The main goal of this research is to contribute to the understanding of nutrient transport and transformations in soil and its impact on groundwater on a large scale. This thesis specifically integrates the physical, chemical and biochemical nitrogen transport processes with a spatial and temporal Land Surface Scheme (LSS). Since the nitrogen biotransformation kinetics highly depends on soil moisture and soil temperature, a vertical soil nitrogen transport and transformations model was coupled with SABAE-HW. The model provides an improved interface for groundwater modeling to simulate soil moisture and soil temperature for a wide range of soil and vegetation. It is assumed that the main source of organic N is from animal manure. A-single-pool nitrogen transformation is designed to simulate nitrogen dynamics. Thus, the complete mathematical model (SABAE-HWS) is able to investigate the effects of nitrogen biochemical reactions in all seasons. This thesis reports the first field comparison of SABAE-HW using an extensive ten-year data set from BOREAS/BERMS project located in Saskatchewan, Canada. The performance of SABAE-HWS is calibrated and verified using 3 years (2002-2004) data from Carberry site in Canada, Manitoba. The effects of three rates of hog manure application, 2500, 5000, and 7500 gal/acre, was investigated to study the distribution of soil ammonium and soil nitrate within the 120 cm of soil profile. The results clearly showed that there is a good agreement between observed and simulated soil ammonium and nitrate for all treatment at the first two years of study. However, it was found a significant difference between observations and simulations at lower depths for 7500 gal/acre by the end of growing season of 2004. Also, 10 years climate data from OJP site was used to evaluate the effect of manure rates on the distribution of soil nitrate at Carberry site. The results indicated that to minimize the risk of nitrate leaching, the rate of manure application, accumulated soil nitrogen from earlier applications and the atmospheric conditions should be all taken into account at the same time. Comparing the results of SABAE-HWS and SHAW model also showed the importance of the crop growth model in simulating soil NH4-N and NO3-N.

The main goal of this research is to contribute to the understanding of nutrient transport and transformations in soil and its impact on groundwater on a large scale. This thesis specifically integrates the physical, chemical and biochemical nitrogen transport processes with a spatial and temporal Land Surface Scheme (LSS). Since the nitrogen biotransformation kinetics highly depends on soil moisture and soil temperature, a vertical soil nitrogen transport and transformations model was coupled with SABAE-HW. The model provides an improved interface for groundwater modeling to simulate soil moisture and soil temperature for a wide range of soil and vegetation. It is assumed that the main source of organic N is from animal manure. A-single-pool nitrogen transformation is designed to simulate nitrogen dynamics. Thus, the complete mathematical model (SABAE-HWS) is able to investigate the effects of nitrogen biochemical reactions in all seasons. This thesis reports the first field comparison of SABAE-HW using an extensive ten-year data set from BOREAS/BERMS project located in Saskatchewan, Canada. The performance of SABAE-HWS is calibrated and verified using 3 years (2002-2004) data from Carberry site in Canada, Manitoba. The effects of three rates of hog manure application, 2500, 5000, and 7500 gal/acre, was investigated to study the distribution of soil ammonium and soil nitrate within the 120 cm of soil profile. The results clearly showed that there is a good agreement between observed and simulated soil ammonium and nitrate for all treatment at the first two years of study. However, it was found a significant difference between observations and simulations at lower depths for 7500 gal/acre by the end of growing season of 2004. Also, 10 years climate data from OJP site was used to evaluate the effect of manure rates on the distribution of soil nitrate at Carberry site. The results indicated that to minimize the risk of nitrate leaching, the rate of manure application, accumulated soil nitrogen from earlier applications and the atmospheric conditions should be all taken into account at the same time. Comparing the results of SABAE-HWS and SHAW model also showed the importance of the crop growth model in simulating soil NH4-N and NO3-N.

Development of the Athabasca Oil Sands Region (AOSR) has increased atmospheric nitrogen emissions, a trend which is expected to increase in the future. The area surrounding development is comprised of Boreal upland forests and peatlands. Improved understanding of the hydrological connectivity between Boreal peatlands and uplands is needed to predict the fate and transport of atmospheric N deposited across the region. Two field sites: Jack Pine High (JPH, located 45 km north of Fort McMurray) and Mariana Lakes (ML, located 100 km south of Fort McMurray) were instrumented with piezometers nests and water table wells for this study (n= 108 sampling locations). The wells were placed along transects that cover target landscape units (bog, fen, upland). Wells were sampled for water isotopes and geochemical parameters during the summers of 2011-2014 to characterize the baseline geochemistry of groundwater in the different landscape units. Inorganic (nitrate, ammonium) and organic forms of nitrogen (dissolved organic nitrogen), major and minor ions and water isotope tracers (18O, 2H and 3H) were measured to identify the various forms of nitrogen in the different landscape units, as well as to assess connectivity and potential for nitrogen transport between the different units. At JPH surface and groundwater flow is from the uplands to the fen. There was little (<0.1-1.5 mg/L) nitrate, ammonium, or dissolved organic nitrate (DON) found throughout JPH. At ML nitrogen concentrations were higher (<0.1-30 mg/l) and concentrations of ammonium and DON increased at depths throughout ML. The distribution of 3H with depth within the peatland reveals limited connectivity between the peat and underlying mineral soils. Tritium sampling at ML indicates that at some locations the wetland residence time is greater than 50 years. Nitrogen movement out of peatlands may take longer due to conversions and storage. At ML nitrogen (NH4 and DON) is produced and stored at depth in the wetlands. At JPH higher nitrogen concentrations are found in the shallow groundwater of the fen. Increases in nitrogen inputs to JPH and ML are likely to be utilized by plants, but dramatic changes to the peatland may cause stored nitrogen to become mobile. / Graduate

<p>Soybean and related legumes export symbiotically-fixed nitrogen from the nodules to the leaves as ureides. The ureide allantoin is hydrolyzed by allantoinase to allantoate then further degraded by other enzymes, releasing ammonia and carbon dioxide. This study aimed to identify allantoinase genes in soybean and their gene expression as well as enzyme activity patterns. The effects of water limitation and allantoin treatment on the expression and activity of allantoinase in N₂-fixing plants were also evaluated. Enzyme activity and ureide content were evaluated using a spectrophotometric assay. Real time RT-PCR was used to quantify the amount of gene products. Four allantoinase genes were identified and were expressed, with <i>GmALN1</i> and <i>2</i> constantly expressed at higher levels. In seedlings, allantoinase was found to be actively synthesized more in cotyledons than in the embryonic axes, as seen by early enzyme activity and higher <i>GmALN 1</i> and <i>2</i> transcript levels. Allantoate produced in these tissues appeared to be mobilized to the developing axes. <i>GmALN1</i> and <i>2</i> were implicated in post-germination nitrogen assimilation during early seedling growth, while <i>GmALN3</i> and <i>4</i> were consistently expressed at very low levels, with an exception in nodules. Transcript abundance in the nodules of N₂-fixing plants, supported by the high enzyme activity and ureide content observed, suggested an important role in the synthesis and transport of allantoate in these tissues. Allantoinase was also detected in non-fixing tissues but may play a different role in these tissues, most probably functioning in the turnover and salvage of purine nucleotides. The effect of exogenous allantoin during water limitation was investigated. The addition of allantoin prior to water limitation seemed to change the sensitivity of soybean to such stress, prolonging its ureide catabolic activity at least up to 5 days without water. Results of this study will aid in our understanding of how ureide catabolism is regulated during soybean development. This information may help address problems in legume crop improvement specifically in enhancing N₂-fixation and yield capacity and in coping with water limitation stress.</p>

<p>Soybean and related legumes export symbiotically-fixed nitrogen from the nodules to the leaves as ureides. The ureide allantoin is hydrolyzed by allantoinase to allantoate then further degraded by other enzymes, releasing ammonia and carbon dioxide. This study aimed to identify allantoinase genes in soybean and their gene expression as well as enzyme activity patterns. The effects of water limitation and allantoin treatment on the expression and activity of allantoinase in N₂-fixing plants were also evaluated. Enzyme activity and ureide content were evaluated using a spectrophotometric assay. Real time RT-PCR was used to quantify the amount of gene products. Four allantoinase genes were identified and were expressed, with <i>GmALN1</i> and <i>2</i> constantly expressed at higher levels. In seedlings, allantoinase was found to be actively synthesized more in cotyledons than in the embryonic axes, as seen by early enzyme activity and higher <i>GmALN 1</i> and <i>2</i> transcript levels. Allantoate produced in these tissues appeared to be mobilized to the developing axes. <i>GmALN1</i> and <i>2</i> were implicated in post-germination nitrogen assimilation during early seedling growth, while <i>GmALN3</i> and <i>4</i> were consistently expressed at very low levels, with an exception in nodules. Transcript abundance in the nodules of N₂-fixing plants, supported by the high enzyme activity and ureide content observed, suggested an important role in the synthesis and transport of allantoate in these tissues. Allantoinase was also detected in non-fixing tissues but may play a different role in these tissues, most probably functioning in the turnover and salvage of purine nucleotides. The effect of exogenous allantoin during water limitation was investigated. The addition of allantoin prior to water limitation seemed to change the sensitivity of soybean to such stress, prolonging its ureide catabolic activity at least up to 5 days without water. Results of this study will aid in our understanding of how ureide catabolism is regulated during soybean development. This information may help address problems in legume crop improvement specifically in enhancing N₂-fixation and yield capacity and in coping with water limitation stress.</p>

Watersheds within northwestern Mississippi, a productive agricultural region referred to as the Delta, were recently identified as contributors of total nitrogen and phosphorus fluxes to the Gulf of Mexico. Water withdrawals for irrigation in the Delta have altered flow paths between surface-water and groundwater systems, allowing for more surface-water losses to the underlying alluvial aquifer. In order to understand how to manage nitrogen in a watershed, it is necessary to identify and quantify hydrologic flow paths and biogeochemical conditions along these flow paths, which ultimately combine to determine transport and fate. In order to evaluate the extent and role of surface-water losses to the alluvial aquifer on the transport of nitrate, a two-dimensional groundwater/surface-water exchange model was developed for a site within the Delta. Results from this model determined that groundwater/surface-water exchange at the site occurred regularly and recharge was laterally extensive into the alluvial aquifer. Nitrate was consistently reported in surface-water samples (n= 52, median concentration = 39.8 micromol/L), although never detected in samples collected from instream or near stream piezometers (n=46). Coupled model and water-quality results support the case for denitrification/ nitrate loss from surface water moving through an anoxic streambed. At larger scale, recent results from two Spatially Referenced Regressions on Watershed attributes (SPARROW) models imply that nitrogen is transported relatively conservatively once it enters the main channel of the Big Sunflower River Basin, which contributes much of the water discharging from the Yazoo River Basin to the Mississippi River. Net loss of nitrogen was assessed by comparing total nitrogen data from Lagrangian sampling events to chloride, drainage area, and predicted total nitrogen flux results from the SPARROW models. Results indicated relatively conservative instream transport of nitrogen at the scale of the Big Sunflower River Basin; however, two potential nitrogen loss mechanisms were identified: (1) transport and transformation of nitrogen through the streambed, and (2) sequestration and transformation of nitrogen above the drainage control structures downstream of Anguilla.

AN ABSTRACT OF THESIS Jarrod Armstrong, for the Master of Science degree in Forestry, presented on December 10, 2014, at Southern Illinois University Carbondale. Title: Nitrogen Availability and Transport Following Drought in Three Agricultural Watersheds in Central Illinois Major Professor: Dr. Karl Williard The use of inorganic nitrogen (N) fertilizers has become an essential part of modern agriculture and has helped increase yields to keep pace with an ever growing population. N is the most dynamic nutrient in nature, and biological activity can transform it into several mobile forms. Nitrate (NO3-N) is the most mobile form of N and is highly susceptible to transport to ground and surface waters. The purpose of this study was to assess N dynamics in three agricultural watersheds during and following a significant drought in 2012. Specifically, the study focuses on the mobilization and transport of residual N. The research was conducted on a ninety‐seven hectare agriculture field in Macon, County Illinois. The study site (BRKA) was divided into three watersheds, with four plots per watershed, and two topographic positions per plot. Volumetric water content (VWC) was measured continuously in each of the two topographic positions. In each watershed, stream stage collected over storm hydrographs using automated water samplers was compared to volumetric water content and NO3-N concentrations over the hydrograph. Four 6.1m groundwater monitoring wells and eight vacuum lysimeters in each watershed were monitored to determine the fate and transport of N to soil water and groundwater. Soil sampling at the 15cm depth was completed on a 0.4 hectare grid over the entire field during the fall of each year of the study. Soil and groundwater samples were analyzed monthly to compare NO3-N concentrations across topographic positions. NO3-N concentrations were highest in soil water, followed by groundwater, and lastly surface runoff. Studies in Illinois and Iowa both confirmed large amounts of residual N in the soil after the growing season in the fall of 2012 (Sawyer 2013, and Nafziger 2013). Residual N was apparent at BRKA in elevated NO3-N concentrations in soil water and groundwater after the 2012 growing season. Runoff events in April 2013 also showed increased NO3-N transport. However, due to precipitation events in the late fall and winter the residual N was flushed from the soil profile rendering it unavailable for the 2013 growing season. The soil NO3-N deficit after the 2012 drought was likely the result of decreased N fixation, N mineralization, nitrification, and leaching of any residual NO3-N. Bottomland positions consistently displayed higher soil water and groundwater NO3-N concentrations compared to uplands. However, due to a lack of plant uptake during the 2012 drought this trend was reversed and caused upland positions to exhibit higher NO3-N concentrations compared to bottomlands. This study demonstrated that even during a soybean year when no N fertilizer was applied significant drought can effectively alter the normal N dynamics at the field scale. Furthermore, this change in dynamics can lead to elevated NO3-N concentrations in soil water and ground water. These findings also suggest that precipitation events following periods of drought, like those observed after the 2012 growing season, can flush excess nutrients from the rooting zone further depleting the NO3-N pool and posing a risk to water quality. Data from a June 15, 2011 storm showed that on the falling limb of the hydrograph subsurface flow flushed soil water from the top of the slope to the bottom of the slope. This is indicative of a variable source area controlled watershed where the near stream zones undergo prolonged saturation from the subsurface drainage of the upland areas. Additionally, the early peak of NO3-N during an April 18, 2013 surface runoff event could be attributed to increased mineralization and nitrification following a rewetting of the soil profile after the 2012 drought. Lastly, topography was shown to have a strong influence on soil NO3-N concentrations across the field. This finding suggests that fertilizer applications based on topography and hydrology could help to mitigate the loss of excess NO3-N from agricultural watersheds. Furthermore, fertilizer applications should be adjusted for drought conditions that extend into the following growing season to account for residual N in the soil.