The root systems of five tree species (Populus deltoides × nigra clone DN-177, Juglans nigra, Quercus rubra, Picea abies, and Thuja occidentalis) are described following non-intrusive imaging using ground penetrating radar (GPR). This research aimed to 1) assess the utility of GPR for in situ root studies and 2) employ GPR to estimate tree root biomass and distribution in an agroforestry system in southern Ontario, Canada. The mean coarse root biomass estimated from GPR analysis was 54.1 ± 8.7 kg tree-1 (± S.E.; n=12), within 1 % of the mean coarse root biomass measured from matched excavations. The vertical distribution of detected roots varied among species, with T. occidentalis and P. abies roots concentrated in the top 20 cm and J. nigra and Q. rubra roots distinctly deeper. I evaluate these root systems based on their C storage potential and complementary root stratification with adjacent crops.

The root systems of five tree species (Populus deltoides × nigra clone DN-177, Juglans nigra, Quercus rubra, Picea abies, and Thuja occidentalis) are described following non-intrusive imaging using ground penetrating radar (GPR). This research aimed to 1) assess the utility of GPR for in situ root studies and 2) employ GPR to estimate tree root biomass and distribution in an agroforestry system in southern Ontario, Canada. The mean coarse root biomass estimated from GPR analysis was 54.1 ± 8.7 kg tree-1 (± S.E.; n=12), within 1 % of the mean coarse root biomass measured from matched excavations. The vertical distribution of detected roots varied among species, with T. occidentalis and P. abies roots concentrated in the top 20 cm and J. nigra and Q. rubra roots distinctly deeper. I evaluate these root systems based on their C storage potential and complementary root stratification with adjacent crops.

Current estimates of terrestrial carbon (C) fluxes overlook explicit hydrological controls. In this research project, a spatially explicit hydro-ecological model, BEPS-TerrainLab V2.0 was further developed to improve our understanding of the non-linearities associated with various hydro-ecological processes. A modeling study was conducted in a humid boreal ecosystem in north central Quebec, Canada. The sizes and nature of various ecosystem-C-pools were comprehensively reconstructed under a climate change and disturbance scenario prior to simulation in order to ensure realistic biogeochemical modeling. Further, several ecosystem processes were simulated and validated using field measurements for two years. A sensitivity analysis was also performed. After gaining confidence in the model’s ability to simulate various hydrologically controlled ecophysiological and biogeochemical processes and having understood that topographically driven sub-surface baseflow is the main process determining the soil moisture regime in humid boreal ecosystem, its influence on ecophysiological and biogeochemical processes were investigated. Three modeling scenarios were designed that represent strategies that are currently used in ecological models to represent hydrological controls. These scenarios were: 1) Explicit, where realistic lateral water routing was considered 2) Implicit, where calculations were based on a bucket-modeling approach 3) NoFlow, where the lateral sub-surface flow was turned off in the model. In general, the Implicit scenario overestimated GPP, ET and NEP, as opposed to the Explicit scenario. The NoFlow scenario underestimated GPP and ET but overestimated NEP. The key processes controlling the differences were due to the combined effects of variations in plant physiology, photosynthesis, heterotrophic respiration, autotrophic respiration and nitrogen mineralization; all of which occurred simultaneously in different directions, at different rates, affecting the spatio-temporal distribution of terrestrial C-sources or sinks (NEP). From these results it was clear that lateral water flow does play a significant role in the net terrestrial C distribution and it was discovered that non-explicit forms of hydrological representations underestimate the sizes of terrestrial C-sources rather than C-sinks. The scientific implication of this work demonstrates that regional or global scale terrestrial C estimates could have significant errors if proper hydrological constraints are not considered for modeling ecological processes due to large topographic variations of the Earth’s surface.

Master of Science / Department of Agronomy / Charles W. Rice / Declining soil health is the underlying cause of decreasing agricultural productivity and environmental degradation. To address this challenge, research was conducted to determine how: (1) cover crops affect soil health in Kansas, USA and (2) direct seeding mulch–based cropping (DMC) systems affect soil health in Nyankpala, Ghana. Soil health indicators assessed include: biomass yield (kg ha[superscript]-1), soil microbial respiration (SMR), soil microbial C and N (MBC & MBN), potentially mineralizable N (PMN), dissolved organic carbon (DOC), soil organic C (SOC), soil total nitrogen (TN), phospholipid fatty acid analysis (PLFA), water stable aggregate (WSA), bulk density, pH, N, P, K, Ca and Mg. DMC systems from Ghana yielded significantly greater biomass compared to the control. High biomass produced by DMC systems did not increase SOC and PMN relative to the control. Fertilizer application had a significant impact on biomass production, which resulted in a significant increase in SOC and PMN in the 0-5 cm soil layer. Soil pH was significantly reduced by cropping systems and fertilizer in the 0-5 cm soil layer. Microbial biomass N, TN, SMR, N, P, Ca and Mg were not affected by the DMC cropping systems. Application of mineral fertilizer increased SMR, MBN, TN, N, and P. Soil K was also significantly affected by cropping systems and mineral fertilizer. The combination of mineral fertilizer and plant residues would be needed to improve soil health and increase crop productivity in the Guinea Savanna Zone of Ghana. Liming would be required to address low soil pH. In the USA, of all the soil health indicators examined, actinomycetes, gram-positive bacteria, fungi-bacteria ratio (F:B), SMR, MBN and WSA, were those significantly influenced by cover crops. The interactive effect of cover cops and N fertilizer also affected gram-positive bacteria, total PLFA, MBN, F:B ratio and WSA. Cover crop residues contributed to the observed differences in these indicators. The low response of soil health indicators suggest further evaluations are needed to determine the effectiveness of the indicators.

Doctor of Philosophy / Agronomy / Charles W. Rice / Substitution of cellulosic biofuel in place of gasoline or diesel could reduce greenhouse gas (GHG) emissions from transportation. However, emissions of nitrous oxide (N₂O) and changes in soil organic carbon (SOC) could have a large impact on the GHG balance of cellulosic biofuel, thus there is a need to quantify these responses in cellulosic biofuel crops. The objectives of this study were to: (i) measure changes in yield, SOC and microbial communities in potential cellulosic biofuel cropping systems (ii) measure and characterize the temporal variation in N₂O emissions from these systems (iii) characterize the yield and N₂O response of switchgrass to N fertilizer and to estimate the costs of production. Sweet sorghum, photoperiod-sensitive sorghum, and miscanthus yielded the highest aboveground biomass (20-32 Mg ha⁻¹). The perennial grasses sequestered SOC over 4 yrs, while SOC stocks did not change in the annual crops. Root stocks were 4-8 times higher in the perennial crops, suggesting greater belowground C inputs. Arbuscular mycorrhizal fungi (AMF) abundance and aggregate mean weight diameter were higher in the perennials. No consistent significant differences were found in N₂O emissions between crops, though miscanthus tended to have the lowest emissions. Most N₂O was emitted during large events of short duration (1-3 days) that occurred after high rainfall events with high soil NO₃₋. There was a weak relationship between IPCC Tier 1 N₂O estimates and measured emissions, and the IPCC method tended to underestimate emissions. The response of N₂O to N rate was nonlinear in 2 of 3 years. Fertilizer induced emission factor (EF) increased from 0.7% at 50 kg N ha⁻¹ to 2.6% at 150 kg N ha⁻¹. Switchgrass yields increased with N inputs up to 100-150 kg N ha⁻¹, but the critical N level for maximum yields decreased each year, suggesting N was being applied in excess at higher N rates. Yield-scaled costs of production were minimized at 100 kg N ha-1 ($70.91 Mg⁻¹). Together, these results show that crop selection and fertilizer management can have large impacts on the productivity and soil GHG emissions biofuel cropping systems.

Doctor of Philosophy / Department of Agronomy / Ganga M. Hettiarachchi / Constructed wetland treatment systems (CWTSs) are an alternative adaptation for flue-gas desulfurization (FGD) wastewater purification. A series of laboratory-based soil column studies mimicking a pilot-scale CWTS was carried out to evaluate the performance of the treatment system in detail. The main objectives of studies were to (1) understand the transport characteristics, retention capacity and transformation of selenium and other FGD constituents in the CWTS, (2) evaluate the effectiveness of soil treatments and influent flow rate on the performance of the CWTS, and (3) develop a mechanistic understanding of the CWTS performance through monitoring interrelationships of selenium (Se), arsenic (As), iron (Fe), and sulfur (S). Ferrihydrite (1% w/w), and labile organic carbon (OC) were used as soil treatments. Different influent flow rates, X (1.42 mL/hour), 2X, or 1/2X were used depending on the objectives of each study. Deoxygenated 1:1 mixture of FGD: raw water was the influent. It was delivered to the saturated columns with an upward flow. Effluent samples were collected continuously, and analyzed for constituents of concern. End of these experiments, soil from sectioned columns were used for total elemental analysis, sequential extraction procedure (SEP) for Se, and synchrotron-based X-ray spectroscopy analyses. Results indicated a complete Se retention by the columns. Boron, and fluorine partially retained whereas sodium, sulfur, and chlorine retention was weak, agreeing with field observations. Some of the initially-retained Se (~ 4 to 5%) was mobilized by changing redox conditions in the soil. Selenium fed with the wastewater accumulated in the bottom 1/3 (inlet) of the soil columns and was mainly sequestrated as stable forms revealed by SEP. Bulk-, and micro-XANES analyses suggested the retention mechanism of Se from the FGD wastewater was via the transformation of Se into reduced/stable forms [Se(IV), organic Se, and Se(0)]. Under wetland conditions, native soil As was mobilized by reductive dissolution of As associated minerals. However, the ferrihydrite amendment suppressed the native soil As mobility. Micro-XRF mapping integrated with As, and Fe-XANES suggested that the mechanism of native soil As retention was the sequestration of released As with newly precipitated secondary Fe minerals. A long-term study carried out with X, 1/2X flow rates, and OC source indicated enhanced S retention by the slow flow rate (1/2X), most likely due to the time dependency of biogenic S reduction. Further, bulk S-, As-, and Fe-XANES revealed that long submergence period and the slow flow rate increased the formation of reduced and/or biogenic S, realgar-like, and greigite-like species. These observations indicated that modified flow rates could have a significant impact on the long-term trace element (such as As) sequestration in the CWTS. Our studies provide useful information to improve the performance, and longevity of a full-scale CWTS for FGD wastewaters.

Master of Science / Department of Biology / John M. Blair / Anthropogenic activities impact ecosystems in numerous direct and indirect ways, affecting the cycling of carbon (C) and nitrogen (N) on local, regional and global scales. North America tallgrass prairie is an ecosystem profoundly altered by anthropogenic activities, with most native prairie converted to alternate land uses or heavily impacted by other environmental changes. While aboveground responses to anthropogenic drivers have received much attention, the responses of belowground biota, ecological processes, and nutrient allocation to land management and environmental change are poorly documented, especially over long timeframes. This research builds upon a long-term experiment (the Belowground Plot Experiment) initiated in 1986 at Konza Prairie Biological Station (Manhattan, KS). I utilized a subset of treatments to address the effects of annual burning vs. fire suppression and/or chronic N additions on soil C and N dynamics and microbial communities in tallgrass prairie. I measured a suite of soil variables related to C and N cycling during the 2012 growing season, including total soil C and N, microbial biomass C and N, in situ net N mineralization, potential N mineralization, in situ CO2 efflux, and potentially mineralizable soil C. I also assessed changes in microbial community composition using microbial phospholipid fatty acids (PLFA) profiles. Annual burning significantly (p≤0.05) increased the soil C:N ratio and in situ CO2 efflux, while decreasing potential ammonification and nitrification rates. Annual burning also increased total PLFA mass and relative abundance of fungi. Chronic N addition (100 kg N ha-1 year-1) significantly reduced the soil C:N ratio, while increasing total soil N and potential nitrification and ammonification rates. Chronic N addition reduced potential C mineralization, microbial biomass C and N, and altered microbial community composition by increasing abundance of bacterial PLFAs and reducing fungal PLFAs. Sampling date also significantly affected many variables. These results indicate that different fire regimes and chronic N enrichment over decades affects soil C and N pools and transformations, as well as microbial biomass and composition. In total, this study highlights the importance of long-term ecological research and identifies likely changes in tallgrass prairie nutrient dynamics and soil microbial communities under increased N and frequent burning.

Doctor of Philosophy / Department of Agronomy / Gary M. Pierzynski / The bioavailability of Pb and Zn is linked to the solubility of solid phases and other soil chemical characteristics, which is associated with their environmental risk, suggesting that in situ stabilization of these elements can be accomplished by influencing their chemistry. However, more research is needed to investigate the effectiveness of different soil amendments on reducing Pb and Zn bioavailability. A lab study was conducted to evaluate the effects of five different P amendments and time on Pb/Zn speciation in a contaminated soil using synchrotron-based techniques, while a field investigation studied the effects of composted beef manure on plant biomass production and the influence on microbial function, size, and community shifts. In the lab study, the Pb-phosphate mineral plumbogummite was found as an intermediate phase of pyromorphite formation, which has not been documented until now. Additionally, all fluid and granular P sources were able to induce Pb-phosphate formation, but fluid phosphoric acid (PA) was the most effective with time and distance from the treatment. However, acidity from PA increased the prescence of soluble Zn species, which can have negative environmental consequences. Granular phosphate rock (PR) and triple super phosphate (TSP) reacted to generate both Pb- and Zn-phosphates, with TSP being more effective at greater distances than PR. In the field study, compost additions of 269 Mg ha[superscript]1 significantly decreased bioavailable Zn, while increasing estimated available water, plant nutrients, and plant biomass as compared to a contaminated control and low addition of compost (45 Mg ha[superscript]1) over three years. Additionally, compost additions of 269 Mg ha[superscript]1 significantly increased microbial enzyme activities, nitrification, and microbial biomass over the contaminated control through the duration of the study. Increases in microbial activity and biomass are related to increases in total C, available water, and extractable P, while negative relationships were found with electrical conductivity and with bioavailable Zn. The addition of lime or lime plus bentonite with compost did not further reduce metal availability, increase plant biomass, or improve the size or function of microbial communities. High compost additions caused a slight shift in microbial community structure according to phospholipids fatty acid analysis. Increases in the mole percents of both Gram-positive (Gm[superscript]+) and Gram negative (Gm[superscript]-) bacteria were found depending on site. Microbial biomass of Gm[superscript]+, Gm[superscript]-, and fungi were also increased by high compost additions. Results indicate that large additions of compost are needed to increase microbial biomass, improve microbial activity, and re-establish a healthy vegetative community. This study proposes that organic matter and P amendments can be used to stabilize and reduce the bioavailability of heavy metals in soils and mine waste materials, but must be managed carefully and intelligently.

Master of Science / Department of Biological & Agricultural Engineering / Stacy L. Hutchinson / Soil erosion is a serious problem resulting in degradation of soil systems and nonpoint source (NPS) pollution of water resources. Concentrated overland flow is the primary transport mechanism for many NPS pollutants including soil, and locating areas where sheet flow transitions into concentrated flow is useful for assessing the potential for soil erosion. The ability to predict areas where overland flow transitions to concentrated flow and soil erosion potential is high assists land managers in implementing best management practices (BMPs) to reduce soil erosion and NPS. An erosion model, called the nLS model, was developed to identify transitional overland flow regions. The model is based on the kinematic wave overland flow theory and uses Manning’s n values, flow length, and slope as inputs to determine where overland flow transitions to sheet flow and soil erosion potential increases. Currently, the model has only been tested and validated for watersheds within Kansas. In order to assess model uncertainties and evaluate the model’s applicability to other regions, a sensitivity analysis on key input parameters was conducted. To assess model operations, several sensitivity analyses were performed on model inputs, including digital elevation models (DEMs) and landuse/landcover data (LULC). The impact of slope was assessed using two methods. First, by modifying the DEMs in a stepwise fashion from flatter to steeper terrains, and second, by modifying the elevation of each DEM cell based on the associated elevation error. To assess difficulties that might arise from the parameterization of surface roughness, LULC classes were assigned Manning’s n values within the suggested range using a Monte Carlo simulation. In addition, the critical threshold value used for locating erosion potential sites was modified, and alternative model calculations were used to assess the potential for improving model accuracy. Finally, the model was run using data from multiple sites, including two study areas in Hawaii and two in Kansas. The outputs for each site were analyzed in an attempt to identify any trends caused by site characteristics. Results from this study showed that the nLS model was sensitive to all of the inputs. Modifying the Manning’s roughness coefficient significantly altered the final nLS values and shifted the critical threshold points, especially in areas of the upper watershed. Changes in the slope value modified the nLS model outputs in a predictable manner, but there was some variability, especially in areas with lower slope values. In addition, discrepancies in the DEM, which may be present due to measurement or processing error, were shown to significantly alter the flow paths of a watershed. These findings suggest that accurate roughness coefficients and LULC data are especially important for regions with a steeper topography, and accurate elevation data is important for regions with lower slope values. The results also suggest that the threshold value for the model plays a vital role in locating potential soil erosion sites, and adjustments to this value could possibly be used as a method for calibrating the nLS model. Finally, the alternative model calculations used in this study did not significantly improve the accuracy of the nLS model, so the existing model is sufficient for obtaining accurate nLS estimates. The information gained from this study can improve the assessment of soil erosion processes due to concentrated overland flow. By successfully implementing a land management program that makes use of the nLS models, it should be possible to improve BMP placement and design, helping to improve water and soil quality.

Doctor of Philosophy / Department of Agronomy / Scott A. Staggenborg / Grain sorghum yield has notably increased from the beginning of hybrid production and commercialization in the late 1950s. The yield increases were the result of improved agronomic practices and hybrid advancement. The objectives of my research were: (1) to determine the magnitude of yield change in the hybrid era in irrigated and rain fed sorghum production, (2) to determine the contribution of agronomic and hybrid changes for yield in the hybrid era, (3) to investigate changes in sorghum morphology, physiology, and water use that contributed to yield increases, (4) to investigate changes that accompanied yield increase with hybrid improvement, and (5) to understand sorghum water and nutrient use and variations between hybrids in these regards. Fifty-two years of grain sorghum hybrid performance trial data (1957-2008), were analyzed and greenhouse and field studies were conducted on five selected hybrids to meet our objectives. The greenhouse and field studies were conducted from the summer of 2007 to the fall of 2009 on five selected hybrids, each representing a decade from the past fifty years. Results indicated that there was an increase in hybrid yield of nearly 50 kg ha-1 yr-1 in dryland sites over the 52 yrs (1957-2008) analyzed. Irrigated grain sorghum yields, however, remained unchanged over the same period. Agronomic practices such as planting date, phosphorus fertilizer use, and planting density changed over these years but were not found to contribute to increased dryland sorghum yields. There was no difference found between old and new hybrids tolerance to different densities. Hybrid advancement and increased nitrogen fertilizer application were responsible for changes in dryland yields. Total water use changed with hybrid advancement. New hybrids used the greatest total water and also had greater root-to-total biomass ratio than the old hybrids. Leaf biomass was also greater for the newest hybrid. There was a difference in amount of total nutrients extracted by hybrids, and there were differences among hybrids in allocation of nutrients to different tissues. In general the yield focus of sorghum hybrid development was effective in dryland sorghum production, likely because of intentional or inadvertent selection of hybrids with better drought tolerance. Results indicated that breeding programs created hybrids with improved morphological characteristics that might have resulted in better resource use (water and nutrient) and ultimately increased yield.