-9942.
Gelsinger, S.L., Coblentz, W.K., Zanton, G.I., Ogden, R.K., Akins, M.S. 2020. Physiological effects of starter-induced ruminal acidosis in calves before, during, and after weaning. Journal of Dairy Science. 103(3):2762-2772.
Coblentz, W.K., Akins, M.S., Cavadini, J.S. 2020. Fermentation characteristics and nutritive value of baled grass silages made from meadow fescue, tall fescue, or an orchardgrass cultivar exhibiting a unique non-flowering growth response. Journal of Dairy Science. 103(4):3219-3233.
Burch, T.R. 2020. Outbreak-based Giardia dose-response model using Bayesian hierarchical Markov chain Monte Carlo analysis. Risk Analysis. 40(4):705-722.
Crook, T., Stewart, B., Sims, M., Weiss, C., Coffey, K., Coblentz, W.K., Beck, P. 2020. The effects of moisture at baling and wrapping delay on storage characteristics of annual ryegrass round bale silage. Crop, Forage & Turfgrass Management. 6(1):e20015.
Klaiber, L.B., Young, E.O., Kramer, S.R. 2020. Impacts of tile drainage on phosphorus losses from edge-of-field plots in the Lake Champlain Basin of New York. Water. 12(2):328.
Young, E.O., Ross, D.S., Jaynes, D.B. 2019. Riparian buffer nutrient dynamics and water quality. Frontiers in Environmental Science. 7:76.
Coblentz, W.K., Akins, M.S., Ogden, R.K., Bauman, L.M., Stammer, A.J. 2019. Effects of sample size on NDF digestibility of triticale forages using the ANKOM daisy II incubator system. Journal of Dairy Science. 102(8):6987-6999.
Griffith, K.E., Young, E.O., Klaiber, L.B., Kramer, S.R. 2020. Winter rye cover crop impacts on runoff water quality in a northern New York (USA) tile-drained maize agroecosystem. Journal of Water Air and Soil Pollution. 231:84.
Murphy, H., Mcginnis, S., Blunt, R., Wu, J., Cagle, A., Denno, D., Spencer, S.K., Stokdyk, J., Firnstahl, A., Borchardt, M.A. 2020. Effects of rainfall and septic systems on the occurrence of human sewage markers and traditional indicator organisms in private wells in southeastern Pennsylvania. Environmental Science and Technology. 54(6):3159-3168.
Niyigena, V., Coffey, K.P., Coblentz, W.K., Philipp, D., Rhein, R.T., Young, A.N., Caldwell, J.D., Shanks, B.C. 2019. Intake and digestibility by gestating sheep offered alfalfa silage wrapped with plastic with or without an oxygen-limiting barrier after extended time delays up to three days. Animal Feed Science and Technology. 254:114193.
Young, E.O., Ross, D.S., Sherman, J.F. 2019. Measuring phosphorus release in laboratory microcosms for water quality assessment. Journal of Visual Experiments. (149) e60072.
Rasmuson, A., Erickson, B., Borchardt, M.A., Muldoon, M., Johnson, W.P. 2019. Pathogen prevalence in fractured versus granular aquifers and the role of forward flow stagnation zones on pore-scale delivery to surfaces. Environmental Science and Technology. 54:137-145.
Sherman, J.F., Young, E.O., Coblentz, W.K., Cavadini, J. 2020. Runoff water quality following low-disturbance manure application in an alfalfa-grass hay crop forage system. Journal of Environmental Quality. 49(3):663-674.
Sherman, J.F., Young, E.O., Jokela, W.E., Cavadini, J. 2020. Influence of low-disturbance fall liquid dairy manure application on corn silage yield, nitrate leaching and rye cover crop growth. Journal of Environmental Quality. J. Environ. Qual.
Stokdyk, J.P., Firnstahl, A.D., Walsh, J.F., Spencer, S.K., De Lambert, J.R., Anderson, A.C., Rezania, L.W., Kieke, B.A., Borchardt, M.A. 2020. Viral, bacterial, and protozoan pathogens and fecal markers in wells supplying groundwater to public water systems in Minnesota, USA. Water Research. 178(1):115814.