Data from: Starch and dextrose at 2 levels of rumen-degradable protein in iso-nitrogenous diets: Effects on lactation performance, ruminal measurements, methane emission, digestibility, and nitrogen balance of dairy cows.

This feeding trial was designed to investigate two separate questions. The first question is, “What are the effects of substituting two non-fiber carbohydrate (NFC) sources at two rumen-degradable protein (RDP) levels in the diet on apparent total-tract nutrient digestibility, manure production and nitrogen (N) excretion in dairy cows?”. This is relevant because most of the N ingested by dairy cows is excreted, resulting in negative effects on environmental quality. The second question is, “Is phenotypic residual feed intake (pRFI) correlated with feed efficiency, N use efficiency, and metabolic energy losses (via urinary N and enteric CH4) in dairy cows?”. The pRFI is the difference between what an animal is expected to eat, given its level of productivity, and what it actually eats. The goal was to determine whether production of CH4, urinary N or fecal N is a driver of pRFI.

This experiment was conducted at the Dairy Cattle Center of University of Wisconsin-Madison. The use and care of animals was approved by the University of Wisconsin-Madison Research Animal and Resource Committee.

Prior to the beginning of the study, 24 multiparous Holstein dairy cows were trained for 7 days to adapt to the GreenFeed (C-Lock Inc., Rapid City, SD) system: a mobile, open circuit gas quantification system that measures CH4 emission with minimal animal disturbance (Dorich et al., 2015). The machine continuously analyzes the CH4 concentration from the exhaled air when the cow consumes delivered feed treats at the trough of the unit. During the GreenFeed adaptation, the 24 cows were fed the herd diet once daily at 0730 h. At each training, each cow was assigned with a score of 1 to 5 depending on how well the cow adapted to the GreenFeed unit (1 = poor; 5 = very good). After the 7-day adaptation to the equipment, the 18 cows that adapted best (18 highest total scores) to the system were selected to conduct the study. All 18 cows were fed the same herd diet during the week before the commencement of this study.

The eighteen cows in the experiment were 148 ±10 days in milk, 3 ± 0.6 parity, 42.3 ± 4.1 kg/day milk yield, 644 ± 41kg body weight (BW) at the commencement of the study (mean + standard deviation). Cows were housed in a tie-stall barn and fed once (starting at 0730 h) and milked twice (0430 and 1630 h) daily. All cows were injected with 500 mg of bST (Posilac; Monsanto, St. Louis, MO) at the beginning of experiment and at 14-day intervals throughout the experiment. The experiment was conducted as a split-plot study. Subplot treatments were 3 refined NFC treatments: 10% refined starch (S), 5% dextrose, 5% refined starch (H), and 10% dextrose (D), as percent of dietary dry matter (DM). Both refined starch (Cargill, Minneapolis, MN) and dextrose (ADM, Decatur, IL) were food-grade products refined from corn starch. The NFC treatments were randomly allocated in three 3 x 3 Latin squares with 3 cows per square. The replicated Latin squares were then randomly assigned to either 11% rumen degradable protein (RDP), 5% rumen un-degraded protein (RUP) (11:5 RDP:RUP ratio) or 9% RDP, 7% RUP (9:7 RDP:RUP ratio), respectively (on a DM basis) in a completely randomized design. The treatments differing in RDP:RUP ratios were achieved by substitution of soybean meal with expeller soybean meal (SoyPLUS, West Central Soy, Ralston, IA) and blood meal. The feeding periods were 28 days in length, with 14 days for adaptation and 14 days for sample collection. The milk production for cows that were fed 11:5 and 9:7 RDP:RUP ratio diets were 43.1 and 41.3 kg/d, respectively.

Experimental diets were offered as total mixed ration (TMR) composed of forage and concentrate at 61:39 ratio (DM basis). The diets were formulated to contain the same concentration of forage (alfalfa silage, corn silage, and wheat straw), to be iso-nitrogenous, and to contain similar concentration of NFC and neutral detergent fiber (NDF). The concentrate for each diet was fed as a customized premix. Due to the availability of forages, different cuts of alfalfa silage were used for each period and corn silage was changed at the beginning of the third period. Due to the minor differences in chemical compositions such as CP and NDF among cuts, the diets were adjusted at the beginning of each period to standardize the chemical compositions.

The cows were fed at 0730 h during the first 2 weeks of each period, whereas during the 3rd and 4th weeks of each period, the 9:7 and 11:5 RDP:RUP ratio diets were offered once daily at 0730 and 0900 h, respectively. The enteric CH4 measurement was staggered between the cows fed the two RDP:RUP ratios accordingly due to the time needed for feed delivery and measurement of CH4 from each RDP:RUP ratio group. All cows were fed ad libitum with TMR adjusted daily to yield 10% orts. The TMR for all the diets were sampled weekly, refusal samples from each of the 18 cows were collected daily during the 3rd and 4th weeks of each period. Forages were sampled for moisture weekly and adjustment in diet was made accordingly to keep the offered diets consistent in each period. All feed samples were stored at -20 oC until dried for further analysis.

Milk yield was recorded daily and milk samples were collected for 4 consecutive milkings from day 18 to day 20, and day 25 to day 27 in each period. Milk was analyzed for milk solids (fat, true protein, and lactose) and milk urea-nitrogen (MUN) concentrations with infrared analysis (Agsource Milk Analysis Laboratory, Menomonie, WI) with a Foss FT6000 (Foss Electric, Hillerød, Denmark). The fat-and-protein-corrected milk (FPCM) was computed based on the equations of International Dairy Federation (IDF, 2015). Body weight (BW) of the cows was taken at 0630 h on days 18,19, 25 and 26 of each period and averaged by week to represent the BW of the cow for the respective week. The average BW of two measurements during the 4th week for each cow was used in estimating the daily urine volume. Feed efficiency (FE) was calculated as FPCM divided by DMI. Dietary nitrogen use efficiency (NUE) was calculated as total nitrogen in milk divided by nitrogen intake (kg of milk true protein/6.38) / (kg of DMI × dietary CP %/6.25).

Eleven spot samplings of enteric CH4 spread over the 24 h feeding cycle were conducted over a 4-day interval during the 3rd week of each period for each cow. The GreenFeed unit was moved from cow to cow fed the same dietary treatment in random order with a minimum of 5 minutes measurement, and 2 minutes interval between samplings for background gas concentration determination. At each sampling, concentrate mix of the corresponding RDP:RUP ratio was delivered into the feed trough to keep the cow’s head inside the trough during analysis of the exhaled breath of the cow. For each sampling, approximately 100 g of concentrate mix was delivered. This amount is less than 2% of the total daily DMI and thus was not included in the DMI calculation, however, it may introduce a source of variation in the substrate available for CH4 production. As a result, CH4 emission measurement was conducted at 1, 2.5, 4, 5.5, 10, 11.5, 13, 14.5, 16, 17.5, and 22.5 h after feeding for both groups of cows. Morning milking was between 5.5 and 10 h; evening milking was between 17.5 and 22.5 h. The GreenFeed unit was zero- and span-calibrated before the start of each sampling period with pure nitrogen carrier gas, CH4 and CO2 (474 and 4497 ppm, respectively). The daily enteric CH4 emission was calculated as the average of the 11 spot samplings for each cow. The hourly emission rate was calculated as the CH4 emission at each of the 11 spot samplings divided by 24.

Feed samples were dried at 60 oC in a forced draft oven for 48 hours. Dried samples were then ground to pass a 1-mm Wiley mill screen (Arthur H. Thomas, Philadelphia, PA). Each feed ingredient (alfalfa silage, corn silage, wheat straw, and concentrate mixes) was composited by the last 2 weeks of each period. Samples were analyzed at Dairyland Laboratories (Arcadia, WI) for nutrient composition. All feed samples were analyzed for total N (AOAC, 1995), amylase-treated NDF (Mertens et al., 2002), ADF and lignin (AOAC, 2000), ether extract (Thiex et al., 2003), ash and OM (Thiex et al., 2012). In addition, starch and water-soluble carbohydrate content of feed samples were analyzed according to Vidal et al. (2009) and Deriaz (1961), respectively. In-situ ruminal incubation was done for each feed ingredient, refusals and fecal samples using 2 ruminally cannulated cows to determine indigestible NDF (iNDF). Duplicate bags were inserted into a nylon laundry mesh bag (38.1 cm x 45.7 cm) (Home Products International, Chicago, IL), which was inserted into the rumen via the rumen cannula of each cow. After 288 hours of incubation, the mesh bags were taken out of the rumen and submerged in cold water and rinsed to remove particles on the surface of bags. Bags were then rinsed with washing machine with cold water for two 12-min rinse cycles. After dried at 55 ºC in a forced-air oven, the bags were washed with α-amylase (Sigma chemical Co., St. Louis, MO) and sodium sulfide to determine the iNDF using an Ankom 200 Fiber Analyzer (Ankom Technology, Fairport, NY).

Blood samples (~10 mL) were collected for each cow from the coccygeal venipuncture with Vacutainer tubes at 4 h after feeding on day 26 of each period. The blood samples were immediately centrifuged at 10,000 × g at 4 °C for 10 minutes and the serum fraction was analyzed for urea nitrogen concentration (SUN, serum urea-nitrogen) with a 96-well plate reader (Synergy H1 Multi-Mode Reader, BioTek, Winooski, VT).

Ruminal fluid of each cow was collected by rumenocentesis at 4 h after feeding on day 27 and day 28 of each period for cows on the 9:7 and 11:5 RDP:RUP ratio diets, respectively, according to the procedure by Nordlund and Garrett (1994). Approximately 10 mL of ruminal fluid was taken from the ventral sac area of the rumen and instantly tested for pH (Laqua Twin pH-meter model B-713; Spectrum Technologies Inc., Plainfield, IL). Then 1-mL aliquots of ruminal fluid were pipetted into microfuge tubes, acidified with 50% trichloroacetic acid solution and stored at – 20 °C for later analysis. For determination of the concentration of volatile fatty acids (VFA), the frozen samples were thawed to room temperature and centrifuged at 10,000 × g at 4 °C for 3 minutes. The supernatant was transferred to gas-chromatography (GC) vials for analysis of VFA concentration using GC (Clarus 500 Gas Chromatograph, PerkinElmer Inc. Shelton, CT). Ammonia nitrogen (NH3-N) concentration of the ruminal fluid was analyzed by a procedure modified from Chaney and Marbach (1962).

Spot urine and feces samples from each cow were collected during the 4th week of each period. The urine and feces were collected at 6 time points on 4-hour intervals to cover the 24 h clock over 3 days (2 spot samples per day for a total of 6 samples for each cow). The urine was obtained through vulval stimulation. Urine samples were acidified with 0.072 M H2SO4 with a 4:1 ratio of acid to urine by volume. At each fecal sampling, approximately 100 g of fresh feces were collected from the rectum of the cow and the feces from the 6 spot samplings were composited for each cow. Both collected urine and feces samples were frozen at -20 °C for later analysis. After thawing at room temperature, urine samples were composited for each cow by period and analyzed for total N (Leco FP-2000 Nitrogen Analyzer, Leco Instruments Inc., St. Joseph, MI). In addition, urinary urea-nitrogen (UUN) concentration and creatinine concentration was analyzed with a colorimetric assay and a picric acid assay (Oser, 1965) adapted to flow-injection analysis, respectively, both using Lachat Quik-Chem 8000 FIA (Lachat Instruments, Milwaukee, WI). Total daily urine volume was estimated with creatinine as internal marker, and using the constant creatinine excretion rate of 29 mg/kg of BW from the 4th week according to Valadares et al. (1999). Concentrations of allantoin and uric acid in urine samples were determined by a colorimetric method (Chen and Gomes, 1992) and InfinityTM uric acid liquid stable reagent (Thermo Fisher Scientific Inc., Middletown, VA), respectively, both with a 96-well plate reader (Synergy H1 Multi-Mode Reader, BioTek, Winooski, VT). Urinary allantoin and uric acid excretions were calculated from the respective concentrations multiplied by estimated total daily urine volume. Urinary purine derivatives (PD) were calculated as the sum of daily allantoin and uric acid excreted in the urine. Fecal samples of each cow were dried at 60 °C in a forced draft oven until for 96 h and then ground through 1-mm Wiley mill screen (Arthur H. Thomas Co., Philadelphia, PA), and analyzed for fecal NDF (with Ankom instrument described above), fecal starch (Vidal et al., 2009) (Dairyland Laboratories, Arcadia, WI), and total N (Leco FP-2000 Nitrogen Analyzer). Fecal crude protein (CP) was calculated as fecal total nitrogen * 6.25. Manure N was calculated as the sum of fecal N and urinary N. Nitrogen retained was calculated as the difference between N intake and N excretion (milk true protein N, fecal N, and urinary N). In addition to iNDF content, feces were also analyzed for total ash by igniting the dry, ground feces sample in a furnace at 600 ºC for 2 hours, the same method used to determine ash in feed samples. Fecal organic matter (OM) was calculated as the difference between feces DM output and ash in feces.

Indigestible NDF served as an internal marker for estimation of feces DM output and in determination of amount of nutrient digested. The marker method was based on the assumption that iNDF present in feed consumed is not digested by the cow and thus equals the amount of iNDF excreted in feces. The iNDF intake is calculated from the iNDF concentration in feed ingredients (measured using the 288-hour rumen incubation described above), multiplied by the daily DMI for each cow. Feces output (DM basis) was estimated with iNDF intake divided by iNDF concentration in feces, which was also determined from the rumen incubation (Cochran et al., 1986). The amount of nutrient intake (OM, NDF, CP, and starch) was calculated from the respective nutrient concentration in feed ingredient multiplied by DMI. Amount of nutrient apparently digested was calculated as the difference of nutrient intake and nutrient in feces for each cow in each period. Total-tract apparent digestibility of nutrients was determined from amount of nutrient in fecal excretion and daily nutrient intake during the 4th week of each period.

This experiment was part of “Climate Change Mitigation and Adaptation in Dairy Production Systems of the Great Lakes Region,” also known as the Dairy Coordinated Agricultural Project (Dairy CAP), funded by the United States Department of Agriculture’s National Institute of Food and Agriculture (award number 2013-68002-20525). The main goal of the Dairy CAP is to improve understanding of the magnitudes and controlling factors over GHG emissions from dairy production in the Great Lakes region. Using this knowledge, the Dairy CAP has improved life cycle analysis (LCA) of GHG production by Great Lakes dairy farms, developing farm management tools, and conducting extension, education and outreach activities.

Data from: Agro-environmental consequences of shifting from nitrogen- to phosphorus-based manure management of corn.

This experiment was designed to measure greenhouse gas (GHG) fluxes and related agronomic characteristics of a long-term corn-alfalfa rotational cropping system fertilized with manure (liquid versus semi-composted separated solids) from dairy animals. Different manure-application treatments were sized to fulfill two conditions: (1) an application rate to meet the agronomic soil nitrogen requirement of corn (“N-based” without manure incorporation, more manure), and (2) an application rate to match or to replace the phosphorus removal by silage corn from soils (“P-based” with incorporation, less manure). In addition, treatments tested the effects of liquid vs. composted-solid manure, and the effects of chemical nitrogen fertilizer. The controls consisted of non-manured inorganic N treatments (sidedress applications). These activities were performed during the 2014 and 2015 growing seasons as part of the Dairy Coordinated Agricultural Project, or Dairy CAP, as described below. The data from this experiment give insight into the factors controlling GHG emissions from similar cropping systems, and may be used for model calibration and validation after careful evaluation of the flagged data.

The experiment was conducted at Cornell University’s Musgrave Research Farm near in Aurora, NY (https://cuaes.cals.cornell.edu/farms/musgrave-research-farm/). Soils are high-pH glacial tills, approximately 55% Lima silt loam (fine-loamy, mixed, active, mesic oxyaquic hapludalfs) and 45% Kendaia and Lyons soils. Slopes range from 0-8%, and there is imperfect tile drainage. Experimental plots were not irrigated. Weather observations from Musgrave Farm can be found at http://newa.cornell.edu/index.php?page=all-weather-data . Manure for the experiment was collected from Aurora Ridge Farm, a commercial dairy. Effluent from an anaerobic manure digester was separated into liquid and solid components using a screw-press, and then solids were further composted (Gooch and Pronto, 2009).

For all experimental plots, seedbeds were prepared by one-time disking followed by rolling with a culti-mulcher. All manure was surface applied. Liquid manure in the “P-based” treatment was immediately incorporated by chisel plow (20 cm depth) to conserve ammonia nitrogen. Liquid manure in the “N-based” treatment and all solid manures were incorporated by chisel plow seven days after application to allow nitrogen volatilization. Starter fertilizer was applied at 5 cm depth and 5 cm to the side of the seed furrow. In 2014, pesticides for general weed control were applied on June 20 to all plots. Single tank mix included S-metolachlor (CAS No. 87392-12-9, 0.94 kg/ha); atrazine (CAS No. 1912-24-9, 0.63 kg/ha); mesotrione (CAS No. 104206-82-8, 0.09kg/ha); isopropylamine salt of glyphosate (CAS No. 38641-94-0, 1.68 kg/ha). In 2015, pesticides were applied on June 25 to all plots. Single tank mix included S-metolachlor (0.93 kg/ha); atrazine (0.75 kg/ha); mesotrione (0.18 kg/ha); isopropylamine salt of glyphosate (2.12 kg/ha). At harvest, crop residue from 10 cm cutting height was left in all plots.

Gas fluxes from soil (CO2, CH4, N2O) were measured on 32 dates in 2014 and 22 dates in 2015, using vented chambers (Dell et al., 2014) and following standard measurement protocols (Parkin and Venterea, 2010). The gas flux measurement chamber was placed between rows. For plots receiving urea and ammonium nitrate fertilizer (UAN), the measurement chamber was placed on the UAN band after application. Chamber deployment time was 45 minutes with sampling intervals of 15 minutes. Samples were analyzed by gas chromatography (GC), and the gas flux rates were calculated by linear regression. Soil samples were treated with the Cornell “Morgan extraction” (Morgan, 2941) to measure available nitrate-nitrogen, phosphorus and potassium. Soil pH and organic matter were also measured, but no soil physical characteristics are available. Organic matter was measured as loss-on-ignition with exposure to 500 degrees Celsius.

This experiment was part of “Climate Change Mitigation and Adaptation in Dairy Production Systems of the Great Lakes Region,” also known as the Dairy Coordinated Agricultural Project (Dairy CAP), funded by the United States Department of Agriculture – National Institute of Food and Agriculture (award number 2013-68002-20525). The main goal of the Dairy CAP is to improve understanding of the magnitudes and controlling factors over GHG emissions from dairy production in the Great Lakes region. Using this knowledge, the Dairy CAP has improved life cycle analysis (LCA) of GHG production by Great Lakes dairy farms, developed farm management tools, and conducted extension, education and outreach activities. 

Carbon Dioxide, Methane, Nitrous Oxide, and Ammonia Emissions from Digested and Separated Dairy Manure during Storage and Land Application

This data set includes measurements of greenhouse gas (GHG) and ammonia fluxes from dairy manure, with accompanying measurements of manure physical and chemical characteristics. The manure was collected from two farms in the Great Lakes region and subjected to varying treatments of anaerobic digestion and liquid-solid separation. Farm 1 was a private farm with a 2,560-cow diary herd. Manure was collected three times daily using skid steers. Both digestion and separation of manure were performed at Farm 1. Farm 2 was the USDA Dairy Forage Research Center in Prairie du Sac, WI with a 350-cow herd and manure collected by scrape daily. Farm 2 had a separator but no digester.

Gas fluxes from manure of each treatment type were monitored both from manure storage barrels ("Storage_GHG" tab of dataset), and from field-applied manure ("Field_GHG" tab). The "Manure" tab gives information about the manure chemical and physical characteristics after treatment (i.e. after digestion and/or separation) and during barrel storage. The "Soil" tab gives information about soil chemical contents during the time period of flux measurements from field-applied manure. Manure storage was during November 2013 – May 2014. In May 2014 the stored manure was surface-applied and immediately incorporated on 3.3 m^2 plots at Farm 2 in a randomized block design, at a rate of 320 kg N/ha. Field corn (maize) was planted in the plots. Note that gas fluxes are given as cumulative mass flux over the monitoring period, with sampling approximately once a week during storage (November 2013 – May 2014) and field monitoring (May 2014 – September 2014). The instrument used to measure both storage barrel and field fluxes was a "Gasmet" brand Fourier Transform Infrared (FTIR) Spectroscopy gas analyzer. Each flux sample was taken over 7 minutes with gas concentrations measured every 20 seconds. Flux data from different manure fraction "treatments" are reported as the measured fluxes, and also as the fluxes normalized to a raw manure (i.e. whole, wet manure) weight basis.

This experiment is part of the project called “Climate Change Mitigation and Adaptation in Dairy Production Systems of the Great Lakes Region,” also known as the Dairy Coordinated Agricultural Project (Dairy CAP). The Dairy CAP is funded by the United States Department of Agriculture – National Institute of Food and Agriculture (award number 2013-68002-20525). The main goal of the Dairy CAP is to improve understanding of the magnitudes and controlling factors over GHG emissions from dairy production in the Great Lakes region. Using this knowledge, the Dairy CAP is improving life cycle analysis (LCA) of GHG production by Great Lakes dairy farms, developing farm management tools, and conducting extension, education and outreach activities.

Data from: Underestimation of N2O emissions in a comparison of the DayCent, DNDC, and EPIC 1 models

Process-based models are increasingly used to study mass and energy fluxes from agro-ecosystems, including nitrous oxide (N2O) emissions from agricultural fields. This data set is the output of three process-based models – DayCent, DNDC, and EPIC – which were used to simulate fluxes of N2O from dairy farm soils. The individual models’ output and the ensemble mean output were evaluated against field observations from two agricultural research stations in Arlington, WI and Marshfield, WI. These sites utilize cropping systems and nitrogen fertilizer management strategies common to Midwest dairy farms.

The models were calibrated and validated using data collected at Arlington and Marshfield over five years (nine years for crop yield). Calibration and validation used observations of soil temperature (n = 887), volumetric soil water content (VSWC, n = 880), crop yield (n = 67), and soil N2O flux (n = 896). The observed data are presented here with the model output to document model calibration and validation; most of these observed data are also held by Ag Data Commons in separate data sets from field experiments at Arlington and Marshfield (http://dx.doi.org/10.15482/USDA.ADC/1361194, http://dx.doi.org/10.15482/USDA.ADC/1401975, http://dx.doi.org/10.15482/USDA.ADC/1399470). The remaining observed data is described in Osterholz et al. 2014.

Model simulations were run from 2010-2015 for the Arlington site and 2013-2015 for the Marshfield site. The three models were parameterized (i.e. calibrated) for each site using the same climate, initial soil physical and chemical conditions, hydraulic properties, initial soil carbon, and management schedules. Weather data for each site (daily minimum and maximum temperature, precipitation, relative humidity, wind speed, and solar radiation) was reconstructed using the NOAA online climate database (NOAA, 2016). Initial soil physical and chemical properties were constructed from available on-site measurements and supplemented using the Web Soil Survey (Soil Survey Staff, 2016). Soil carbon data was available for each site, and to prioritize model agreement initial soil carbon for the 0-20cm layer was set at 55.7 Mg C ha-1 for Arlington (Sanford et al., 2012), and at 52.6 Mg C ha-1 for Marshfield. Following parameterization of soil C, a 17 year spin-up period (1993-2009) at each site was simulated prior to the years during which data was collected (2010-2015). While DayCent developers typically recommend a spin-up of at least 1000 years, DNDC has been run with spin-up periods as low as 2 years (Zhang et al., 2015). Given that observations of soil C were available, a 17 year spin-up was chosen to reflect the duration between initial soil C sampling (Sanford et al., 2012) and the first measurement of N2O in our data set (Osterholz et al., 2014). Management and input schedules were constructed from on-site data and record-keeping; these are available in the supplementary online data of the primary journal paper. All other initial parameters, such as crop-specific productivity or soil carbon turnover rate, were independently established by each model in calibration.

This work was part of “Climate Change Mitigation and Adaptation in Dairy Production Systems of the Great Lakes Region,” also known as the Dairy Coordinated Agricultural Project (Dairy CAP), funded by the United States Department of Agriculture – National Institute of Food and Agriculture (award number 2013-68002-20525). The main goal of the Dairy CAP was to improve understanding of the magnitudes and controlling factors over greenhouse gas (GHG) emissions from dairy production in the Great Lakes region. Using this knowledge, the Dairy CAP has improved life cycle analysis (LCA) of GHG production by Great Lakes dairy farms, developing farm management tools, and conducting extension, education and outreach activities.

Data from: Gas emissions from dairy barnyards

To assess the magnitude of greenhouse gas (GHG) fluxes, nutrient runoff and leaching from dairy barnyards and to characterize factors controlling these fluxes, nine barnyards were built at the U.S. Dairy Forage Research Center Farm in Prairie du Sac, WI (latitude 43.33N, longitude 89.71W). The barnyards were designed to simulate outdoor cattle-holding areas on commercial dairy farms in Wisconsin. Each barnyard was approximately 7m x 7m; areas of barnyards 1-9 were 51.91, 47.29, 50.97, 46.32, 45.64, 46.30, 48.93, 48.78, 46.73 square meters, respectively. Factors investigated included three different surface materials (bark, sand, soil) and timing of cattle corralling. Each barnyard included a gravity drainage system that allowed leachate to be pumped out and analyzed. Each soil-covered barnyard also included a system to intercept runoff at the perimeter and drain to a pumping port, similar to the leachate systems.

From October 2010 to October 2015, dairy heifers were placed onto experimental barnyards for approximately 7-day periods four times per year, generally in mid-spring, late-spring / early summer, mid-to-late summer and early-to-mid autumn. Heifers were fed once per day from total mixed rations consisting mostly of corn (maize) and alfalfa silages. Feed offered and feed refused were both weighed and analyzed for total nitrogen (N), carbon (C), phosphorus (P) and cell wall components (neutral detergent fiber, NDF). Leachate was pumped out of plots frequently enough to prevent saturation of surface materials and potential anaerobic conditions. Leachate was also pumped out the day before any gas flux measurements. Leachate total volume and nitrogen species were measured, and from “soil” barnyards the runoff was also measured. The starting bulk density, pH, total carbon (C) and total N of barnyard surface materials were analyzed. Decomposed bark in barnyards was replaced with new bark in 2013, before the spring flux measurements. Please note: the data presented here includes observations made in 2015; the original paper included observations through 2014 only.

Gas fluxes (carbon dioxide, CO2; methane, CH4; ammonia, NH3; and nitrous oxide, N2O) were measured during the two days before heifers were corralled in barnyards, and during the two days after heifers were moved off the barnyards. During the first day of each two-day measurement period, gas fluxes were measured at two randomly selected locations within each barnyard. Each location was sampled once in the morning and once in the afternoon. During the second day, this procedure was repeated with two new randomly selected locations in each barnyard.

This experiment was partially funded by a project called “Climate Change Mitigation and Adaptation in Dairy Production Systems of the Great Lakes Region,” also known as the Dairy Coordinated Agricultural Project (Dairy CAP). The Dairy CAP is funded by the United States Department of Agriculture – National Institute of Food and Agriculture (award number 2013-68002-20525). The main goal of the Dairy CAP is to improve understanding of the magnitudes and controlling factors over GHG emissions from dairy production in the Great Lakes region. Using this knowledge, the Dairy CAP is improving life cycle analysis (LCA) of GHG production by Great Lakes dairy farms, developing farm management tools, and conducting extension, education and outreach activities.

Greenhouse gas fluxes from a dairy cropping system at the Wisconsin Integrated Cropping System Trials

This experiment was designed to measure the greenhouse gas (GHG) fluxes and related agronomic characteristics of a dairy forage cropping system. The cropping system rotation consisted of one year of corn (Zea mays) followed by three years of alfalfa (Medicago sativa). Liquid dairy manure was applied in the fall following corn and the final year of alfalfa. The primary purpose of this study was to gain insight into GHG dynamics of corn and alfalfa crops receiving manure as fertilizer. These observations have also been used for parameterization and validation of computer simulation models of GHG emissions from dairy farms (Gaillard et al., in preparation), and for evaluation of the effects of biomass manipulation within static chambers on nitrous oxide emissions from soil (Collier et al., 2016). These activities were performed as part of the Dairy CAP, described below.

The experiment was conducted at the Wisconsin Integrated Cropping System Trials (http://wicst.wisc.edu/) at the University of Wisconsin’s Arlington Agricultural Research Station in Arlington, WI. WICST is a long-term study of the productivity, profitability and environmental impact of six representative Wisconsin cropping systems. The site’s conversion from prairie vegetation to cropland began in the mid-1800s, primarily for the production of wheat. From the 1860’s until ~ 1960 the land was used to produce feed for dairy cattle; from 1960 until the initiation of WICST the predominant crop rotations were corn (Zea mays L.) and alfalfa (Medicago sativa L.) with dairy manure serving as the primary source of nutrients. The treatments in the current experiment corresponded with the four phases of the rotation. Each of the three blocks used at WICST contained all four phases every year, so that twelve plots were used in total. Please note that some of the field operations included in the “Experimental_Set-up” section of the data set, especially tillage and manure application, were made in the fall in preparation for the next growing season. Weather data for WICST are available at (http://agwx.soils.wisc.edu/uwex_agwx/awon).

The soil at WICST is “Plano silt loam” (Mollisol, Typic Argiudoll) according to the USDA-NRCS soil classification system. Soil slope is 0-2%, with no impermeable layers at less than 1 meter depth. Samples for soil carbon, nitrogen and bulk density analysis were taken in 2009, prior to this experiment (n=12, see Sanford et al., 2012). Soils were sampled on April 27, 2015 for pH, phosphorus, potassium, cation exchange capacity (K+, Ca+ and Mg2+ only), soil organic matter, and soil texture. At this latter sampling, two cores per plot were taken between the GHG-measurement chambers (n=24) and composited by block before analysis at the University of Wisconsin Soil & Forage Analysis Laboratory (https://uwlab.soils.wisc.edu/). Soil chemical and physical characteristics are given on a dry soil basis (0% water).

The manure applied in this experiment was liquid / slurry manure from the dairy herd at the University of Wisconsin’s Blaine Dairy Cattle Research Center (W6723 Badger Ln., Arlington, WI 53911). The herd had 430 milking cows, 100 dry cows and more than 50 calves in a free-stall barn with sand bedding. Manure was stored in an earthen pit. In 2013, three manure samples were collected: one each at the beginning, middle and end of the field application day. In 2014 and 2015, two samples were taken. Sampling in 2012 was similar to 2014 and 2015, but only averages were retained by field management. Samples were frozen until analysis at the UW Soil & Forage Analysis Laboratory. Manure chemical and physical characteristics are given on a dry manure basis (0% water).

GHG fluxes (CO2, CH4, N2O) were measured using vented static chambers as described in Collier et al. (2014). Soil temperature, moisture, NO3- and NH4+ contents were also measured. Chamber dimensions were 40.5 cm diameter in 2013, and 76.2 cm long by 42.2 cm wide in 2014 and 2015, with variable height including extensions for alfalfa and accounting for uneven soil surface. Chamber deployment time was 20-36 minutes to yield 4-5 time points. Gas samples were analyzed by gas chromatography (7890A GC System, Agilent). Linear regression of gas concentrations (with visual inspection for quality control) was used to calculate GHG flux rates. Soil samples for nitrate + nitrite and ammonium contents were collected on selected gas sampling dates during 2014 and 2015.

This experiment was part of “Climate Change Mitigation and Adaptation in Dairy Production Systems of the Great Lakes Region,” also known as the Dairy Coordinated Agricultural Project (Dairy CAP), funded by the United States Department of Agriculture – National Institute of Food and Agriculture (award number 2013-68002-20525). The main goal of the Dairy CAP is to improve understanding of the magnitudes and controlling factors over GHG emissions from dairy production in the Great Lakes region. Using this knowledge, the Dairy CAP has improved life cycle analysis (LCA) of GHG production by Great Lakes dairy farms, developing farm management tools, and conducting extension, education and outreach activities. Support was also provided by National Science Foundation grant number 1215858, “Translating agricultural greenhouse gas emissions modeling into decision making on landscapes.”