Thompson, Karen

In Ontario, farmers commonly use a MZ (Maize (Zea mays L.))-SB (Soybean (Glycine max))/WW (Winter wheat (Triticum aestivum)) – CC (mixed cover crop) rotation to maximize economic benefits. This study aimed to investigate the short-term impacts of the crop rotation phases and their associated management practices in this diversified cash crop rotation on soil health and the abundance of nitrogen (N)-cycling soil microbial communities (SMCs). Additionally, the abundance of N-cycling SMCs and plant-available N in both surface (0-5 cm) and rooting zone (5-15 cm) depths were characterized in tile-drained (TD) and non-TD fields. In the present study, soils collected under the CC phase had the highest labile carbon levels (10-17% higher) and water-stable aggregates (35-50% higher) compared to the other two crop phases. Lower nitrifying (amoA) gene abundances and soil NO3--N levels were observed in the CC phase compared to the MZ and SB-WW phases, suggesting a potential for decreased nitrification in the CC phase. The presence of SB potentially influenced the soil N concentration in the subsequent WW phase likely due to the release of symbiotically fixed N in the SB-WW phase. Further, higher amoA abundances and NO3--N in the SB-WW phase imply a potential for increased nitrification in the SB-WW phase. Additionally, higher amoA/nosZI and nirS+nirK/nosZI ratios were observed in the MZ phase than in SB-WW and CC phases, suggesting a potential capacity for increased N2O emissions from the reactions mediated by N-cycling SMCs in soils planted to MZ during fall sampling days. In the TD and NTD field study, higher NO3--N levels were observed in TD-SB-WW fields at 5-15 cm vs. 0-5 cm depths, which was possibly facilitated by tile drainage. The TD-CC fields displayed higher nosZI gene abundances and lower nirS+nirK/nosZI abundance ratios, suggesting a greater potential capacity for decreased N2O emissions in soils planted to CCs during the spring sampling days. When examining changes in plant available N by soil depth, reduced downward movement of NO3- through shallow soil depths (0-15 cm depth) was observed in the CC phase compared to cash crops. This short-term study highlights the potential contribution of the CC phase, particularly within TD agricultural fields, for improving soil health and reducing potential N2O emissions. Together, these results suggest that management-associated differences in crop rotation phases have temporary effects on soil health and the abundance of SMCs. Future studies linking N-cycling SMC's potential activity and field-scale N2O fluxes will provide a better insight into the longer-term sustainability of Ontario's cash crop management systems.

Author Keywords: denitrification, maize-soybean-winter wheat- cover crop rotation, nitrification, soil depth, Sustainable agriculture, tile-drainage

In an effort to improve upon existing analytical methods, electrochemical sensors offer portable, cost-effective alternatives to traditional lab-based techniques. Recent advances in supramolecular chemistry offer a unique alternative to achieve high selectivity while also benefitting from facile scaling for mass production. Thus, by incorporating host-guest chemistry with electrochemical sensors, the development of simple and selective sensors is possible. To that extent, novel hosts and electroactive ion pairs were investigated for their ability to transduce an electrochemical signal representative of host-guest complexation. Results demonstrated that the upper rim modifications of resorcinarene hosts attenuated their affinity for electroactive probes whilst maintaining structural integrity upon extended cycling. Further work revealed that guests may be directly quantified via their complexation with electroactive hosts. The sensing method was further validated by quantification of surfactant pollutants in the Otonabee River. Through a fundamental understanding of the electrochemical behaviour of host-guest systems a general sensing platform can be developed, where hosts are interchangeable for specificity towards any desired analyte. Therefore, moving away from expensive lab-based methods and significantly reducing the barriers for biological or environmental monitoring.

Author Keywords: Electrochemistry, Ferrocene, Host-Guest, Resorcinarenes, Supramolecular Chemistry, Surfactants

Eutrophication is an ongoing global problem and agriculture is an important non-point source of nutrient loading. Specifically, nitrogen (N) and phosphorus (P) losses from agricultural landscapes continue to drive water quality issues. In southern Ontario, agriculture has intensified in recent decades, with major expansions of cash crop production and extensive tile drainage (TD). Through intensive monitoring of 12 tile outlets draining operational fields under the conventional corn-soybean-wheat rotation, this study examined differences in measured and volume-weighted total P, total N, and nitrate-N concentrations and loads over 28 months (October 2020- April 2023) amongst crop covers and between growing (GS; May – September) and non-growing seasons (NGS; October – April). Nitrogen concentrations (i.e., TN and NO3-N) in TD eluent were consistently high both between seasons and were found to be significantly highest from winter wheat (WW) fields in the NGS, and corn fields in the GS. Volume-weighted TP concentrations were not significantly different either amongst crop covers or between seasons, although TP losses tended to be highest from the cover crop (CC) fields in the NGS. Differences in N and P losses between years and amongst crop covers were attributed to differences in legacy soil nutrients, the establishment and decomposition of over-winter cover crops, and physical soil properties. The results of this study can inform agricultural management by addressing the urgent need for improved information around the relationship between agricultural practices and nutrient losses, especially in the NGS.

Author Keywords: Best management practices, Crop rotation, Over-winter cover crops, Seasonality, Tile drainage, Water quality

Glyphosate burndown and tillage, followed by the cultivation of cash crops, are frequently used techniques in LUC from perennial cropping systems (PS) to annual cropping systems (AS). Agricultural LUC can result in the loss of soil nitrogen (N) via emission of nitrous oxide (N2O), a potent greenhouse gas (GHG). The purpose of this thesis is to investigate the short-term impacts of agricultural LUC from PS to AS on soil health parameters and the nitrogen (N)-cycling bacterial communities responsible for nitrification and denitrification processes that result in the emission of N2O. The study field site was in Stone Mills, Ontario and comprised of four fields: two annual cropping systems were regularly cultivated for cash crops (AS), and two perennial cropping systems had not been cultivated for cash crops for over 50 years (PS). One PS was left intact while the other PS was subjected to LUC (converted system [CS]) from PS to AS within the study period. The results of this study indicate that PS promotes soil health, as illustrated through higher soil organic matter % (2.3 ± 0.2 %), beta-glucosidase activity (0.41 ± 0.04 mmol g-1 dry soil h-1), and N-acetylglucosaminidase activity (0.18 ± 0.03 mmol g-1 dry soil h-1). The PS soils exhibited higher nitrifier (6.0  0.3 log10 copies per g dry soil) and denitrifier (nirS, nirK and nosZI: 7.8  0.05, 8.1  0.1 and 5.0  0.1 log10 copies per g dry soil, respectively) gene abundances compared to AS (amoA, nirS, nirK and nosZI: 5.7  0.1, 7.7  0.04, 7.9  0.1 and 4.8  0.1 log10 copies per g dry soil, respectively). Moreover, LUC from PS to AS deteriorated soil health parameters and significantly decreased the nosZI/16S rRNA gene ratio, leading to potential N loss through N2O emissions. A laboratory incubation study revealed that the use of N-containing fertilizer in conjunction with easily metabolized C cumulatively resulted in 64.2% increase in N2O and 42.1% increase in CO2 fluxes in AS soils compared to PS soils. The AS soils also produced 69.8% more N2O and 13.4% more CO2 when compared to CS soils. The results suggest that the availability of C and N promote R-strategists, leading to increased production of CO2 and N2O. Additionally, results also suggest that LUC mediates fluxes depending on resource availability. The findings of this research demonstrate the significance of LUC in shaping N-cycling microbial communities and GHG emissions, emphasizing the importance of transitioning towards less intensive management practices to ensure the long-term sustainability of the agri-food system.

Author Keywords: annual, denitrification, greenhouse gas, laboratory incubation, nitrification, perennial

Forests play a critical role in the global carbon cycle, acting as carbon sinks that remove and store an estimated 0.4 to 4.1 Pg of atmospheric carbon annually. However, historical acid deposition and timber harvesting have disrupted nutrient cycles, leading to nutrient-deficient soils that hinder tree growth, particularly for sugar maple (Acer saccharum), a keystone species in Ontario sensitive to soil acidity and calcium (Ca) depletion. This study evaluates the effects of non-industrial wood ash (NIWA) applied at 0, 2, 4, 6, and 12 Mg ha-1 on soil chemistry, nutrient concentrations, microbial activity, CO2 fluxes, and sugar maple growth over two years. NIWA increased soil pH and exchangeable base cations, especially in the organic horizon, with some increase in forest floor metals, though foliar levels remained safe. Enzyme activity responses were minimal, and fine root biomass declined at higher doses. Soil CO₂ fluxes rose sharply at 12 Mg ha⁻¹, suggesting pH-driven effects. NIWA improves soil chemistry, but long-term impacts remain uncertain.

Author Keywords: carbon flux, extracellular soil enzyme, non-industrial wood ash, sugar maple

Agricultural and urban land uses have been linked to the recent resurgence of eutrophication and salinization issues in the lower Great Lakes. This thesis examined the relationship between watershed land use and stream nitrate-nitrogen (NO3-N), total phosphorus (TP), and chloride (Cl) concentrations across southern Ontario. Using a self-organizing map analysis, the watersheds were classified into eight distinct spatial clusters, representing four agricultural, two urban, and two natural clusters. Agricultural clusters under intensive row crop agriculture exhibited NO3-N and TP concentrations up to twelve and five times higher, respectively, than the most natural-dominated cluster. Urban clusters had Cl concentrations up to nine times greater than the natural-dominated clusters. Three agricultural land use practices, namely continuous corn-soybean rotation, synthetic fertilizer application, and tile drainage, were positively correlated with stream NO3-N concentrations, whereas Cl concentrations increased with urban area and human population density. This thesis also characterized sampling trends of the provincial stream water quality monitoring program and found that sampling frequency has declined since the mid-1990s, while current sites are monitored almost exclusively during the ice-free period. Sampling year-round is critical to capture seasonal variations in NO3-N and Cl, while sampling across a full range of flow conditions is important for describing TP. Exclusion of sampling sites in close proximity of downstream municipal wastewater treatment plants and greenhouses can help isolate and better understand water quality impacts of non-point sources. Although intensive agricultural watersheds in southwestern Ontario draining into Lake Erie remain a priority for research and management, regions experiencing row crop expansion such as along the northern shore of Lake Ontario as well as rapidly urbanizing areas require further attention as these land use shifts will likely increase stream NO3-N and Cl concentrations, placing further pressure on water resources in the lower Great Lakes.

Author Keywords: Chloride, Nitrogen, Phosphorus, Self-organizing map, Southern Ontario, Water quality

Diversified agroecosystems supporting greater genetic, structural, and functional diversity improve soil health and ecosystem function. However, there is limited understanding of how multiple forms of diversification, such as mixing cover crop species and adding arbuscular mycorrhizal fungi (AMF), alter belowground carbon supply to soil. In a controlled environment experiment using rhizoboxes, I investigated the belowgound response of cover crops – red clover (Trifolium pratense) and barley (Hordeum vulgare) – grown in monoculture or mixture, with and without AMF inoculation. Root morphological and mycorrhizal traits that characterize the hypothesized root economics spectrum (RES) were integrated with novel sampling of dissoved organic carbon fluxes and easily extractable glomlin in rhizosphere soil. Results revealed species-specific shifts on the RES suggesting that diversification through species mixing and AMF additions can alter belowground carbon allocation pathways, with potential implacations for plant performance and soil carbon stabilization in agroecosystems.

Author Keywords: Arbuscular mycorrhizal fungi, carbon sequestration, cover crops

In Ontario, farmers commonly use a MZ (Maize (Zea mays L.))-SB (Soybean (Glycine max))/WW (Winter wheat (Triticum aestivum)) – CC (mixed cover crop) rotation to maximize economic benefits. This study aimed to investigate the short-term impacts of the crop rotation phases and their associated management practices in this diversified cash crop rotation on soil health and the abundance of nitrogen (N)-cycling soil microbial communities (SMCs). Additionally, the abundance of N-cycling SMCs and plant-available N in both surface (0-5 cm) and rooting zone (5-15 cm) depths were characterized in tile-drained (TD) and non-TD fields. In the present study, soils collected under the CC phase had the highest labile carbon levels (10-17% higher) and water-stable aggregates (35-50% higher) compared to the other two crop phases. Lower nitrifying (amoA) gene abundances and soil NO3--N levels were observed in the CC phase compared to the MZ and SB-WW phases, suggesting a potential for decreased nitrification in the CC phase. The presence of SB potentially influenced the soil N concentration in the subsequent WW phase likely due to the release of symbiotically fixed N in the SB-WW phase. Further, higher amoA abundances and NO3--N in the SB-WW phase imply a potential for increased nitrification in the SB-WW phase. Additionally, higher amoA/nosZI and nirS+nirK/nosZI ratios were observed in the MZ phase than in SB-WW and CC phases, suggesting a potential capacity for increased N2O emissions from the reactions mediated by N-cycling SMCs in soils planted to MZ during fall sampling days. In the TD and NTD field study, higher NO3--N levels were observed in TD-SB-WW fields at 5-15 cm vs. 0-5 cm depths, which was possibly facilitated by tile drainage. The TD-CC fields displayed higher nosZI gene abundances and lower nirS+nirK/nosZI abundance ratios, suggesting a greater potential capacity for decreased N2O emissions in soils planted to CCs during the spring sampling days. When examining changes in plant available N by soil depth, reduced downward movement of NO3- through shallow soil depths (0-15 cm depth) was observed in the CC phase compared to cash crops. This short-term study highlights the potential contribution of the CC phase, particularly within TD agricultural fields, for improving soil health and reducing potential N2O emissions. Together, these results suggest that management-associated differences in crop rotation phases have temporary effects on soil health and the abundance of SMCs. Future studies linking N-cycling SMC's potential activity and field-scale N2O fluxes will provide a better insight into the longer-term sustainability of Ontario's cash crop management systems.

Author Keywords: denitrification, maize-soybean-winter wheat- cover crop rotation, nitrification, soil depth, Sustainable agriculture, tile-drainage

Eutrophication is an ongoing global problem and agriculture is an important non-point source of nutrient loading. Specifically, nitrogen (N) and phosphorus (P) losses from agricultural landscapes continue to drive water quality issues. In southern Ontario, agriculture has intensified in recent decades, with major expansions of cash crop production and extensive tile drainage (TD). Through intensive monitoring of 12 tile outlets draining operational fields under the conventional corn-soybean-wheat rotation, this study examined differences in measured and volume-weighted total P, total N, and nitrate-N concentrations and loads over 28 months (October 2020- April 2023) amongst crop covers and between growing (GS; May – September) and non-growing seasons (NGS; October – April). Nitrogen concentrations (i.e., TN and NO3-N) in TD eluent were consistently high both between seasons and were found to be significantly highest from winter wheat (WW) fields in the NGS, and corn fields in the GS. Volume-weighted TP concentrations were not significantly different either amongst crop covers or between seasons, although TP losses tended to be highest from the cover crop (CC) fields in the NGS. Differences in N and P losses between years and amongst crop covers were attributed to differences in legacy soil nutrients, the establishment and decomposition of over-winter cover crops, and physical soil properties. The results of this study can inform agricultural management by addressing the urgent need for improved information around the relationship between agricultural practices and nutrient losses, especially in the NGS.

Author Keywords: Best management practices, Crop rotation, Over-winter cover crops, Seasonality, Tile drainage, Water quality

Glyphosate burndown and tillage, followed by the cultivation of cash crops, are frequently used techniques in LUC from perennial cropping systems (PS) to annual cropping systems (AS). Agricultural LUC can result in the loss of soil nitrogen (N) via emission of nitrous oxide (N2O), a potent greenhouse gas (GHG). The purpose of this thesis is to investigate the short-term impacts of agricultural LUC from PS to AS on soil health parameters and the nitrogen (N)-cycling bacterial communities responsible for nitrification and denitrification processes that result in the emission of N2O. The study field site was in Stone Mills, Ontario and comprised of four fields: two annual cropping systems were regularly cultivated for cash crops (AS), and two perennial cropping systems had not been cultivated for cash crops for over 50 years (PS). One PS was left intact while the other PS was subjected to LUC (converted system [CS]) from PS to AS within the study period. The results of this study indicate that PS promotes soil health, as illustrated through higher soil organic matter % (2.3 ± 0.2 %), beta-glucosidase activity (0.41 ± 0.04 mmol g-1 dry soil h-1), and N-acetylglucosaminidase activity (0.18 ± 0.03 mmol g-1 dry soil h-1). The PS soils exhibited higher nitrifier (6.0  0.3 log10 copies per g dry soil) and denitrifier (nirS, nirK and nosZI: 7.8  0.05, 8.1  0.1 and 5.0  0.1 log10 copies per g dry soil, respectively) gene abundances compared to AS (amoA, nirS, nirK and nosZI: 5.7  0.1, 7.7  0.04, 7.9  0.1 and 4.8  0.1 log10 copies per g dry soil, respectively). Moreover, LUC from PS to AS deteriorated soil health parameters and significantly decreased the nosZI/16S rRNA gene ratio, leading to potential N loss through N2O emissions. A laboratory incubation study revealed that the use of N-containing fertilizer in conjunction with easily metabolized C cumulatively resulted in 64.2% increase in N2O and 42.1% increase in CO2 fluxes in AS soils compared to PS soils. The AS soils also produced 69.8% more N2O and 13.4% more CO2 when compared to CS soils. The results suggest that the availability of C and N promote R-strategists, leading to increased production of CO2 and N2O. Additionally, results also suggest that LUC mediates fluxes depending on resource availability. The findings of this research demonstrate the significance of LUC in shaping N-cycling microbial communities and GHG emissions, emphasizing the importance of transitioning towards less intensive management practices to ensure the long-term sustainability of the agri-food system.

Author Keywords: annual, denitrification, greenhouse gas, laboratory incubation, nitrification, perennial