Environmental and Life Sciences

Arctic breeding shorebirds are often considered alternate or secondary prey to avian and terrestrial predators that primarily feed on cyclic populations of rodents. Predation risk can strongly influence habitat selection; however, there is limited understanding of how nest placement by shorebirds and subsequent risk of nest predation are affected by spatiotemporal patterns involving the indirect effects of alternate prey on predator activity. I examined nest fates of Whimbrel (Numenius phaeopus) and Dunlin (Calidris alpina) at the southernmost edge of their breeding ranges at Polar Bear Provincial Park, Ontario, using field surveys including direct observations, camera monitors and thermal probes. I used resource selection functions (RSFs) to compare used and available habitat features near shorebird nests. I assessed whether shorebird nest predation was affected by spatial patterns in avian predator activity, habitat, and small mammal alternate prey and annual variation in cyclic small mammal abundance. RSFs confirmed strong habitat selection for graminoid fen habitats with avoidance of tundra heath, presumably to avoid terrestrial predators that may use them as travel corridors. Shorebird nest predation was not affected by the spatial variation in avian predator activity. However, Dunlin nest predation risk was affected by spatial variation in small mammal abundance. Further, the effect was strongest in years consistent with peaks in the small mammal population cycle. These findings highlight the important effects of spatiotemporal variation of alternate prey densities on Arctic-Subarctic food webs, providing insights on the complex relationships affecting shorebird nest success.

Author Keywords: apparent competetion, Dunlin, Empirical Bayesian Kriging, Shorebird, Subarctic, Whimbrel

ABSTRACT

Development of Forest Degradation Indicators from Long-term Trajectories of Multispectral Satellite Images, and their Projections into the Future under Climate Change, in Ontario, Canada

Md. Mozammel Hoque

Ontario forests are affected by natural and anthropogenic disturbances leading to forest degradation, which significantly impact local ecosystems, health, safety, and economy. This thesis develops a methodology for the continuous assessment, mapping, and monitoring of present and historic (1972–2020) forest disturbances, and future forest degradation trends and projections, using remote sensing data, ground measurements, and predictive models in an Ontario forested area. After testing four supervised classification algorithms, support vector machine was found to be the most robust, consistent, and effective for land cover classification. Seven vegetation indices derived from Landsat and MODIS platforms were used to derive forest degradation indicators (FDIs), which were combined into one composite forest degradation indicator (CFDI) for each year, using the principal component analysis image fusion approach. The CFDI was the most informative indicator. The computed FDIs from available large multispectral image stacks were statistically related to historical climate variables. These relationships were used to project future FDIs related to climate variables derived from General Circulation Models through multiple linear regression models. Spatially-explicit maps of relevant climatic variables and of long-term historical forest degradation were developed from the LandTrendr trajectory analysis. Climate variables P, MA1, MA2, and CFDI were strongly correlated, allowing for the development of a model with a high coefficient of determination, R2 (0.93), and low RMSE (0.28) to predict future values. Forest disturbances (as CFDI) were also monitored from 1972–2020. Overall, these relationships allowed for to the creation of spatially-explicit, long-term historical forest degradation maps derived from the Landtrendr trajectory analysis. Historical and future forest degradation maps identified the areas with projected high vulnerability to climate change, as well as the actual and potential changes in forest cover under climate change. The results indicated 2050 will experience an average temperature increase of 3.0°C, projected yearly decrease in precipitation of 109.5 mm, evapotranspiration increase of 73.0 mm, and moisture deficits of 28.47 mm (MA1) and 37.60 mm (MA2), leading to increased forest degradation.

Author Keywords: Climate change impacts, Forest degradation indicators, Forest disturbance and degradation, Land cover classification, Projections of 2050 forest degradation under climate change, Remote sensing technology

This thesis determined the temporal dynamics of microplastics in the biosolid and final effluent of a WWTP for one year (October 2020–September 2021). The WWTP exported 354.1 ± 24.7 billion microplastic particles, or 296.7 ± 39.4 kg of microplastics; of this, 85.7% of counts and 86.6% of mass was exported via biosolids. As such, microplastic loads in biosolids need to be reduced before they are land applied. This thesis further examined the ability of settling treatments to liberate microplastics from biosolids under the effect of four variables (harvest method, stirring, settling time, and biosolid type). Across all treatments, average microplastic removal was 9.01 ± 5.82% in terms of count, and 6.91 ± 4.98% in terms of mass. Overall, this thesis contributed to our understanding of annual microplastic burden in a WWTP and set the foundation for the development of settling-based biosolids treatments to reduce microplastic emissions to the environment.

Author Keywords: Biosolid, Count Concentration, Final Effluent, Mass Concentration, Polymer, Treatment

Giardia intestinalis is a parasitic protozoan that possesses a flavohemoglobin (gFlHb), an enzyme that plays a role in the detoxification of reactive nitrogen species (RNS) and reactive oxygen species (ROS) via its nitric oxide dioxygenase (NOD) activity as well as its NADH-oxidase activity. This enzyme is a potential target for imidazole-based antigiardial drugs that act as ligands of the iron within its heme cofactor. In this work, two rapid and relatively inexpensive assays, the colorimetric Griess assay and a fluorescence assay, were adapted, optimized, and implemented to screen for flavohemoglobin inhibitors in parallel studies that compared the response of gFlHb to that of Hmp (Escherichia coli flavohemoglobin) when a group of six different imidazole-based compounds was tested. These assays displayed isotype selectivity, showing how the different drugs elicited different responses from the two enzymes. Comparative results for gFlHb and Hmp revealed that bulkier compounds elicited higher inhibition of Hmp, while smaller compounds resulted in better inhibition of gFlHb, which might be explained by the presence of different amino acid residues in the active sites of the enzymes, with two large amino acid sequence inserts being a unique feature of gFlHb, thus blocking the active site from being reached and blocked by larger compounds.

Author Keywords: 2.3-diaminonaphthalene, Flavohemoglobin, Giardia intestinalis, Griess Assay, imidazole-based drugs, nitric oxide detoxification

Mutations in the CLN7 (MFSD8) gene, causes CLN7 disease, a subtype of neuronal ceroid lipofuscinosis. MFSD8 is a lysosomal transmembrane protein that transports chloride across membranes. Experimentation regarding Dictyostelium discoideum revealed that mfsd8 deficiency altered lysosomal enzyme activity. During starvation, the aggregation of mfsd8¬¬- cells was delayed, and cells formed more mounds that were smaller in size, phenotypes that were attributed to reduced cell-substrate adhesion and altered lysosomal enzymatic activities. This study examines the possible transcriptomic and secretomic basis for these phenotypes. This work generated new datasets for examining the effect of mfsd8 loss on the transcriptome and secretome. The validity of these datasets was supported by use of western blotting and RT-PCR along with a set of assays probing relevant biological processes. Together these results elucidate the biological mechanisms behind the observed phenotypes and lay the foundation for future studies to further study the cellular role of MFSD8.

Author Keywords: Battens disease, CLN7, Dictyostelium discoideum, MFSD8, Secretome, Transcriptome

Darwinian fitness is determined by the outcome of allocations of energy and nutrients to plant growth, survival, and reproduction. Allocations to reproduction differ from allocations to growth and survival because the products of reproduction (pollen, ovules, and fruits) are dispersed away from the plant and so the resources used to produce them cannot be re-allocated. As a result, and because the total resource pool available to a plant is limited, allocations to reproduction can reduce future growth, reproduction, and/or survival, yielding fitness costs of reproduction. This study provides a novel approach to detecting the costs of reproduction through multiple reproductive currencies, including both biomass and nitrogen allocations and their temporal effects on current and future plant performance. My results demonstrate the environmental dependence of the costs of reproduction and show that under certain conditions, males can bear greater costs than females, contrary to the prevailing view.

Author Keywords: Cost of reproduction, dioecy, flower removal, life-history trade-offs, photosynthetic machinery, sexual dimorphism

The TATA-binding protein (TBP) is a key regulator of eukaryotic transcription initiation. The TBP homolog from Giardia intestinalis (gTBP) is highly divergent among all TBPs; notably lacking three of the four phenylalanine residues to unwind double- stranded DNA. I show that gTBP preferentially binds to single-stranded DNA (ssDNA) in two modes based on sequence and protein concentration. The proposed A mode likely represents multimeric binding of gTBP to ssDNA with four or more consecutive guanine bases. The B mode involves monomeric binding utilizing the structural properties of the ssDNA. To demonstrate this, I developed a novel technique using base stacking energy potentials to approximate the per-nucleotide flexibility of ssDNA. I also attempted to create a polynomial regression model to predict binding; however, further work is required to improve accuracy. Overall, this thesis presents a new perspective on eukaryotic transcription regulation based on the discovery of unconventional binding between gTBP and ssDNA.

Author Keywords: computer modelling, DNA binding protein, DNA structure, DNA transcription, general transcription factor (GTF), parasite

Innovative strategies to manage copious waste streams by upcycling feedstocks to valorized products which are then used in environmental remediation applications is an attractive circular economy model. This thesis explores this approach using waste wood generated from the milling of Chlorocardium rodiei (greenheart), a tropical hardwood species abundant in Guyana. We evaluate the thermochemical conversion of this feedstock, using phosphoric acid as the activant, to super activated carbons with surface areas of more than 2200 m2/g. Owing to the presence of surface heteroatoms, these adsorbents are amenable to further surface modifications including base-treatment, O-functionalization and N-functionalization. Using a facile oxidation procedure and shrimp waste-based dopants, we increase oxygen and nitrogen content by 8-fold and 5-fold respectively. These increases are realized without catastrophic loss of surface area and porosity as generally occurs with many reported functionalization approaches. Functionalized materials demonstrated efficient removal of both metal ions and the chlorinated herbicides 2,4-dichlorophenoxy acetic acid and paraquat. Pristine and base-washed ACs removed more than 90% of iron, aluminum and manganese from natural pit-lake waters. O-functionalized adsorbents also showed excellent removal efficiencies for aluminum and lead but only removed moderate amounts of manganese. Nitrogen-enriched composites fabricated with the addition of commercial chitosan removed 67% 2,4-D and 89% paraquat from model solutions at environmentally relevant concentrations of 4 ppm and 40 ppm respectively. Their versatility is further demonstrated in their ability to remove both herbicides from binary mixtures albeit to different extents. Shrimp chitin-based composites were most effective at removing 2,4-D from model solutions with a maximum adsorption capacity of 101 mg/g. Both surface area and surface nitrogen had strong influences on the adsorption capacity of adsorbents. Mechanistically, physisorption interactions predominate the synergistic or antagonistic interaction between N-functionalized composites and herbicide species. These green adsorbent materials, fabricated from sustainable biopolymers, are promising candidates for diverse environmental remediation applications.

Author Keywords: adsorption, Environmental remediation, N-functionalization, O-functionalization, tropical hardwood waste, waste valorization

Forests play a critical role in the global carbon cycle, acting as carbon sinks that remove and store an estimated 0.4 to 4.1 Pg of atmospheric carbon annually. However, historical acid deposition and timber harvesting have disrupted nutrient cycles, leading to nutrient-deficient soils that hinder tree growth, particularly for sugar maple (Acer saccharum), a keystone species in Ontario sensitive to soil acidity and calcium (Ca) depletion. This study evaluates the effects of non-industrial wood ash (NIWA) applied at 0, 2, 4, 6, and 12 Mg ha-1 on soil chemistry, nutrient concentrations, microbial activity, CO2 fluxes, and sugar maple growth over two years. NIWA increased soil pH and exchangeable base cations, especially in the organic horizon, with some increase in forest floor metals, though foliar levels remained safe. Enzyme activity responses were minimal, and fine root biomass declined at higher doses. Soil CO₂ fluxes rose sharply at 12 Mg ha⁻¹, suggesting pH-driven effects. NIWA improves soil chemistry, but long-term impacts remain uncertain.

Author Keywords: carbon flux, extracellular soil enzyme, non-industrial wood ash, sugar maple

Microplastics are intricate plastic particles (<5 mm in length) with complex chemical mixtures that are pervasive globally. Nonetheless, our understanding of microplastic contamination in the Canadian Arctic is limited. Therefore, this thesis aimed to investigate the concentration and characteristics of microplastics in and surrounding the community of Iqaluit, Nunavut. Our findings suggest Iqaluit is a local source of microplastics in the Arctic based on their concentration in road dust (2.83 ± 3.72 µg/g). Microplastic concentrations were comparable to those in metropolitan areas and given their abundance in parking lots it is suggested that these are temporary reservoirs for microplastics and tire wear particles. Further, lakes predominately upwind of Iqaluit had a greater concentration of microplastics (134 ± 204 µg/L) than lakes downwind (30.8 ± 55.5 µg/L). These findings underscore the importance of assessing both local-scale and long-range sources when examining microplastic contamination in the Arctic.

Author Keywords: Atmospheric microplastics, Biomonitoring, Canadian Arctic, Fourier-Transform Infrared Spectroscopy (FTIR), Plastic pollution