Environmental and Life Sciences

Chromophoric dissolved organic matter (CDOM), a chemically diverse family of organic compounds defined by their ability to absorb ultraviolet and visible light, is a critical constituent of numerous environmental systems, including freshwater lakes. Industrial operations in the Athabasca Oil Sands Region (AOSR, Alberta, Canada) are major sources of acidic inorganic gases and organic contaminants to the atmosphere, the subsequent deposition of which posed the potential to alter the composition of natural CDOM within surrounding lake surface-waters. The objective of this thesis was to determine if OS sources measurably impacted CDOM quality within 50 regionally monitored acid sensitive lakes by means of a) altered acid-base chemical processes or b) industrial atmospheric CDOM inputs. Ultraviolet-visible light spectroscopy and excitation emission matrix (EEM) fluorescence spectroscopy were applied to characterize CDOM within regional lake surface-waters to identify the primary sources (e.g., natural, anthropogenic) and process (e.g., acid-base chemistry) influencing chromophoric organic matter quality. These spectroscopic techniques were further used to evaluate industrial CDOM within atmospheric aerosols and deposition to assist with the identification of industrial CDOM within lake waters. Spectroscopic analysis of regional lake surface-water found weak associations between CDOM and acid-base variables, suggesting that acid inputs from OS sources would have limited influence over surface-water chromophoric organic matter. A distinct fluorescent component (i.e., fluorophore) measured within the lake samples (C3) displayed decreasing emission intensity as a function of distance from OS sources and positive correlations with surface-water polycyclic aromatic compounds, implying industrial influence. Spectral similarity between C3 and industrial fluorophores observed from regional aerosol and atmospheric deposition samples further confirmed the lake fluorophore was linked to OS sources. This research suggests that EEM fluorescence spectroscopy could be used as a cost-effective technique to detect industrial pollution within lake surface-waters throughout the AOSR.

Author Keywords: atmospheric brown carbon, atmospheric deposition, atmospheric pollution, dissolved organic matter, fluorescence spectroscopy, lake chemistry

Decades of sulphur and nitrogen deposition acidified forest ecosystems across northeastern North America causing declines in pH and exchangeable base cation concentrations, negatively affecting biota. To assist natural recovery, researchers are investigating using alkaline soil amendments such as wood ash. However, much remains unknown about its use. This thesis evaluated the effects of non-industrial wood ash application (between 0 – 12 Mg ha-1) on soil chemistry, understory vascular plant communities and sugar maple (Acer saccharum Marsh.) regeneration in central Ontario. Wood ash increased soil pH and concentrations of calcium, magnesium and several metals. Vascular plant species abundance, richness, and diversity exhibited no consistent treatment effect. Sugar maple seedling survivorship was adversely affected by wood ash applications > 4 Mg ha-1, while growth was unaffected. These results support related research regarding the ability for wood ash to increase soil pH and base cation status but raises uncertainty regarding consequences for vascular plants.

Author Keywords: Acer saccharum, Acid deposition, Ecosystem regeneration, Soil amendment, Understory vegetation, Wood ash

Measuring biodiversity has become increasingly complex as biologists and ecologists have gradually learned more about how biotic systems are structured and interact. Given the wide range of tools, techniques and approaches now in use to quantify biological diversity, it is useful to consider different "dimensions of diversity" to classify these measurements and provide context for their interpretation. Even within the genetic dimension of diversity alone, recent improvements in theory, technology, and statistics has generated several approaches which can provide distinct insights into natural systems. In this thesis, I use multiple "axes of diversity" to subdivide the dimension of genetic diversity to better understand a complex ecological system - the unisexual Ambystoma complex on Pelee Island, Ontario. By focusing on the genomotype axis, I found that the composition of local unisexual Ambystoma assemblages generally reflects the current relative abundance of the local sexual host populations. This suggests that sexual hosts can be thought of as a keystone species for the complex not only because they are required for unisexual Ambystoma to reproduce, but also because their relative abundance governs the composition of entire unisexual Ambystoma assemblages. Comparatively, when assessing the lineage axis of genetic diversity, unisexual Ambystoma assemblage diversity patterns primarily reflected historic landscape structure, and spatial patterns of increased lineage richness were linked to areas where both potential hosts were locally available (currently or historically). Thus, while both of the investigated axes of diversity are forms of genetic diversity, each revealed distinct factors that have shaped contemporary diversity patterns across the landscape operating at different spatial and temporal scales. Critically, our understanding of complex ecological systems is likely to be broadened by including additional axes of diversity (e.g., allelic, loci, or chromosomal structure axes), and such investigations are not limited to clonal hybrid systems. Overall, this work illustrates the importance of combining insights from distinct conceptual and analytical toolkits to generate a comprehensive understanding of the factors which have shaped the patterns of diversity we observe today.

Author Keywords: Biological diversity, Dimensions of diversity, Ecological genetics, Metacommunity ecology, Unisexual Ambystoma

Frog virus 3 (FV3) belongs to the genus Ranavirus within the Iridoviridae family.Its 105,903 base genome encodes 98 open reading frames (ORFs), including ORF 97R, a putative apoptosis regulator sharing 31% structural similarity with the anti-apoptotic Bcl- 2 family protein, myeloid cell leukemia 1 (Mcl-1). 97R contains a BH1 domain, implicated in apoptosis regulation, and a predicted C-terminal transmembrane domain, which acts as a membrane-anchoring domain, localizing 97R to the ER membrane. To study its role in host cell modulation, 97R was cloned into a vector and transfected into HeLa cells. Immunofluorescence revealed a time-dependent decrease in Protein Disulfide Isomerase (PDI) in 97R-transfected cells. Immunoprecipitation and western blotting revealed that 97R interacts with Prohibitin 1 (PHB1), a host protein involved in apoptosis regulation. This research provides insight into the novel functional role of 97R in host cells, enhancing our understanding of how FV3 may manipulate its host.

Author Keywords: Bcl-2 protein family, frog virus 3, Iridoviridae, ORF 97R, Protein-protein interactions, Ranavirus

Wildlife translocation programs are widely employed as a strategy to reintroduce extirpated species into regions they once inhabited but no longer do. Reintroduction programs can be successful at re-establishing extirpated populations and also provide unique opportunities to study post-reintroduction population dynamics and behavioural ecology. The wild turkey (Meleagris gallopavo) is a forest generalist species that, prior to European colonization, inhabited much of the Carolinian zone in Ontario. This species was hunted to extirpation in the early 1900's and reintroduced in the mid-1980's through a series of wildlife trade agreements and coordinated trap and transfer efforts. Ontario's contemporary populations are seemingly thriving, with wild turkey harvest permitted in many regions of the province. However, given this species history of extirpation, understanding the size, distribution, and behavioural ecology of Ontario's reintroduced population of wild turkeys is essential to their long-term persistence in the province. We captured and radio-tagged 77 wild turkeys over four years in Peterborough, Ontario and studied their movement, sociality, and habitat preferences. My findings indicate that Ontario may contain relatively high densities of this species when compared with other parts of their range. My analyses also elucidated interesting aspects of this species habitat selection patterns within an anthropogenic landscape, in addition to novel findings surrounding wild turkey sociality and genetic structure.

Author Keywords: behaviour, genetics, Ontario, reintroduction, wild turkey, wildlife management

Heterogeneous environments impose discordant selective pressures on natural populations, where disparate biotic/abiotic factors and variable population connectivity, yield mosaic patterns of genetic variation on the landscape. The ability to maintain or change genetic mosaics of populations becomes key to persistence, as species increasingly need to adapt to rapidly changing environmental and human-associated selective pressures. Specifically, infectious diseases can impose strong and rapid selective pressures on populations, where anthropogenic disruptions of co-evolutionary patterns and altered distributions of hosts and pathogens exacerbate disease risk. Genomic tools provide means to evaluate disease-associated impacts on the genetic landscape of host populations and facilitate implementation of informed conservation efforts. In this thesis, I evaluate disease dynamics in: 1) a long-standing arctic rabies/arctic fox (Vulpes lagopus) system affected by influxes of red fox (V. vulpes), and 2) an invasive bat pathogen system, where the North American introduction of Pseudogymnoascus destructans (Pd) has had variable impacts on bat species and populations. In these systems, signatures of host selection were estimated from temporal and spatial shifts in allelic diversity within genomic regions associated with immune response, highlighting different host mechanisms to enzootic and invasive diseases. In the arctic rabies/fox system, pathogen variants did not influence red fox local disease responses, reflecting more recent expansions of this host to Arctic regions. In contrast, arctic fox revealed genomic patterns consistent with long-term, co-evolutionary processes. In Pd/bat systems, genomic evidence supported the hypothesis that eastern small-footed bats (Myotis leibii) were inherently resistant or tolerant to Pd, the causative agent of white-nose syndrome (WNS). In contrast, WNS-impacted little brown bat (M. lucifugus) populations had varied genomic impacts subsequent to strong selective sweeps from disease. My research illustrates how immunogenetic profiling, in context of demographic processes inferred from neutral genetics, enhances understanding of the varied impacts of changing disease landscapes on host populations/species; insights relevant to other host-pathogen systems. Building on this thesis, future explorations of low coverage genomes, host-imposed reciprocal selection, and impacts on methylation, transcriptomic and proteomic patterns associated with shifts in genetic diversity, would enable more holistic understanding of the geographic mosaics within these disease systems.

Author Keywords: Disease Dynamics, High-throughput Sequencing, Immune System, Natural Selection, Population Genetics, Reduced Representation Sequencing

Dissolved organic matter (DOM) plays a vital role in lake ecosystems, yet its temporal and spatial variations in lakes remain poorly understood. This study investigates DOM dynamics in boreal lakes during the warm season and the Laurentian Great Lakes ice during winter. Sampling 10 boreal lakes in early and late June 2022, revealed subtle changes in DOM in the epilimnion and hypolimnion related to factors such as water residence time and stratification strength. In ice from the Great Lakes, lower dissolved organic carbon concentrations and a higher proportion of protein-like DOM were found compared to water, which mostly contained terrestrial-like DOM. Ice DOM composition varied with factors such as ice thickness, water nutrients, and DOM concentration in ice and water. In addition, we found that the potential release of protein-like DOM from ice to the water during spring melt is considerable and may fuel heterotrophic microbial metabolism.

In situ chlorophyll sensors are beneficial for monitoring of long-term impacts of algal blooms and accessing water quality issues in bodies of water. However, more research is needed to validate their efficacy and understand how environmental conditions can influence sensor measurements. I assessed the performance of an in situ chlorophyll sensor under controlled environmental conditions and used the same sensor to collect vertical phytoplankton patterns in south-central Ontario boreal lakes. The performance of the sensor was assessed by examining the precision of chlorophyll measurements and determining the suitable timing length that would produce precise results. In general, the sensor was relatively insensitive to conditions under lower algal concentrations and the decent of the sensor should be slowed for vertical lake profiling in lakes with higher algal biomass. Most variation resulted from the movement of particle bound algal cells. We described chlorophyll profile characteristics including surface chlorophyll levels and chlorophyll peak depth and width and investigated the relationships of these features with environmental controls. The lakes showed a typical chlorophyll profile of low phytoplankton biomass lakes. Our results showed that dissolved organic carbon was a strong predictor of epilimnetic biomass while light attenuation and dissolved organic carbon were both strong predictors of peak depth. Light attenuation and surface area were small but significant predictors of peak width. We acknowledged that any uncertainties in sensor chlorophyll readings were not an issue in our lakes due to the overall low chlorophyll biomass.

Author Keywords: chlorophyll, chlorophyll fluorescence, in situ profiling, lakes, phytoplankton biomass, water quality 

Using Drosophila deficiency (Df) and Over Expression (OE) (GAL4/UAS>dCas9-VPR; sgRNA) gene systems, it was demonstrated that Dmel_CG31381 and Dmel_CG11089 are functional tRNA isopentenyltransferase (EC 2.5.1.8) genes (tRNA IPT1 and IPT2) critical to the first committed step in insect cytokinin biosynthesis. IPT Df mutants showed significant decreases in total CK levels and IPT1/IPT2 transcript levels compared to parent lines. IPT OE mutants showed significant increases in total CK levels and IPT1/IPT2 transcript levels compared to parent lines. Further, endogenous CK analyte levels and qPCR relative fold gene expression of Dmel_CG31381 and Dmel_CG11089 (tRNA IPT1 and IPT2) genes demonstrated expression patterns with functional confirmation corresponding to the predicted IPT mutant variants. The functional confirmation of tRNA IPT1 and IPT2 as the first committed step was further supported by the bioinformatic detection of putative gene homologs to corroborate seven remaining enzyme transcripts supporting the novel description of a CK biosynthesis pathway in insects.

Author Keywords: Cytokinin Biosynthesis, Drosophila, gene expression, Insect Gall, mass spectrometry, tRNA IPT

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