Environmental and Life Sciences

This work presents a new online method using gas chromatography coupled to the multicollector-inductively coupled plasma-mass spectrometer for methylmercury (MMHg) isotope ratio measurement. An extraction method using distillation was developed that effectively extracted MMHg from up to 5 grams of sediment, imparting no isotope fractionation on MMHg during extraction. Isotope ratios from transient signals were calculated using three different data treatment approaches, facilitated by a data processing application, IsoCor. Peak Area Integration using 80% of the peak gave the most accurate and precise results. Using the proposed methodology, an external precision (2 SD) of ± 0.59‰ for NIST 3177 was measured. This method can be applied to samples with MMHg concentration as low as 0.1 ng/g and was successfully applied to real sediment samples however, additional research to improve the precision of the method is required for the detection of small differences between samples.

Author Keywords: compound specific isotopic ratios, isotope ratio measurement, MC-ICP-MS, methylmercury

Agriculture may result in soil disturbances, including contamination by rare earth elements (REE) and trace elements (TEs) from agricultural inputs (e.g. fertilizers, pesticides). Regulations concerning agricultural inputs currently do not consider TE background concentrations, concurrent use of inputs, and emerging contaminants. Therefore, they may not sufficiently protect against TE contamination, including that of REEs as emerging contaminants. The objective of this work was to assess the concentration and distribution of TEs and REEs in agricultural soil and whether agricultural management alters soil geochemistry. Fourteen farms were sampled in southeastern Ontario, and the geochemistry of soils was analysed using ICP-MS and ED-XRF. Trace element concentrations exceeded environmental safety standards in some sites, including those characterized by historical contamination or elevated background concentrations. Concentrations of REEs are reported in Ontario agricultural soils, and the normalized REE values indicated enrichment of the middle REEs. Geographic location drives site geochemistry more than agricultural management.

Author Keywords: agriculture, phosphate fertilizer, rare earth elements, soil geochemistry, trace elements

This thesis presents a case of the aquatic plant species Fanwort (Cabomba caroliniana) significantly naturalizing in Kasshabog Lake in bays where it had been invasive. This significant naturalization presents major implications for invasive species management and invasion biology because the naturalization of invasive species is a phenomenon that has been largely omitted from study within ecology. There are several reasons for this: 1) the most used definition of the term naturalization within invasion biology categorically excluded the sense in which naturalization refers to community integration; 2) the most cited frameworks that have been created and used to describe and study biological invasions have no conception of invasive species naturalization; 3) boundary work has been conducted to exclude consideration of the naturalization of invasive species. Incorporation of an understanding of naturalization into science and management of biological invasions will make our understanding of them more complete.

Author Keywords: Ecological Restoration, Invasion Biology, Invasive Species, Naturalization

Many communities in Canada rely on water sourced from boreal forest headwaters for their drinking water. The Boreal Shield Ecozone is highly susceptible to climate change which threatens to exacerbate the effects of natural and human-driven disturbances such as wildfire, insect infestation and harvesting on water quality. Therefore, examining source water quality in headwater catchments within the Boreal Shield Ecozone is crucial to elucidating the potential implications of these disturbances to water treatment processes in the context of a changing climate. A synoptic water sampling investigation was conducted to evaluate how dissolved organic carbon (DOC) quantity and quality and disinfection by-product formation-potential (DBP-FP) quantity varied across space and time in the Algoma region of central Ontario. Over a five-month timeframe (June 2021 - October 2021), 168 streamflow estimates and 176 water samples were collected across 30 catchments (catchment areas from 0.2 - 106.8 km2) which varied in their forest disturbance histories. DOC concentration ([DOC]) ranged from 2.4 - 38.2 mg L-1 and tended to be higher in harvest-dominated sites, while no discernible differences in SUVA254 were observed between catchment types. DOC export estimates ranged from 1.0 - 63.2 g C m-2 over a 141-day period (June 5th - Oct. 23nd, 2021). Fluorescence indices for quantifying DOC composition suggested that all catchments were dominated by humified and terrestrially sourced carbon. DBP-FP values were positively correlated to UV-254 (r = 0.76 - 0.78) and [DOC] (r = 0.85 - 0.88), such that DBP-FP spatiotemporal patterns were strongly coupled to DOC dynamics. Multiple linear regression analysis identified that open water was negatively related to [DOC] and SUVA254 and explained the most variability in their spatiotemporal patterns. In addition, catchment area, which was negatively related to [DOC] and SUVA254, and legacy insect infestation and harvesting disturbance helped improve model explanatory power. Other predictor variables, such as slope, wetland cover, coniferous forest cover and recent forest disturbance (i.e., 5-year harvesting and 5-year insect infestation), showed relatively poor explanatory power. Variability in DOC export estimates may be explained by harvesting disturbance (adjusted r2 = 0.68 - 0.82). The results of this study emphasise that complex processes across the terrestrial-aquatic continuum, which are influenced by several factors, such as runoff, forest disturbance and landscape heterogeneity, govern the spatiotemporal patterns in water quality across boreal headwaters within the Algoma region.

Long-term avian population declines, particularly for the avian insectivore guild, are a conservation concern. With widespread and continuing population trends, climate change and its negative effects on avian food resources is a plausible cross-species driver. My goal was to evaluate whether bottom-up trophic effects of climate change could be influencing avian populations. I used a space-for-time approach to assess the influence of snowpack and soil moisture variability on arthropods and subsequent effects on nest survival. In the 2010 and 2011 growing seasons, I sampled arthropods, soil moisture (soil volumetric water content; VWC), snowpack (snow water equivalent; SWE), forest floor depth (L, F, H layers) and soil texture in conifer plantations and mixed deciduous forest in Southern Ontario's Ganaraska Forest (~4, 400 ha). I used additive linear mixed effects models to assess the responses of arthropod groups' (e.g., order or class) relative biomass (g/day) and abundance (count/day) to those variables. Influences for each arthropod group's biomass and abundance were typically in the same direction. Maximum annual SWE significantly positively influenced most arthropod groups and annual relative difference in VWC positively influenced one quarter. In mixed directions, forest type influenced half of the groups and soil texture and forest floor depth each affected less than one quarter. I then used structural equation models to evaluate relationships between SWE, VWC, the biomass of three arthropod functional guilds, and logistic-exposure model calculated daily nest survival rates for American Robin (Turdus migratorius), Eastern Wood-Pewee (Contopus virens), Least Flycatcher (Empidonax minimus), Ovenbird (Seiurus aurocapilla), and Red-eyed Vireo (Vireo olivaceus). Arthropod guilds included diet-based food, predaceous arthropods and soil-dwelling bioindicators. SWE significantly positively influenced food biomass in all five models and negatively influenced predaceous arthropods in three models. Soil moisture had a mix of positive, negative, and null effects. Eastern Wood-Pewee and Red-eyed Vireo nest survival positively related to food and negatively related to predaceous arthropod biomass. American Robin, Least Flycatcher and Ovenbird nest survival did not appear to be related to arthropod biomasses. Through bottom-up relationships, predicted climate change-induced reductions in snowpack may cause food resource declines and negatively affect some forest breeding bird populations.

Author Keywords: Arthropod biomass, Bottom-up, Forest birds, Nest survival, Path analysis, Precipitation

Giardia intestinalis is the causative agent of a diarrheal disease in mammals, but the mechanisms of disease pathogenesis are unclear. While proteins secreted by Giardia affect the host cells, the potential of hormone secretion has not been investigated to date. Cytokinins (CKs) are classified as phytohormones, but little is known about their role beyond plants. Mass spectrometry-based intracellular analysis revealed CKs typical of tRNA degradation, and extracellular analysis showed CK-riboside scavenging by Giardia with concurrent secretion of CK-free bases. Metabolomics profiling of culture supernatants showed similar trends where nucleosides were up taken, and nucleobases were secreted. The dynamics of amino acids, nucleosides and nucleobases were altered by CK-supplementation during encystation, along with inhibition of encystation. In summary, this is the first study to report CK synthesis and metabolism by Giardia along with the effects of CKs on the metabolite secretome of Giardia, while establishing a link between CK and nucleoside metabolism.

Author Keywords: Cytokinins, Giardia, mass spectrometry, metabolomics, parasite, secretome

The neuronal ceroid lipofuscinoses (NCLs), commonly known as Batten disease, are a family of fatal neurodegenerative disorders that primarily affect children. Several subtypes of NCLs have been reported, each being caused by a mutation in a distinct ceroid lipofuscinosis neuronal (CLN) gene; this results in aberrant lysosome function and the accumulation of lipoprotein aggregates (known as ceroid lipofuscin) within cells. Several innate cellular pathways exist to alleviate the stress caused by the buildup of aggregates. The endoplasmic reticulum (ER) is an essential organelle in this process because it is responsible for maintaining cellular homeostasis through protein production, quality control, and regulating several signalling pathways. The unfolded protein response (UPR) consists of several conserved pathways devoted to attenuating ER stress caused by an accumulation of misfolded proteins or aggregates; at the center of this stress response is GRP78, a molecular chaperone that binds to misfolded proteins to facilitate proper folding. The social amoeba Dictyostelium discoideum is an excellent model system for studying NCLs as it encodes more CLN-like proteins when compared to other classical model organisms (e.g., yeast, worm, fruit fly). In this study, D. discoideum was used to elucidate the effects of ER stress and build an understanding of how cells cope with increased stress. Beyond this, ER stress in D. discoideum models for CLN3 disease and CLN5 disease were evaluated. First and foremost, during the induction of ER stress by tunicamycin, there was an increase in intracellular and extracellular amounts of Grp78 accompanied by an increase in stress-related changes to the ER. Furthermore, models of CLN3 disease and CLN5 disease displayed increased amounts of Grp78 as well as a disrupted ER morphology. Interestingly, wildtype D. discoideum, AX3 cells, treated with tunicamycin displayed a similarly disrupted ER when compared to CLN models. Finally, when subjected to tunicamycin-induced ER stress, these NCL models displayed a trend towards increased Grp78 amounts, however, these cells appear to have a reduced sensitivity to tunicamycin-induced stress compared to wild-type cells. In summary, this study highlights D. discoideum as a model for studying ER stress through the conserved role of Grp78 in the stress response and concludes that an aberrant ER stress underlies the pathology of the NCLs.

Author Keywords: Batten disease, Dictyostelium discoideum, ER stress, GRP78, neuronal ceroid lipofuscinoses (NCLs)

Lake Huron's food web has experienced drastic changes in response to multiple stressors including declines in offshore productivity, decreased trophic transfer efficiency and a transformation of the benthic food web. However, how these changes have affected the diets and isotopic niches of predatory fish is largely unexplored. My diet study analysed stomach contents from five predatory fish species (lake trout, lake whitefish, chinook salmon, rainbow trout, and walleye) from the Ontario waters of Lake Huron. My isotopic study focused on lake trout and lake whitefish, based on community concerns that recovering lake trout are competing with or consuming lake whitefish. By contrast, I found that lake whitefish were a minimal component of lake trout diets, and the diet and isotopic overlap between these two species was low overall, but varied regionally. Both the dietary and isotope analyses reflect the high regional diversity of energy sources used by predatory fish.

Author Keywords: Food web, Isotopic Niche, Lake Huron, Predator-prey, Regime shift, Regional Energy Sources

Animal migration is defined as the seasonal movement from one independent and non-overlapping range to another. Understanding how and why animals migrate is important not only to understand their life history processes but also for informing other important ecological processes such as the spread of wildlife disease and habitat alteration. Animal migrations have been impacted by human activity with instances of complete loss of migrations in human-altered areas. Understanding the drivers of migration can help predict responses to future environmental changes and potentially help conserve these phenomena. Seasonal movements of white-tailed deer (deer; Odocoileus virginianus; Zimmerman, 1780) have been linked to seasonal changes in environmental conditions that impact their ability to find food resources and risk of predation. The human shield hypothesis posits that prey species will select habitat close to people to use predator fear of humans to protect themselves from predation. Using global positioning system (GPS) collars, we examined the onset of deer migrations and assessed how environmental variables including snow, temperature, and plant biomass influenced migration departure dates using time-to-event models. We compared deer locations to data from GPS collared coyotes (Canis latrans; Say, 1823) within the same study area to explore daily space-use differences and examine if deer migrations were food or predation-risk driven using generalized linear mixed effects regression models. We found substantial annual and individual variation in deer migration dates. Snow depth was the strongest and most consistent predictor of deer migration, with individuals departing earlier with greater snow depth. Our regression analyses showed that deer selected for habitats closer to and with greater density of anthropogenic structures than coyotes at all times. After removing the animal locations close to areas with active supplemental feeding, these effects were diminished showing no differences in proximity or density of structures. Overall, we found more support for a food driven migration rather than a predator driven human shield. With the reduction in natural food caused by snow cover, we suggest that supplemental feeding is likely influencing the use of wintering areas by deer. The high proportion of deer migrating to human developed areas with supplemental feeders highlights the need for continued research into the impacts of human activity on animal behaviour.

Author Keywords: coyote, human shield, migration, supplemental feeding, white-tailed deer

Globally, wildlife populations are experiencing increasing rates of range loss, population decline, and extinction. Caribou (Rangifer tarandus) have experienced dramatic declines in both range and population size across Canada over the past century. Boreal caribou (R. t. caribou), one of twelve Designatable Units, have lost approximately half of their historic range in the last 150 years, particularly along the southern edge of their distribution. Despite this northward contraction, some populations have persisted at the trailing range edge, over 150 km south of the boreal continuous range (BCR) in Ontario, along the coast and near-shore islands of Lake Superior. Better understanding the population structure and evolutionary history of caribou in the Lake Superior range (LSR) could help to inform conservation and management actions, such as the delineation of conservation or management units or translocations between populations. In this thesis, I use whole genome sequences from boreal, eastern migratory and barren-ground caribou sampled in Manitoba, Ontario, and Quebec to investigate evolutionary history and population structure. I discovered that the LSR caribou form a distinct group but also some evidence of gene flow with the BCR. Notably, caribou from the LSR demonstrated relatively high levels of inbreeding (measured as Runs of Homozygosity; ROH) and genetic drift, which may contribute to the differentiation observed between caribou occupying the two ranges. Despite inbreeding, the LSR caribou retained Heterozygosity Rich Regions (HRR). I found genomic structure among caribou populations from the LSR and BCR but found these two ranges had similar demographic histories. My analyses indicate that the LSR caribou display distinct genomic characteristics but share ancestry with the BCR, with historical gene flow between these two ranges. Collectively, this dissertation characterizes the population structure and evolutionary history of caribou from the southernmost range in Ontario, providing key insights for the conservation and management of these small and isolated populations.