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Title: Simulating agroecosystem soil inorganic nitrogen dynamics under long-term management with an improved SWAT-C model
Despite the extensive application of the Soil and Water Assessment Tool (SWAT) for water quality modeling, its ability to simulate soil inorganic nitrogen (SIN) dynamics in agricultural landscapes has not been directly verified. Here, we improved and evaluated the SWAT–Carbon (SWAT-C) model for simulating long-term (1984–2020) dynamics of SIN for 40 cropping system treatments in the U.S. Midwest. We added one new nitrification and two new denitrification algorithms to the default SWAT version, resulting in six combinations of nitrification and denitrification options with varying performance in simulating SIN. The combination of the existing nitrification method in SWAT and the second newly added denitrification method performed the best, achieving R, NSE, PBIAS, and RMSE of 0.63, 0.29, −4.7 %, and 16.0 kg N ha−1, respectively. This represents a significant improvement compared to the existing methods. In general, the revised SWAT-C model's performance was comparable to or better than other agroecosystem models tested in previous studies for assessing the availability of SIN for plant growth in different cropping systems. Sensitivity analysis showed that parameters controlling soil organic matter decomposition, nitrification, and denitrification were most sensitive for SIN simulation. Using SWAT-C for improved prediction of plant-available SIN is expected to better inform agroecosystem management decisions to ensure crop productivity while minimizing the negative environmental impacts caused by fertilizer application.  more » « less
Award ID(s):
1639327 2224712
Author(s) / Creator(s):
; ; ; ; ; ; ; ;
Publisher / Repository:
Science of The Total Environment
Date Published:
Journal Name:
Science of The Total Environment
Page Range / eLocation ID:
Medium: X
Sponsoring Org:
National Science Foundation
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This site is a part of the Great Lakes Bioenergy Research Center ( and is a Long-term Ecological Research site ( Soils are mesic Typic Hapludalfs developed on glacial outwash54 with high sand content (76% in the upper 150 cm) intermixed with silt-rich loess in the upper 50 cm55. The water table lies approximately 12–14 m below the surface. The climate is humid temperate with a mean annual air temperature of 9.1 °C and annual precipitation of 1005 mm, 511 mm of which falls between May and September (1981–2010)56,57. The BCSE was established as a randomized complete block design in 2008 on preexisting farmland. Prior to BCSE establishment, the field was used for grain crop and alfalfa (Medicago sativa L.) production for several decades. Between 2003 and 2007, the field received a total of ~ 300 kg P ha−1 as manure, and the southern half, which contains one of four replicate plots, received an additional 206 kg P ha−1 as inorganic fertilizer. The experimental design consists of five randomized blocks each containing one replicate plot (28 by 40 m) of 10 cropping systems (treatments) (Supplementary Fig. S1; also see Sanford et al.58). Block 5 is not included in the present study. Details on experimental design and site history are provided in Robertson and Hamilton57 and Gelfand et al.59. Leaching of P is analyzed in six of the cropping systems: (i) continuous no-till corn, (ii) switchgrass, (iii) miscanthus, (iv) a mixture of five species of native grasses, (v) a restored native prairie containing 18 plant species (Supplementary Table S1), and (vi) hybrid poplar. Agronomic management Phenological cameras and field observations indicated that the perennial herbaceous crops emerged each year between mid-April and mid-May. Corn was planted each year in early May. Herbaceous crops were harvested at the end of each growing season with the timing depending on weather: between October and November for corn and between November and December for herbaceous perennial crops. Corn stover was harvested shortly after corn grain, leaving approximately 10 cm height of stubble above the ground. The poplar was harvested only once, as the culmination of a 6-year rotation, in the winter of 2013–2014. Leaf emergence and senescence based on daily phenological images indicated the beginning and end of the poplar growing season, respectively, in each year. Application of inorganic fertilizers to the different crops followed a management approach typical for the region (Table 1). Corn was fertilized with 13 kg P ha−1 year−1 as starter fertilizer (N-P-K of 19-17-0) at the time of planting and an additional 33 kg P ha−1 year−1 was added as superphosphate in spring 2015. Corn also received N fertilizer around the time of planting and in mid-June at typical rates for the region (Table 1). No P fertilizer was applied to the perennial grassland or poplar systems (Table 1). All perennial grasses (except restored prairie) were provided 56 kg N ha−1 year−1 of N fertilizer in early summer between 2010 and 2016; an additional 77 kg N ha−1 was applied to miscanthus in 2009. Poplar was fertilized once with 157 kg N ha−1 in 2010 after the canopy had closed. Sampling of subsurface soil water and soil for P determination Subsurface soil water samples were collected beneath the root zone (1.2 m depth) using samplers installed at approximately 20 cm into the unconsolidated sand of 2Bt2 and 2E/Bt horizons (soils at the site are described in Crum and Collins54). Soil water was collected from two kinds of samplers: Prenart samplers constructed of Teflon and silica ( in replicate blocks 1 and 2 and Eijkelkamp ceramic samplers ( in blocks 3 and 4 (Supplementary Fig. S1). The samplers were installed in 2008 at an angle using a hydraulic corer, with the sampling tubes buried underground within the plots and the sampler located about 9 m from the plot edge. There were no consistent differences in TDP concentrations between the two sampler types. Beginning in the 2009 growing season, subsurface soil water was sampled at weekly to biweekly intervals during non-frozen periods (April–November) by applying 50 kPa of vacuum to each sampler for 24 h, during which the extracted water was collected in glass bottles. Samples were filtered using different filter types (all 0.45 µm pore size) depending on the volume of leachate collected: 33-mm dia. cellulose acetate membrane filters when volumes were less than 50 mL; and 47-mm dia. Supor 450 polyethersulfone membrane filters for larger volumes. 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Sampling of water samples from lakes, streams and wells for P determination In addition to chemistry of soil and subsurface soil water in the BCSE, waters from lakes, streams, and residential water supply wells were also sampled during 2009–2016 for TDP analysis using Supor 450 membrane filters and the same analytical method as for soil water. These water bodies are within 15 km of the study site, within a landscape mosaic of row crops, grasslands, deciduous forest, and wetlands, with some residential development (Supplementary Fig. S2, Supplementary Table S2). Details of land use and cover change in the vicinity of KBS are given in Hamilton et al.48, and patterns in nutrient concentrations in local surface waters are further discussed in Hamilton62. 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Volume-weighted mean TDP concentrations in leachate for each crop-year and for the entire 7-year study period were calculated as the total dissolved P leaching flux (kg ha−1) divided by the total drainage (m3 ha−1). One-way ANOVA with time (crop-year) as the fixed factor was conducted to compare total annual drainage rates, P leaching rates, volume-weighted mean TDP concentrations, and maximum aboveground biomass among the cropping systems over all seven crop-years as well as with TDP concentrations from local lakes, streams, and groundwater wells. When a significant (α = 0.05) difference was detected among the groups, we used the Tukey honest significant difference (HSD) post-hoc test to make pairwise comparisons among the groups. In the case of maximum aboveground biomass, we used the Tukey–Kramer method to make pairwise comparisons among the groups because the absence of poplar data after the 2013 harvest resulted in unequal sample sizes. We also used the Tukey–Kramer method to compare the frequency distributions of TDP concentrations in all of the soil leachate samples with concentrations in lakes, streams, and groundwater wells, since each sample category had very different numbers of measurements. Individual spreadsheets in “data table_leaching_dissolved organic carbon and nitrogen.xls” 1.    annual precip_drainage 2.    biomass_corn, perennial grasses 3.    biomass_poplar 4.    annual N leaching _vol-wtd conc 5.    Summary_N leached 6.    annual DOC leachin_vol-wtd conc 7.    growing season length 8.    correlation_nh4 VS no3 9.    correlations_don VS no3_doc VS don Each spreadsheet is described below along with an explanation of variates. Note that ‘nan’ indicate data are missing or not available. First row indicates header; second row indicates units 1. Spreadsheet: annual precip_drainage Description: Precipitation measured from nearby Kellogg Biological Station (KBS) Long Term Ecological Research (LTER) Weather station, over 2009-2016 study period. Data shown in Figure 1; original data source for precipitation ( Drainage estimated from SALUS crop model. Note that drainage is percolation out of the root zone (0-125 cm). Annual precipitation and drainage values shown here are calculated for growing and non-growing crop periods. Variate    Description year    year of the observation crop    “corn” “switchgrass” “miscanthus” “nativegrass” “restored prairie” “poplar” precip_G    precipitation during growing period (milliMeter) precip_NG    precipitation during non-growing period (milliMeter) drainage_G    drainage during growing period (milliMeter) drainage_NG    drainage during non-growing period (milliMeter)      2. Spreadsheet: biomass_corn, perennial grasses Description: Maximum aboveground biomass measurements from corn, switchgrass, miscanthus, native grass and restored prairie plots in Great Lakes Bioenergy Research Center (GLBRC) Biomass Cropping System Experiment (BCSE) during 2009-2015. Data shown in Figure 2.   Variate    Description year    year of the observation date    day of the observation (mm/dd/yyyy) crop    “corn” “switchgrass” “miscanthus” “nativegrass” “restored prairie” “poplar” replicate    each crop has four replicated plots, R1, R2, R3 and R4 station    stations (S1, S2 and S3) of samplings within the plot. For more details, refer to link ( species    plant species that are rooted within the quadrat during the time of maximum biomass harvest. See protocol for more information, refer to link ( For maize biomass, grain and whole biomass reported in the paper (weed biomass or surface litter are excluded). Surface litter biomass not included in any crops; weed biomass not included in switchgrass and miscanthus, but included in grass mixture and prairie. fraction    Fraction of biomass biomass_plot    biomass per plot on dry-weight basis (Grams_Per_SquareMeter) biomass_ha    biomass (megaGrams_Per_Hectare) by multiplying column biomass per plot with 0.01 3. Spreadsheet: biomass_poplar Description: Maximum aboveground biomass measurements from poplar plots in Great Lakes Bioenergy Research Center (GLBRC) Biomass Cropping System Experiment (BCSE) during 2009-2015. Data shown in Figure 2. Note that poplar biomass was estimated from crop growth curves until the poplar was harvested in the winter of 2013-14. Variate    Description year    year of the observation method    methods of poplar biomass sampling date    day of the observation (mm/dd/yyyy) replicate    each crop has four replicated plots, R1, R2, R3 and R4 diameter_at_ground    poplar diameter (milliMeter) at the ground diameter_at_15cm    poplar diameter (milliMeter) at 15 cm height biomass_tree    biomass per plot (Grams_Per_Tree) biomass_ha    biomass (megaGrams_Per_Hectare) by multiplying biomass per tree with 0.01 4. Spreadsheet: annual N leaching_vol-wtd conc Description: Annual leaching rate (kiloGrams_N_Per_Hectare) and volume-weighted mean N concentrations (milliGrams_N_Per_Liter) of nitrate (no3) and dissolved organic nitrogen (don) in the leachate samples collected from corn, switchgrass, miscanthus, native grass, restored prairie and poplar plots in Great Lakes Bioenergy Research Center (GLBRC) Biomass Cropping System Experiment (BCSE) during 2009-2016. Data for nitrogen leached and volume-wtd mean N concentration shown in Figure 3a and Figure 3b, respectively. Note that ammonium (nh4) concentration were much lower and often undetectable (<0.07 milliGrams_N_Per_Liter). Also note that in 2009 and 2010 crop-years, data from some replicates are missing.    Variate    Description crop    “corn” “switchgrass” “miscanthus” “nativegrass” “restored prairie” “poplar” crop-year    year of the observation replicate    each crop has four replicated plots, R1, R2, R3 and R4 no3 leached    annual leaching rates of nitrate (kiloGrams_N_Per_Hectare) don leached    annual leaching rates of don (kiloGrams_N_Per_Hectare) vol-wtd no3 conc.    Volume-weighted mean no3 concentration (milliGrams_N_Per_Liter) vol-wtd don conc.    Volume-weighted mean don concentration (milliGrams_N_Per_Liter) 5. Spreadsheet: summary_N leached Description: Summary of total amount and forms of N leached (kiloGrams_N_Per_Hectare) and the percent of applied N lost to leaching over the seven years for corn, switchgrass, miscanthus, native grass, restored prairie and poplar plots in Great Lakes Bioenergy Research Center (GLBRC) Biomass Cropping System Experiment (BCSE) during 2009-2016. Data for nitrogen amount leached shown in Figure 4a and percent of applied N lost shown in Figure 4b. Note the fraction of unleached N includes in harvest, accumulation in root biomass, soil organic matter or gaseous N emissions were not measured in the study. Variate    Description crop    “corn” “switchgrass” “miscanthus” “nativegrass” “restored prairie” “poplar” no3 leached    annual leaching rates of nitrate (kiloGrams_N_Per_Hectare) don leached    annual leaching rates of don (kiloGrams_N_Per_Hectare) N unleached    N unleached (kiloGrams_N_Per_Hectare) in other sources are not studied % of N applied N lost to leaching    % of N applied N lost to leaching 6. Spreadsheet: annual DOC leachin_vol-wtd conc Description: Annual leaching rate (kiloGrams_Per_Hectare) and volume-weighted mean N concentrations (milliGrams_Per_Liter) of dissolved organic carbon (DOC) in the leachate samples collected from corn, switchgrass, miscanthus, native grass, restored prairie and poplar plots in Great Lakes Bioenergy Research Center (GLBRC) Biomass Cropping System Experiment (BCSE) during 2009-2016. Data for DOC leached and volume-wtd mean DOC concentration shown in Figure 5a and Figure 5b, respectively. Note that in 2009 and 2010 crop-years, water samples were not available for DOC measurements.     Variate    Description crop    “corn” “switchgrass” “miscanthus” “nativegrass” “restored prairie” “poplar” crop-year    year of the observation replicate    each crop has four replicated plots, R1, R2, R3 and R4 doc leached    annual leaching rates of nitrate (kiloGrams_Per_Hectare) vol-wtd doc conc.    volume-weighted mean doc concentration (milliGrams_Per_Liter) 7. Spreadsheet: growing season length Description: Growing season length (days) of corn, switchgrass, miscanthus, native grass, restored prairie and poplar plots in the Great Lakes Bioenergy Research Center (GLBRC) Biomass Cropping System Experiment (BCSE) during 2009-2015. Date shown in Figure S2. Note that growing season is from the date of planting or emergence to the date of harvest (or leaf senescence in case of poplar).   Variate    Description crop    “corn” “switchgrass” “miscanthus” “nativegrass” “restored prairie” “poplar” year    year of the observation growing season length    growing season length (days) 8. Spreadsheet: correlation_nh4 VS no3 Description: Correlation of ammonium (nh4+) and nitrate (no3-) concentrations (milliGrams_N_Per_Liter) in the leachate samples from corn, switchgrass, miscanthus, native grass, restored prairie and poplar plots in Great Lakes Bioenergy Research Center (GLBRC) Biomass Cropping System Experiment (BCSE) during 2013-2015. Data shown in Figure S3. Note that nh4+ concentration in the leachates was very low compared to no3- and don concentration and often undetectable in three crop-years (2013-2015) when measurements are available. Variate    Description crop    “corn” “switchgrass” “miscanthus” “nativegrass” “restored prairie” “poplar” date    date of the observation (mm/dd/yyyy) replicate    each crop has four replicated plots, R1, R2, R3 and R4 nh4 conc    nh4 concentration (milliGrams_N_Per_Liter) no3 conc    no3 concentration (milliGrams_N_Per_Liter)   9. Spreadsheet: correlations_don VS no3_doc VS don Description: Correlations of don and nitrate concentrations (milliGrams_N_Per_Liter); and doc (milliGrams_Per_Liter) and don concentrations (milliGrams_N_Per_Liter) in the leachate samples of corn, switchgrass, miscanthus, native grass, restored prairie and poplar plots in Great Lakes Bioenergy Research Center (GLBRC) Biomass Cropping System Experiment (BCSE) during 2013-2015. Data of correlation of don and nitrate concentrations shown in Figure S4 a and doc and don concentrations shown in Figure S4 b. Variate    Description crop    “corn” “switchgrass” “miscanthus” “nativegrass” “restored prairie” “poplar” year    year of the observation don    don concentration (milliGrams_N_Per_Liter) no3     no3 concentration (milliGrams_N_Per_Liter) doc    doc concentration (milliGrams_Per_Liter) 
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