Eimers, Catherine

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

A meta-analysis revealed that while there is often a greater degree of contamination of soils and sediments with metals, contamination by mercury (Hg) is a large concern owing to its toxicity at low concentrations. The case study in Guyana characterized Hg and concentrations of other metals (As, Cd, Co, Cu, Mn, Ni, Pb, and Zn) in soil and sediment within gold mined areas. Metal concentrations were low in soil and sediment of sampled gold mines, while the concentrations of Hg were much higher in soil and sediment and contamination was not localized to the mine site. Moss bags and Hg passive air samplers (MerPAS) were deployed to measure atmospheric Hg around a gold mine in Mahdia, Guyana over a 90-day period as well as a 2-day period that encompassed a periodic burn (typically 2-hr). Mercury in moss and MerPAS were positively correlated over both deployment periods, but Hg concentrations measured during the 2-day event were several-fold higher in both moss and MerPAS compared with the 90-day exposure demonstrating that most of the Hg sorbed to both moss and passive samplers is lost during periods of inactivity. Using the 2-day deployment as a conservative estimate of atmospheric Hg exposure, Hg air concentrations around the burning station exceeded 100,000 ng m-3 averaged over a 48-hr period, and moss Hg concentrations were greater than 250,000 ng g-1 around the burning station, although Hg concentrations in both media decreased rapidly with distance. Mercury concentration in soil and sediment was strongly related to organic matter content, which tended to be higher away from the mine site. These controls of organic matter (carbon; C) cycling on Hg distribution and movement are clear at sites exposed to high atmospheric Hg and exist at the global scale, although Hg:C ratios in environmental media are greatly elevated at the gold mine site compared with the global average. Locally sourced biochar did not sufficiently improve physical properties (porosity) in overburden soil, which showed the worse plant response, possibly due to the high clay content that contributes to the "baked" condition of these soils and restrict root growth.

Author Keywords: Biochar, Environmental contamination, Gold mining, Mercury, Metals, Organic matter

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

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

The accelerated recovery of base-poor soils from the legacy effects of acidic deposition may be possible by applying industrial wood ash as a soil amendment. Wood ash may be an effective soil amendment due to its high alkalinity and concentrations of several essential nutrients, such as calcium, magnesium, potassium, and phosphorus, that are retained after the volatilization of the parent material. However, wood ash can also contain trace amounts of metals that could be released into the soil and soil solution. The short-term (<3 years) biogeochemical response of soils, microbial communities, and sugar maple (Acer saccharum Marsh.) trees were assessed following wood ash application at Porridge Lake, Ontario. The study design consisted of five blocks containing three treatment plots each (2.5, 5.0, 7.5 Mg ha-1) and a control. Soil solution pH, base cation, and trace metal concentrations were monitored for three years, using tension lysimeters at depths of 30 and 60 cm and zero-tension lysimeters for forest floor percolate within each plot. In the last year of the trial, soil, foliage, and fine root samples were collected and analyzed for trace elements. Also, soil samples were analyzed for the abundance of 16S and ITS DNA through metabarcoding to ascertain the microbial response to wood ash. Significant changes in soil solution pH were measured within the forest floor horizon in the first year of the trial. Significant increases in calcium (Ca), magnesium (Mg) and calcium/aluminum (Ca/Al) ratios were also observed in the second year of the trial, along with decreases in dissolved organic carbon (DOC), sulphate (SO4) and nitrate (NO3) in the LFH horizon. By the third year of the trial, significant increases in soil solution pH and potassium (K) concentrations and decreases in Al were observed to a depth of 30 cm. Changes in trace metal concentrations in soil water were notably variable, with concentrations of chromium, copper, lead, nickel, and selenium remaining unresponsive, whereas concentrations of cadmium, manganese and zinc decreased by the third year. The metalloid arsenic showed a significant increase in the third year of the trial but remained below regulatory guidelines, similar to all other trace metals. Soil measurements conducted in the third year of the trial showed positive pH responses in the FH horizon and increases in Ca and Mg in the Ah and Bm soil horizons, but foliar base cation and metal concentrations were unchanged. Diversity analysis on the soil prokaryotic and eukaryotic groups indicated increased bacterial alpha diversity in the FH horizon and bacterial dominance in the litter horizon. Analysis of relative abundance at the phylum level for prokaryotes and at the order for eukaryotes did not indicate any compositional shifts due to the wood ash treatments. Changes in the length and diameter of sugar maple and mycorrhizal fine root may point to pH shock being an issue at higher ash doses. The results from this study indicate that wood ash has a strong ameliorative effect on soil properties and does not pose a risk to soil communities. 

Author Keywords: DNA, mycorrhizae, soil acidication, soil amendments, soil solution, sugar maple

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

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