Environmental and Life Sciences

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by progressive loss in function of motor neurons. Elevated levels of biologically important metal ions, such as copper (II) (Cu(II)), zinc (II) (Zn(II)) or iron (III) (Fe(III)), may contribute to the disease. Moreover, Cu(II) interactions with other proteins associated with ALS have been investigated; however, the effects of metallation on TAR DNA-binding protein of 43 kDa (TDP-43) are less known. The aim of the thesis was to evaluate interactions between full-length TDP-43 and metal ions, and gain insight into the mechanisms of these interactions. In Chapter 2, electrochemical methods were used to evaluate the coordination of Cu(II) ions to immobilized TDP-43. Cu(II)-TDP-43 binding was favourable at a neutral pH. Surface characterization confirmed protein immobilization and Cu(II)-TDP-43 coordination. Competitive Zn(II) ion binding studies revealed Zn(II) increases Cu(II) binding. In Chapter 3, Fe(III) ion binding studies revealed that Fe(III) reduces Cu(II) binding when co-exposed to the TDP-43-Au surface. Data shows significant uptake of Cu(II) by TDP-43 protein which may have important implications in normal and diseased states of TDP-43, indicating surface bioelectrochemistry is a viable tool for fundamental exploration of proteins and metals, and their interactions, as they inform disease mechanisms, disease detection and drug screening.

Author Keywords: Amyotrophic Lateral Sclerosis, bioelectrochemistry, electrochemistry, metalloprotein, surface characterization, TDP-43

Nutrient losses from forest soils caused by decades of acid deposition and intensive tree harvesting have affected tree growth and forest health in North America and Europe. Non-industrial wood ash (NIWA), a substance rich in macronutrients, may be a potential remediation strategy to return lost nutrients to forest. However, the chemical composition of NIWA and its effects on soil and tree growth are poorly understood. This thesis evaluated the chemical variability of non-industrial wood ash, and its short-term effects on soil properties, sugar maple (Acer saccharum) foliar chemistry, tree growth, and understory vegetation community composition at three sugar bushes in Muskoka, Ontario. The chemical analysis of NIWA samples obtained from the residents of Muskoka, showed that NIWA contains high levels of macro nutrients such as calcium, magnesium, and potassium and contains relatively low concentrations of trace metals. Ash mixtures amalgamated in the field were relatively homogenous in their chemical composition and metal concentrations were generally below Ontario NASM regulation guidelines for land application. Concentrations of copper and zinc exceeded CM1 guidelines, however, were always below restricted metals land application limits (CM2). Ten months after NIWA application to three sugar bush sites, soil pH and exchangeable base cations increased significantly in the litter and FH horizons at all treatment plots compared with control plots. Few treatment effects were recorded for the surface (0 – 10 cm) mineral horizon, with only potassium increasing in mineral soil at all three study sites. Elevated concentrations of most metals and metalloids (aluminum (Al), boron (B), cadmium (Cd), copper (Cu), Iron (Fe), manganese (Mn), nickel (Ni), lead (Pb), zinc (Zn)) were recorded in soil at all treatment plots, however these effects were generally restricted to the litter horizon. Diagnosis and recommendation integrated system analysis (DRIS) conducted on the sugar maple foliage indicated that potassium was the most limiting nutrient at all three study sites, and significant increases were recorded in foliar potassium concentrations ten months after ash application in sapling and mature trees at all treatment plots. Increases in foliar calcium and magnesium concentrations were small and variable amongst the study sites. No significant treatment effects of NIWA application were observed on sugar maple tree growth two years after ash application, while changes in understory composition were generally limited, but these also varied among sites.

Author Keywords: Acer saccharum, Base cations, Calcium decline, Forest soil amendment, non-industrial wood ash, Trace metals

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

This study reports on as series of laboratory wind tunnel experiments aimed at furtheringour understanding of aggregate breakdown and dust release during aeolian transport, and thereby, has implications for air quality and the management of dust emission through water application. Particles aggregates 500 um in diameter were formed and isolated by the wetting, drying, and screening of playa sediments collected from Owens Lake. They were then released into a boundary-layer flow within the Trent Environmental Wind Tunnel (TEWT), whereupon they either slid, rolled and/or saltated downwind. The concentration of PM10 and the particle size of the aggregates were monitored throughout each test along the central axis of the tunnel. The results confirm that aggregate breakdown did occur, resulting in the production and emission of dust. The relative efficiency of aggregate abrasion in the production of silt sized particles during aeolian transport was calculated using normalized indices, providing a starting point for the modelling of similar systems in a natural setting. The results indicate that for every metre of transport, the abrasion of a 500 um aggregate formed from playa sediment may release a volume of dust roughly equivalent to that of a single silt particle that is 60 um diameter. Conversely, aggregate formation is found to produce 1-4% of dust as compared to an equivalent volume of disaggregated silt when exposed to a given airflow above the threshold for saltation.

Author Keywords: Aeolian abrasion, Aggregate breakdown, Owens Lake, PM10, Saltation, Wind Tunnel

Migratory fish can influence the rivers where they spawn by depositing nutrients and organic matter which increase primary and secondary production. Past research in the Laurentian Great Lakes has focused on individual tributaries, accordingly, the spatial extent of subsidies and how environmental factors influence subsidies are not clear. To determine which tributaries received subsidies, I compared stable carbon isotope values (δ13C) of resident stream fishes above and below 54 barriers in 37 tributaries. Subsidies were found in found across 43 of the barriers. The subsidy magnitude varied among the lakes, with Lake Superior having significantly larger subsidies. Correspondence analysis of environmental factors showed that large differences in δ13C were associated with steeper river channels on the Canadian Shield with little agricultural land-use. Migratory fish supply resource subsidies to rivers across the Great Lakes basin, though their magnitude is contextually dependent.

Author Keywords: barriers, Great Lakes, migratory fish, resident stream fish, resource subsidies, stable isotopes

Mineral feedstocks, including alkaline mine wastes, can sequester CO2 as a dissolved phase (e.g., HCO3-) or a solid carbonate via enhanced rock weathering (ERW). For this thesis, the release of easily accessible Ca and Mg from non-carbonate sources was determined for kimberlite residues from several diamond mines and commonly proposed ERW rock types, including wollastonite and olivine. Batch leaches determined the CO2 sequestration potentials of kimberlites to be in the range of 3–12 kg CO2/t, which was exceeded by most ERW feedstocks. Leaches also assessed the release of Ni and Cr, elements of concern in ERW settings, and P and K, which benefit agricultural soils. Year-long leaching columns were deployed using kimberlite from the Gahcho Kué and Venetia diamond mines, wollastonite skarn, and olivine sand from the initial assessment. The kimberlite residues sequestered 0.03 kg CO2/t as dissolved inorganic carbon and 0.6 kg CO2/t as solid total inorganic carbon. Weathering of wollastonite skarn resulted in CO2 removal rates via mineral trapping of CO2 of 6.31 kg CO2/t, while the olivine sand yielded rates of 0.5 kg CO2/t via solubility trapping. Both methodologies used in this study demonstrated value in the prediction and monitoring of drainage chemistry as it relates to ERW and CO2 mineralization. Implementation of these strategies can progress ERW efforts by providing confidence in feedstock selection and the verification of carbon offsets.

Author Keywords: CO2 mineralization, Drainage chemistry, Enhanced weathering, Mine wastes, Mineral trapping, Solubility trapping

Mining and smelting degraded landscapes are characterised by heavily eroded soils that are acidic, contaminated with toxic metals, and depleted of essential nutrients. Regreening degraded landscapes has been proposed to support global carbon (C) mitigation measures and protect biodiversity. One of the world's largest regreening programs in the City of Greater Sudbury, Canada has been ongoing since 1978 and involves liming and fertilizing selected areas followed by planting primarily jack pine (Pinus banksiana Lamb.) and red pine (Pinus resinosa Ait.) trees. The main objective of this thesis was to improve our understanding of biogeochemistry in the City of Greater Sudbury regreened forests, and to determine how nutrient pools and cycling change as stands age. I established a chronosequence of forested sites between 15–40 years-old and to account for the effects of erosion, each site was categorized as "stable" (<10% bedrock cover) or "eroded" (>30% bedrock cover). Individual tree growth and nutrient accumulation in aboveground biomass (AGB) did not differ between stable and eroded sites and were comparable to rates reported from pine plantations in similar ecozones. Aboveground nitrogen (N) pools were six times larger than N applied in fertilizer, suggesting N limitation is most likely not a concern. Rates of C cycling were generally similar to those measured at unimpacted jack and red pine plantations. The exception being a decrease in mineral soil and aggregate C concentrations. However, at the ecosystem-scale the loss of soil C is trivial in comparison to increases in AGB C pools, leading to an overall increase in total ecosystem C following regreening (550,547 Mg in aboveground C across the 19,649 ha regreening landscape). Litter decomposition rates were higher at the regreening sites using a site-specific litter compared to a general common litter, indicating a home-field advantage for local decomposers. Soil temperature varied at the regreening sites and higher soil temperatures were related to higher rates of soil respiration. The regreening sites are rich in calcium (Ca) and magnesium (Mg); and while soils were generally poor in phosphorous (P) and potassium (K), foliar concentrations of P and K were comparable to those of "healthy" red pines. Overall, the regreening program appears to have increased tree growth and produced jack and red pine plantations that are biogeochemically similar to conifer plantations unimpacted by over a century of mining and smelting impacts.

Author Keywords: biogeochemistry, degraded landscape, forests, nutrient cycling, regreening, soil carbon

A significant portion (15-20%) of mercury (Hg) in the Arctic Ocean is believed to originate from Arctic rivers, such as the Mackenzie River watershed in the NWT. Recent (2005- 2020) Hg monitoring data of freshwater and fish tissue and environmental model outputs were compiled and used to develop a Bayesian Network Relative Risk model (BN-RRM), a probabilistic model capable of analyzing causal relationships. The objectives of the model were to estimate the risk posed to fish health and the subsequent dietary Hg-exposure to humans; to compare the relative risks between regions of the watershed; and to identify the influential Hg sources. The output of the BN-RRMs differed significantly throughout the watershed, with atmospheric Hg deposition and soil erosion Hg release consistently flagged as important explanatory variables. Analysis of the endpoint uncertainties revealed gaps in knowledge and in Hg datasets, which should be the focus of study for future monitoring programs.

Author Keywords: Aquatic Ecosystems, Arctic, Bayesian Network, Mercury, Risk Assessment, Toxicology

Understanding snowpack variability is important as it plays an imperative role in environmental, hydrologic, and atmospheric systems. Research questions related to three linked areas were investigated in this thesis: 1) scaling issues in snow hydrology, 2) forest-snowpack relationships, and 3) methods of integrating snow water equivalent (SWE) into a hydrologic model for a large, forested drainage basin in central Ontario. The first study evaluated differences in SWE across process, measurement, and model scales. Point scale snowpack measurements could be bias corrected using scaling factors derived from a limited number of transect measurements and appropriately stratified point scale measurements may be suitable for replacing transect scale mean SWE when transect data are not possible to collect. Comparison of modelled products to measurements highlighted the importance of understanding the spatial representativeness of in-situ measurements and the processes those measurements represent when validating snow products or assimilating data into models.The second study investigated the efficacy of field-based, and remotely sensed datasets to describe forest structure and resolve forest-snowpack relationships. Canopy cover was highly correlated with melt rate and timing at the site scale however, significant correlations were present in 2016 but not 2017, which was attributed to interannual differences in climate. Peak SWE metrics did not correlate well with forest metrics. This was likely due to mid-winter melt events throughout both study years, where a mix of accumulation and melt processes confounded forest-snowpack relationships. The third study evaluated the accuracy of the Copernicus SWE product and assessed the impact of calibrating and assimilating SWE data on model performance. The bias corrected Copernicus product agreed with measured data and provided a good estimate of mean basin SWE. Calibration of a hydrologic model to subbasin SWE substantially improved modelled SWE performance. Modelled SWE skill was not improved by assimilating SWE into the calibrated model. All models evaluated had similar streamflow performance, indicating streamflow in the study basin can be accurately estimated using a model with a poor representation of SWE. The findings from this work improved knowledge and understanding of snow processes in the hydrologically significant Great Lakes-St Lawrence Forest region of central Ontario.

Author Keywords: data assimilation, hydrologic model, multi-objective calibration, remote sensing, scale, snow

Cytokinins (CKs) are a pervasive group of growth-promoting signaling molecules spanning every kingdom of life. Their roles are best known in plants, where they act as phytohormones controlling nearly all aspects of plant growth and development. CKs continue to be detected in new organisms, posing questions about their roles in such widespread forms of life. The research presented in this thesis, therefore, investigated CK dynamics in a non-plant system using the simple eukaryotic model, Dictyostelium discoideum. Prior to this thesis, CKs were established as key intercellular signals necessary for proper development of D. discoideum – specifically in the induction of sporulation and maintenance of spore dormancy. However, there were no documented roles of CKs prior to the late stages of multicellular development. Comprehensive mass spectrometric screening for CKs detected six novel CK forms during all stages of D. discoideum growth and development. Based on these findings, a model was proposed that mapped CK biosynthesis in D. discoideum. The CK profiles indicate that there are differing dominant CK forms during vegetative growth and early development compared to those detected during late multicellular development. This led to the hypothesis that CKs have different roles during the distinctive life cycle stages of D. discoideum. This hypothesis was tested by generating knockout and overexpression strains of the key, primary CK biosynthesis gene, iptA, to investigate potential expanded roles for CKs during growth and the early stages of D. discoideum development. iptA-deficiency resulted in cytokinesis defects and both iptA-deficiency and overexpression caused altered mitochondrial morphology, dysregulated TCA cycle and amino acid metabolism, as well as increased levels of the energy metabolite, AMP. These combined phenotypes were suggestive of mitochondrial-associated dysfunction in vegetative growth and provided the first evidence of expanded roles of CKs during the D. discoideum life cycle. This was the first metabolomics-based evidence of CKs influencing mitochondrial function in D. discoideum. Lastly, a key CK-activating enzyme was functionally characterized, DdLOG, and additional CK biosynthesis enzymes were identified for future examination. Together, the findings of this thesis provide insights into: CK biosynthesis in a non-plant associated model; new roles for CKs during the D. discoideum life cycle; and CK interactions with mitochondria. The methods established as part of this thesis can be used as a foundation for characterizing further CK biosynthesis enzymes and as a guide for detecting subtle sub-cellular phenotypes related to CK metabolism in D. discoideum and other CK-producing organisms.

Author Keywords: cytokinin biosynthesis, cytokinins, Dictyostelium discoideum, IptA, mass spectrometry, mitochondria