A Process-Based Nutrient Model for the Bedpack Manure of Confined Beef Systems

Final Report for GNC12-148

Project Type: Graduate Student
Funds awarded in 2012: $9,860.00
Projected End Date: 12/31/2014
Grant Recipient: South Dakota State University
Region: North Central
State: South Dakota
Graduate Student:
Faculty Advisor:
Dr. Erin Cortus
South Dakota State University
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Project Information


Manure management is a concern for beef cattle producers and the general public. However, the manure and bedding material mixed with manure can be a valuable fertilizer. We conducted a lab-scale experiment to investigate how manure storage time, bedding material, and temperature affect ammonia (NH3), greenhouse gases (carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O)), moisture content, and nutrient content (nitrogen (N), phosphorus (P), and potassium (K)) in lab-scaled simulated beef cattle bedded manure packs. The study showed that NH3 and GHG concentrations were higher under hot conditions (approaching 104°F) compared to moderate conditions (at temperatures around 50°C). Storage time did not affect NH3 and N2O losses, whereas CH4 and CO2 emissions are expected to increase with longer storage. During hot, dry summer months, bedded manure packs are expected to be drier and have less N content because of increased gaseous loss of N. Ammonia emission and K concentration are expected to be higher when corn stover bedding is used compared to soybean stubble. Results of the lab-scaled study inform a model of N, P and K transformations and movements in bedded manure packs with respect to different manure storage time, bedding material, and ambient air temperature. A survey with beef producers and consultant/planners in Minnesota, South Dakota, Iowa, and, Nebraska was conducted to identify the most useful format of input and output parameter to this model. A process-based model has been conceived that predicts amount and volume of manure produced, fertilizer (N-P-K) content and monetary value, and NH3 and N2O emissions. Using this model, manure storage space and nutrient losses as gaseous emission can be estimated, and manure over- and under-application can be reduced. In the future, producers can use this information to make best decisions on manure management practices and obtain sustainable beef cattle manure management.


Traditionally, beef cattle have been kept outside on pasture or in open or partially covered feedlots. In the Northern Great Plains, there is an increasing interest in raising beef cattle in confined housing, such as hoop and mono-slope barns. As reasons for building confinement facilities, producers cite the ability to mitigate extreme weather conditions, complete containment of feedlot runoff, and/or high land prices that make it cost prohibitive to build additional open feedlots. A variety of management styles are used in these confined facilities. Typically, beef producers apply bedding material once per week or every other week to manage manure and moisture, and to provide comfort for the animals (Doran et al., 2010). Some producers let the manure and bedding build up to a bedded manure pack that is compacted over time by cattle activity. In this management style, manure is only removed from the bunk apron once or twice weekly to establish a bedded pack in the center of the pen. The bedded pack might be removed between groups of cattle (once or twice per year) or may be maintained for several years (Doran et al., 2010). Other producers remove all bedding and manure as frequently as once per week to avoid a bedded pack. Either way, removed manure with bedding needs to be managed properly and is either stored, applied directly to cropland as fertilizer, or treated (e.g. by composting) prior to field application.

Improved understanding of the nutrient composition of manure from bedded beef facilities provides beef producers with information to guide manure management decisions that reduce nutrient losses to the environment. Spiehs et al. (2011) provided baseline information on nutrient composition (nitrogen (N), phosphorus (P), potassium (K), and dry matter) of beef cattle bedded manure packs. Yet, it is unknown how storage temperature and bedded manure characteristics affect manure nutrient composition, nutrient value, and moisture content over time. There is limited information on how manure management practices impact ammonia (NH3) and greenhouse gas emissions from beef cattle bedded manure. A better understanding of nutrient transformations and movements will help optimize nutrient and moisture management practices of bedded packs and increase profitability and crop yields.

Modeling can help describe the processes occurring in manure and predict the fate of nutrients in the manure. The advantage of a process-based model over an empirical model is that it can also be applied for conditions that diverge from the original data which was used to develop the model. There are only limited models available that predict GHG and NH3 emissions from livestock farms relating to environmental factors: the Manure-DNDC model (Li et al., 2012) and the Integrated Farm System Model (IFSM) (Rotz et al., 2014). These accessible models lack prediction capabilities for manure quantity and nutrient content from bedded beef systems. In addition, no data from mono-slope barns were used to calibrate these models. A model is needed that describes the combined processes occurring within a bedded beef barn system with respect to both different bedding material and manure removal frequencies. The model should predict manure quantity, nutrient content, and fertilizer (N-P-K) value for a sustainable beef cattle facility.



Doran, B. E., Euken, R., & Spiehs, M. J. (2010). Hoops and Mono-slopes: What we have learned about management and performance. Feedlot Forum 2010.

Li, C. S., W. Salas, R. H. Zhang, C. Krauter, A. Rotz, and F. Mitloehner. 2012. Manure-DNDC: a biogeochemical process model for quantifying greenhouse gas and ammonia emissions from livestock manure systems. Nutrient Cycling in Agroecosystems 93(2):163-200.

Rotz, C.A., Corson, M.S., Chianese, D.S., Montes, F., Hafner, S.D., Bonifacio, H.F., Coiner, C.U., 2014. The Integrated Farm System Model Reference Manual, Version 4.1. USDA-Agricultural Research Service. Avaialble at: http://www.ars.usda.gov/sp2UserFiles/Place/80700500/Reference%20Manual.pdf. Accessed 25 February 2015.

Spiehs, M. J., Woodbury, B. L., Doran, B. E., Eigenberg, R. A., Kohl, K. D., Varel, V. H., Berry, E. D., & Wells, J. E. (2011). Environmental conditions in beef deep-bedded monoslope facilities: a descriptive study. Transacttions of the ASABE, 54(2), 663-673.

Project Objectives:

The objective of my research was to develop a process-based model that estimates manure quantity, nutrient content, fertilizer (N-P-K) value, and gaseous emission (NH3, N2O) for the bedded manure mixture. The model should simulate the physical, chemical and biological transformations and movements of N, P and K from the bedded manure pack surface with respect to different storage length, bedding material, and ambient air temperature. The important and relevant input variables include bedding material, manure storage time, bedded pack depth, and ambient temperature. Output parameters include amount, fertilizer (N-P-K) and monetary value of manure produced, and NH3 and N2O emissions.

Physical, chemical, and biological transformations of N, P, and K from simulated bedded packs have been measured. However, model development is still progressing. A framework, inputs and outputs to the model exist. Calculations still have to be fine-tuned before the model can be calibrated and validated with data from the experimental study. The model performance will be evaluated with different measures to detect bias and errors in the model that might cause wrong predictions. The utility of the model will be validated with NH3 emission and manure N-P-K concentration estimates from field-scale studies.


Click linked name(s) to expand/collapse or show everyone's info
  • Dr. Erin Cortus
  • Daniel Miller
  • Dr. Mindy Spiehs


Materials and methods:

I designed a survey for beef cattle producers, consultants/planners and researchers to identify the most useful format of inputs and outputs to the nutrient model. During a stakeholder meeting with scientists and beef producers from SD, IA, and NE, I presented the plan of developing a manure nutrient model and the corresponding experiments I conducted. I discussed the questionnaire with the stakeholders to gather their feedback on the model and available input parameters and desired outputs. The discussion during the meeting helped me refine the questionnaire, discuss methods to reach producers and receive their feedback on the development of a beef cattle bedded manure nutrient calculator. After the stakeholder meeting, I revised the questionnaire and sent the survey to beef producers, consultant/planners and researchers in Minnesota, South Dakota, Iowa, and, Nebraska to gather their feedback. Overall, 40 participants completed the survey.

We conducted lab-scale experiments to understand how manure handling impacts nutrient flow and transformations in the bedded manure. We evaluated NH3, carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4) concentrations in the headspace above the bedded packs based on storage time, bedding material, temperature and depth within the pack. We also measured moisture content, free air space, nutrient value and enzyme activity within the bedded packs. Nutrients measured included total ammonium-N, total N, total P, and total K. We measured short-term nitrification activity potential, and denitrification enzyme activity as indicators of N transformation within the bedded pack. The simulated bedded manure packs were prepared and maintained in 10-gallon plastic containers in temperature and humidity-controlled chambers by adding 0.9 pounds bedding material, two pounds freshly deposited cattle feces from an open beef feedlot, and two pounds previously frozen urine to each container on a weekly basis (Figure 1). Based on stakeholders’ input and Doran et al. (2010), producers commonly use corn stover as bedding material, while some also use soybean stubble. Therefore, we selected corn stover and soybean stubble as the two bedding materials. At the start of the experiment, 36 bedded manure packs were constructed (three per treatment). The bedded packs were monitored over three weeks at 50°F and 104°F. Instead of three different temperature settings as initially proposed, we chose two different temperature settings because of limited space in the environmental chambers. After material addition, an iron rod was used to slightly agitate the surface of the packs until the material was mixed (Figure 2). This was done to imitate cattle hoof action observed in confined beef systems with bedded packs. At each interval of six weeks prior, three weeks prior and at the start of the monitoring period, twelve bedded manure packs were constructed. The 0-3, 3-6 and 6-9 week old bedded packs were zero, three and six weeks old, respectively, at the start of the monitoring period. A water leak contaminated one of the 3-6 week old bedded packs in the 50°F chamber containing corn stover and was eliminated from the study, resulting in only two replicates for this treatment.

At fixed intervals, gas concentrations were determined through static flux chamber measurements from the headspace of the bedded packs with simultaneous pH and temperature measurements (Figure 3). Each week during the three-week monitoring period, greenhouse gas concentrations were measured 0, 22, 46 and 142 h after material was added to bedded packs. Ammonia concentrations were sampled at 0, 5, 8, 22, 32, 46, and 142 h after material addition since the majority of NH3 losses occur within the first 24 h. Gas measurements were only collected from two of the three replicates (n=2) per treatment due to limited amount of static flux chambers available for the 20 minute collections.

Immediately prior to weekly addition of fresh material, samples were taken from one, two and three different depths for 0-3, 3-6 and 6-9 week-old packs, respectively, to measure nutrient content and enzyme activity (Figure 4 and 5). As material was added to the simulated packs, the depth increased and distinct zones developed. Grab samples from 0-3, 3-6 and 6-9 week old bedded packs were collected from one, two and three depths, respectively. Top zone samples were taken approximately one inch below the surface of the dried material, middle zones from the approximate middle, and bottom zones samples from the area approximately one inch above the bottom of bedded packs. Since 0-3 week old bedded packs were shallow and had not developed distinct zones, all samples collected from these fresh bedded packs were designated as sampled from the top zones. Similarly, 3-6 week old pack samples were designated as collected from top or bottom zones, and samples from 6-9 week old packs were designated as coming from top, middle or bottom zones. Denitrification enzyme activity and nitrification activity potential were only determined for week 2 and 3 of the monitoring period.

A modified version of IFSM (not yet released) was used to predict water movement through the bedded manure packs. The processes considered for vertical water movement include evaporation, percolation and unsaturated flow. The process-based water movement model has to be adapted to estimate the water content of the pack over time for different environmental conditions, bedding materials, and storage times at varying depths within the bedded pack. After calibrating and validating the water movement model with moisture content data obtained from the lab-scale experiments, the water will be used to estimate N, P and K movements through the different zones of the bedded pack. The IPCC (2006) Tier 2 approach will be used to estimate N2O emission from the surface of the bedded pack. Ammonia emission predictions will be based on IFSM.

I will use the data collected from the lab-scale experiment to calibrate and validate the bedpack model. The model performance will be evaluated by calculating the mean absolute error and the root mean square error. I will use estimates from calculators currently available for beef manure that do not consider bedding material and age of the bedpack, and NH3 emission and manure N-P-K concentration estimates from field-scale studies to evaluate the utility of the model. The model development will be presented at the 2015 Waste to Worth National Conference in Seattle, WA, March 30-April 3, 2015, and the final model will then be accessible to the public on eXtension.org.


IPCC. 2006. Guidelines for national greenhouse inventories. Vol. 4: Agriculture, forestry and other land use. Intergovernmental Panel on Climate Change. Available at: http://www.ipcc-nggip.iges.or.jp/public/2006gl/vol4.html Accessed 25 February 2015.

Research results and discussion:

Lab-scale experiment results

All physical, biological and chemical properties were affected by the storage temperature, as were the gaseous releases of NH3, CO2, CH4 and N2O concentration. As temperature increased from 50°F to 104°F, NH3, CO2 and CH4 concentrations increased two-fold. The bedding material impacted moisture content, total N, total C, ammonium-N and total K concentration. For gas concentrations, bedding only affected NH3 concentration which increased with corn stover bedding at 104°F. Methane increased with storage length, while CO2 increased with storage time only at 50°F. Ammonia and N2O were not affected by storage length. Ammonium-N, total P and total K concentration were higher in areas closer to the bottom of the packs where the water accumulated when compared to areas closer to the surface.

Producers make decisions regarding the choice of the bedding material and how frequently to remove the manure and bedding mixture. These decisions are made in conjunction with the current and predicted weather patterns, bedding availability and labor. The decisions producers make impact the nutrient content and monetary fertilizer value and the weight/volume of the manure. According to the results obtained from this lab-scale experiment, manure management decisions may be affected in the following ways:

  • During the hot summer season (temperatures approaching 104°F), bedded packs will be drier and producers can expect more NH3, CO2, CH4 and N2O release from the bedded pack compared to the moderate season (around 50°F).
  • Increased volatilization of N as NH3 and N2O during hot conditions will decrease total N and ammonium-N concentrations in the bedded packs. Total P and total K concentration will increase towards the bottom of the bedded packs during summer months where the water accumulates. Thus, thoroughly sampling the bedded packs from top to the bottom is needed to obtain accurate estimates of the nutrient value, especially during warm season when the bedded pack is drier.
  • The moisture content of the bedded pack will decrease with storage length at high temperatures. Manure with lower moisture content may decrease transportation cost per unit of nutrient. Knowing the moisture content help producers estimate the volume that is required for storage of the bedded manure.
  • Producers can expect higher moisture content, increased NH3 release, and higher total K and ammonium-N concentrations when using corn stover compared to soybean stubble. Total P, Total N, CO2, CH4 and N2O concentration are not expected to vary with the choice of bedding material.
  • Maintaining a bedded manure pack leads to higher total N concentration with longer storage and higher CO2 and CH4 concentration during moderate season. In contrast, ammonium-N, total K, NH3 and N2O concentration are not expected to change as the bedded manure accumulates.

Depending on the nutrient to be managed, decisions on manure removing frequencies may be more critical during the summer months. More frequent removal of the manure during the warmer weather will reduce gaseous emissions within the barn. The choice of the bedding material appears to be important year round. The available space for storage of removed manure and/or producer’s ability to apply the manure needs to be considered when making decisions on cleaning frequencies.

Survey results

The survey responses provided useful information on how to design the input and output parameters of the model. The responses also showed the interest of the participants and proved the utility of the future model: 69% of consultants and planners and 63% of producers found the manure nutrient calculator useful. Only 24% of the consultants and planners and 13% of the producers found it not useful (Figure 6). The majority of beef producers stated that yearly estimates of amount of manure produced are needed while consultants/planners answers varied (Figure 7). Consultants/planners’ and producers’ answers showed that the most important output of the model would be the N-P-K value of the manure followed by the monetary fertilizer value (Figure 8). The answers also indicated that producers found model estimates of gaseous emission not important and needed only yearly estimates (Figure 9).

Economic Analysis

As an example for what the model will predict, we used the manure estimator “What’s manure worth” by Bob Koehler, Bill Lazarus, and Will Meland, available on extension.umn.edu to calculate differences in manure monetary value for manure bedded with different bedding materials at different temperatures. We used bedded manure N, P, and K values obtained from our experiment for four different settings (corn stover and soybean stubble bedded manure at 50°F and 104°F). The calculator showed that there were differences in monetary value for the different manure mixtures. Manure bedded with soybean stubble and corn stover from the hot chambers at 104°F had the same net value in excess of application cost ($4,748). Bedded manure from cold chambers at 50°F with soybean stubble had a higher net value ($4,295) than bedded manure with corn stover ($4,063).

Participation Summary

Educational & Outreach Activities

Participation Summary:

Education/outreach description:

The results and conclusions of the gas concentration data were presented at The 2013 Waste to Worth National Conference in Denver, Colorado, April 1-5, 2013. The presentation, abstract, and proceedings under the title “Ammonia and greenhouse gas surface concentration measurements from beef bedded manure packs” are available on extension.org. Waste to Worth is a national conference hosted by the Livestock and Poultry Environmental Learning Center and focuses on solutions for issues related to manure management. The audience consists of farmers/growers, researchers, consultants, extension, people who are involved in environmental management decisions in livestock production.

At the 2014 ASABE Intersectional Meeting in Brookings, South Dakota, I presented a poster on moisture and nutrient composition of different depths and ages of simulated beef bedded manure packs. This poster placed second in the graduate student poster competition.

Two manuscripts describing the simulated beef cattle bedded manure pack studies are under review for the Transactions of the ASABE. I am working on an additional manuscript that describes the model development, model calibration and validation and will be submitted to the Transactions of the ASABE. In April 2015, I will present part of the model development at the Waste to Worth 2015 Conference in Seattle. The abstract and proceedings of the presentation and a link to the final model will then be available on extension.org.


Project Outcomes

Project outcomes:

The results from the experimental study improve the understanding on how storage temperature, storage length, depth of the bedded manure and choice of bedding material affect NH3 and greenhouse gas concentration, nutrient content and monetary value over time for the bedded manure. Seasonal management is expected to impact gas production in the bedded packs. Carbon dioxide and CH4 concentration are expected to be higher with increased length of storage during moderate seasons (around 50°F), while NH3 concentrations are expected to be higher when using corn stover compared to soybean stubble in hot summer months (approaching 104°F). So to reduce NH3 concentrations in warmer seasons, soybean stubble could be used as the bedding instead of corn stubble. During cooler more humid season with lower evaporation, corn stover could be applied to keep the bedpack drier because corn stover has a higher water absorption capacity than soybean stubble. Nutrient content and monetary value vary also with season because of the difference in moisture content in the pack. During cooler seasons, with higher moisture in the pack, total P and K concentration will be lower on a wet mass basis compared to a drier pack, whereas N concentration is expected to be higher. In addition, transportation costs will increase and additional manure storage space will be needed for the bedded pack with higher moisture content.

The data from the lab-scaled experiments is being used to develop a process-based model in form of a calculator that will facilitate beef cattle producers’ work, reduce nutrient losses to the environment, and increase profitability by improving manure monetary value and manure management practices in confined beef cattle barns. Proper manure management reduces the risk of nutrient release into the soil, water and air of the surrounding environment. When applying this tool, beef producers can predict quantity and nutrient content of the beef bedded manure and thus avoid over-application of manure to compensate for uncertainty in the manure nutrient content. Over-application of manure increases the risk of N and P loss through runoff and/or leaching, and can contaminate surface and ground water. At the same time over-application of N leads to NH3 emission which can contribute to eutrophication of ecosystems, soil acidification and irritate upper respiratory tracts of humans and animals. Under-application of nutrients may result in decreased crop yield. Other potential model uses include estimating storage volume needs, and over- and under application of manure.

Economic Analysis

Addressed above in Results and Discussion/Milestones section.

Farmer Adoption

The discussion at the stakeholder meeting showed that beef cattle producers were very interested in a manure nutrient tool that will optimize manure management decisions. Producers particularly want to understand the impact of manure removal frequency on NH3 emission. The written survey responses also showed that the participants were interested in a manure nutrient calculator. One participant of the written survey commented that “what has been lacking is an estimate of the volume of the manure produced per day per head…what leaves the barn… Look forward to seeing your results”. Another participant commented, “Good luck, this is a very good idea, I am excited to see the results”.

Using this tool can reduce manure nutrient losses to the environment that occur which pollute air, water and soil quality. Following land application of manure, nutrient losses may occur through N and P runoff and/or leaching that contaminate surface and ground water. The tool will guide producers’ decision on manure removing frequency and bedding material related to season to optimize nutrient retention. Applying the nutrient calculator will improve manure management to optimize nutrient retention and reduce emission.


Areas needing additional study

After the model development, the model will be calibrated and validated with data obtained from the experimental study and data from previous field-scale experiments. Further field-scale studies should be conducted to validate the utility of the model for N2O emission and N-P-K values from different depth of confined beef systems with a bedded manure pack.

Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.