Environmental and Life Sciences

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

Advanced generation/backcrossed (non-F1) hybrids can be challenging to identify when their traits are similar to those of parental taxa, F1 hybrids, or both. This is particularly evident in the North American hybrid zone involving Typha latifolia, T. angustifolia, F1 T. × glauca and non-F1 hybrids. Cattails are challenging to differentiate based on gross morphological characteristics. Microscopic characteristics in female inflorescences have not been previously studied to differentiate parental taxa from non-F1 hybrids. To investigate whether researchers can use microscopic floret and bracteole characteristics for taxonomic identification, I compared pistillate flower length, bracteole length and width, and bracteole colour among taxa. I found that floret and bracteole characteristics can be useful for identifying T. latifolia but cannot accurately differentiate T. angustifolia and F1 T. × glauca from non-F1 hybrids. Further, a flowering bias can lead to the underestimation of the frequency of T. latifolia when using floral characters to examine the relative abundance of cattail taxa.

Author Keywords: advanced-generation hybrids, backcrossed hybrids, invasive species, morphology, species identification, Typha spp.

Cadmium is a toxic metal that has detrimental effects on blood vessel development and function. To examine the effect of varying concentrations of cadmium on angiogenesis, two in vitro assays were used. First, developing yolk sac blood vessels were studied in gestation day 8 mouse embryos exposed to medium alone, 1.25, or 1.75 μM cadmium chloride (CdCl2). Embryos exposed to 1.25 μM cadmium experienced a significant increase in the number of vessels formed; however, they were smaller in size. Vessel morphology and signalling pathways were also investigated using the mouse aortic ring assay, with exposures of 0.0, 0.5, 1.0, 5.0, or 10.0 μM CdCl2. Samples exposed to 10 μM experienced a significant increase in vessel length. However, no significant differences in phosphorylated PTEN and AKT were observed. The results of this study suggest that low levels of cadmium may disrupt angiogenesis, particularly the development of the embryonic vasculature in the yolk sac.

Author Keywords: Angiogenesis, Cadmium, Embryonic Development, Teratogenicity, Vascular Development, Vasculogenesis

Animals are essential to freshwater biogeochemistry and productivity. Through their excretion, aquatic consumers release bioavailable nutrients and carbon that can vary with animal taxonomic rank, trophic position, and abiotic factors such as light and nutrient supply. In fresh waters, light and nutrient supply is often modulated by dissolved organic matter (DOM), a "murky" component in the water that gives it a brown color and that may indirectly affect animal nutrient and carbon excretion. Additionally, contaminants can impact animal physiology, altering metabolism and inducing stress, further affecting nutrient and contaminant excretion. The size and structure of the ecosystem, including community composition and biomass, can also impact the contribution of aquatic animals to the elemental pool. To understand these dynamics, I examined animal‐mediated elemental cycling in freshwater ecosystems across gradients of DOM concentration and composition and under contaminant exposure. I tested fish and invertebrate nitrogen, phosphorus, and DOM excretion across trophic positions during two sampling events in Lake Erie and in naturally DOM-variable streams and lakes. I also investigated the effects of chronic exposure to silver nanoparticles (AgNP) under environmentally relevant conditions on fish nutrient and silver (Ag) release. I found that aquatic animals can be a substantial nutrient contributor to the nutrient pool, particularly when their population biomass is high and ambient nutrient concentrations are low. I also detected nonlinear relationships between animal nutrient excretion and DOM characteristics that varied with taxonomic rank and trophic position and that dampened at larger ecological scales. Importantly, I identified several fish DOM excretion signatures that differed relative to ambient DOM and reported the first fish Ag excretion rates under AgNPs exposure. My results underscore the context-dependency and variability inherent in animal-mediated elemental cycling, highlighting the critical role of animals as both modifiers and conduits of nutrients, DOM, and contaminants in aquatic ecosystems.

Author Keywords: carbon, consumer-nutrient driven dynamics, ecological stoichiometry, nitrogen, phosphorus, silver nanoparticles

Phosphorus is the growth-limiting nutrient in freshwater environments. Dissolved organic phosphorus (DOP) refers to phosphorus within dissolved organic matter (DOM). Much of DOP is bioavailable, but it is poorly understood due to its complexity. This thesis explores the export DOP to Lake Erie from its tributaries, by investigating its speciation and concentration seasonally through weekly sampling of two tributaries and spatially across a river to lake transect. The rivermouth was a site of rapid transition, with lower concentrations of DOP in the lake than in the river and a greater proportion of P as DOP in the lake. Phosphomonoesters and aromatic DOM were coupled in the medium-sized Grand River, but not in the Upper Great Lakes-influenced Detroit River. Phosphodiesters and highly processed DOM were coupled in the Detroit River, but only during periods of low terrestrial inputs. Finally, we found that DOP is a large contributor to tributary phosphorus exports.

Author Keywords: dissolved organic matter, dissolved organic phosphorus, enzymatic hydrolysis, Lake Erie, nutrient export, rivermouth

The neuronal ceroid lipofuscinoses (NCLs), collectively referred to as Batten disease, are a group of neurodegenerative diseases that affect all ages, primarily children. Batten disease is caused by mutations in 1 of the 13 ceroid lipofuscinosis neuronal (CLN) genes (CLN1-CLN8, CLN10-CLN14), each of which causes an NCL subtype when mutated. One of the NCL subtypes, CLN5 disease, is caused by mutations in the CLN5 gene. CLN5 is a soluble lysosomal protein that localizes to the endoplasmic reticulum (ER), the Golgi complex, the cytoplasm, and extracellularly. CLN5 has four putative molecular functions, including as a ceramide synthase, glycoside hydrolase, depalmitoylase, and bis(monoacylglycerol)phosphate synthase. CLN5 plays various roles within the cell, such as lipid metabolism, autophagy, and proteasome degradation. However, the function and the exact pathway in which CLN5 is involved are unclear. In addition, CLN5 is a secreted protein that, as shown via bioinformatics analysis, contains a signal peptide sequence. Furthermore, there are currently 70 CLN5 disease-causing mutations reported in the NCL mutation database. 12 CLN5 disease-causing mutations have been studied thus far in terms of their cellular impact, as well as the release of CLN5 to a certain extent. However, there is a lack of research into the functionality of the signal peptide in CLN5 and an in-depth analysis of the molecular impact of mutations in CLN5 disease. Consequently, this Ph.D. thesis focused on using comparative transcriptomics to reveal biological pathways affected by cln5-deficiency, revealing mechanisms that regulate the secretion of Cln5 and CtsD, and using Dictyostelium to gain insights into the molecular effects of mutations in CLN5 disease. Comparative transcriptomics reveal many differentially expressed genes that are linked to phenotypes observed in cln5-deficient cells and identified pathways affected in other CLN5 disease models, such as autophagy. Furthermore, novel findings, like affected expression of lysosomal enzymes and pathways, including secretion, are identified within the comparative transcriptomics analysis. Subsequently, this research also shows the secretory role of the signal peptide in Cln5 and CtsD. Finally, this Ph.D. thesis revealed that mutations in CLN5 disease affect the lysosomal biology and secretion of Cln5 and other lysosomal enzymes.

Author Keywords: Batten disease, CLN5, Dictyostelium discoideum, Enzymes, Lysosome, Secretion

Since the mid-Pleistocene, evolutionary histories of North American species were shaped by extreme climatic oscillations involving major range and habitat shifts at a rapid pace. The peopling of the continent and the subsequent human colonisation waves created further pressures affecting North American faunal and plant populations. Cervidae (deer family) are a diverse group which arrived in North America approximately 5 million years ago, and is represented on the continent by several extant species. The overarching aim of my thesis is to understand how North America's dynamic history shaped the evolutionary trajectory of the region's Cervidae species. In Chapter 2, I investigated the speciation and hybridisation history of the sister species white-tailed (Odocoileus virginianus) and mule deer (Odocoileus hemionus) using whole genome data of individuals from across their ranges, including zones of sympatry and allopatry. I found negligible patterns of ancient gene-flow suggesting white-tailed and mule deer divergence occurred via drift and their hybridisation is the result of secondary contact. In Chapter 3, I furthered our understanding of the Odocoileus species pair evolutionary history through explicit demographic inference and selection analyses. I used deer samples from across North America and found strong signals of climate- and human-induced population declines. Particularly, this work highlights the impact of European settlers and patterns of conservation concerns for mule deer. For Chapter 4, I clarified the phylogenetic relationship of a contentious taxon, Torontoceros hypogaeus, that went extinct during the late Pleistocene extinction event. I analysed 11k years old DNA of the single specimen representing the species, performed phylogenetic and divergence analyses, and found it belongs to the Odocoileus genus as Odocoileus (Torontoceros) hypogaeus which should be included in North America's late Pleistocene extinction list. Finally, in Chapter 5, I investigated genetic diversity over time in five North American Cervidae using contemporary and ancient DNA. I found patterns of change in genetic diversity that are consistent with known dispersal and demographic histories of our target species. Altogether, my thesis provides valuable insight into the evolutionary history of Northern American Cervidae, and on how they have been impacted by the continent's dynamic past.

Author Keywords: Cervidae, Demographic history, Extinction, Human impact, Hybridisation, Speciation genomics

Rare earth elements (REEs) are in high demand globally for the green transition and high technologies. The growing demand leads to their release into aquatic ecosystems from various point and non-point sources, which creates urgency to investigate their fate and enrichment. This thesis further investigates the biogeochemical fate and REE uptake mechanisms throughout aquatic ecosystems. Rare earth element concentrations and fractionations were quantified to determine the natural uptake mechanism of three REE exposure pathways (dissolved, diet, and particulate) into aquatic organisms. Pelagic organisms accumulated heavy REEs, indicating they primarily uptake dissolved REEs. Benthic organisms were characterized by REE patterns specific for diet and particulate REEs. Furthermore, lanthanum (La) enrichment was investigated in a lake treated with La-based coagulants using La anomalies. Lanthanum enrichment in the water and organisms were directly related to La dispersion from sediments. This research provides information on preferential exposure pathways and REE enrichment in aquatic ecosystems.

Author Keywords: bioaccumulation potential, fractionations, lanthanum enrichment, metal organotropism, rare earth elements, uptake mechanisms

Acid mine drainage (AMD) and metal-contaminated tailings represent some of the most inhospitable aquatic environments on Earth, characterized by low pH, elevated metal concentrations, and chronic carbon limitation. Yet these systems support microbial consortia with remarkable resilience. Among the most conspicuous inhabitants is Euglena mutabilis, an acidophilic protist traditionally regarded as an indicator species of AMD but seldom thoroughly investigated. This thesis reframes E. mutabilis at the center of a fungal-algal-bacterial (FAB) consortium, demonstrating that its cadmium tolerance and persistence are emergent properties of the consortium.

Culture-based experiments revealed that E. mutabilis survival under cadmium stress declined when fungal and bacterial partners were disrupted, underscoring their indispensability. Glucose supplementation revealed the consortium's capacity for structural and metabolic reorganization: fungal hyphae bound algal cells into flocs, bacterial associates proliferated, and hormone production shifted. Hormone profiling suggested a distributed signaling system in which fungi contributed cytokinins (CKs) and gibberellins while algae produced methyl-thiolated CKs, jasmonic acid, and salicylic acid. Transmission electron microscopy revealed bacterial-like inclusions within algal vacuoles, suggesting facultative endosymbiosis or phagotrophic retention. Transcriptomic analyses revealed that cadmium stress suppresses light-harvesting complexes and growth-promoting hormone biosynthesis while activating metal transporters and chloroplast sequestration mechanisms.

Beyond stress physiology, the FAB consortium unlocked chemical diversity inaccessible to axenic cultures. Molecular networking revealed that environmental consortia consistently produced unique metabolite families, often linked to silent biosynthetic pathways. Metagenomic sequencing linked these products to bacterial gene clusters further supporting the view that metabolic innovation is an emergent property of the collective.

Together, these findings suggest that the FAB consortium should be understood not as a loose association but as a microbial superorganism. This framing extends beyond the holobiont concept by dissolving the hierarchy between host and symbiont: E. mutabilis, fungi, and bacteria are all indispensable, and the identity of the host itself becomes blurred.

By reframing E. mutabilis as the nucleus of a microbial superorganism, this work highlights both theoretical and applied significance. It advances ecological understanding of how life persists under geochemical extremes, while pointing to new opportunities for sustainable bioremediation and natural product discovery through the deliberate cultivation of naturally evolved microbial consortia.

Author Keywords: Algal symbiosis, Bioremediation, Co-culture, Hormones, Microscopy, Transcrioptomics

Wetlands are highly susceptible to the invasion of invasive species. The invasive hybrid cattail (Typha × glauca) is prevalent in the southeastern Prairie Pothole Region (PPR) wetlands. However, concerns arise about its recent proliferation in the northwestern PPR without maternal T. angustifolia. To determine taxonomic distribution, I used species-specific PCR-RFLP and microsatellite markers for genotyping 245 samples from 50 northwest PPR sites. I found 75% T. latifolia, 7% T. angustifolia, 16% T. × glauca, and 2% backcrossed or advanced-generation hybrids. F1 T. × glauca has expanded in western PPR without its mother species, and the low occurrence of later-generation hybrids indicates their recent range expansion. Additionally, T. angustifolia offspring make fewer hybrids, which suggests that reproductive barriers may limit hybridization between parental species. This study highlights the vulnerability of prairies to cryptic invasions by Typha hybrids, and early detection of invasive species is a critical factor in wetland management success.