Environmental Microbiology and Microbial Ecology Commons^™

Investigating Soil Microbiome Changes During Panax Quinquefolius Cultivation In New Gardens, Pok Man Paul Wan

Electronic Thesis and Dissertation Repository

Ginseng (Panax quinquefolius) is susceptible to ginseng replant disease (GRD), resulting in root rot and decreased yield when ginseng is grown in soils previously used for ginseng crops. Although fungal and oomycete pathogens are implicated, GRD is a complex disease and the changes in the soil when initially cultivating ginseng that lead to GRD remain unclear. This thesis reported changes in the soil microbiome from three new gardens in Norfolk County, Ontario over three years starting from seeding with ginseng. Over this period of cultivation, metabarcoding of the V4 region of the 16S ribosomal RNA gene clearly showed …

Towards More Complete Metagenomic Analyses Through Circularized Genomes And Conjugative Elements, Benjamin R. Joris

Electronic Thesis and Dissertation Repository

Advancements in sequencing technologies have revolutionized biological sciences and led to the emergence of a number of fields of research. One such field of research is metagenomics, which is the study of the genomic content of complex communities of bacteria. The goal of this thesis was to contribute computational methodology that can maximize the data generated in these studies and to apply these protocols human and environmental metagenomic samples.

Standard metagenomic analyses include a step for binning of assembled contigs, which has previously been shown to exclude mobile genetic elements, and I demonstrated that this phenomenon extends to all conjugative …

Response Of The Soil Bacterial Community, Resistome, And Mobilome To A Decade Of Macrolide Antibiotic Contamination, Liam Paul Brown

Electronic Thesis and Dissertation Repository

Biosolids (treated sewage sludge) are used as agricultural fertilizer but are frequently contaminated with macrolide antibiotics, to which resistance is rising among historically susceptible bacteria. To determine if the land-application of macrolides carried in biosolids could promote antibiotic resistance in soil bacteria, soil plots were exposed annually to environmentally realistic or high doses of macrolides for ten years. I sequenced the bacterial 16S ribosomal DNA, metagenomic DNA, and integron gene cassettes within the treated and antibiotic-free soil to compare the compositions and diversities of the bacterial communities, antibiotic resistance genes, and mobile genetic elements. I determined that the high dose …

Microbial Innovations For Disease Management In Honey Bees, Brendan A. Daisley

Electronic Thesis and Dissertation Repository

Arguably the most important insect pollinator, honey bees (Apis mellifera) are threatened by infectious disease, pesticide exposure, and nutritional deficits resulting from habitat loss.

The major goals of this thesis were to advance our understanding of the immune and microbiota factors underpinning synergistic interactions between the threats, and to develop a honey bee-specific probiotic with strain-level functions to alleviate cumulative stress burden.

Drosophila melanogaster was used as a high-throughput discovery platform in molecularly characterizing the effects of candidate probiotic lactobacilli and neonicotinoid-neuroimmune-microbiota mechanisms prior to experimentation in honey bees. Imd pathway activation by lactobacilli was identified to be …

Investigation Of Shocked Basalts From Vargeão Dome And Vista Alegre: Implications For The Search For Life On Mars, Nikol Posnov

Electronic Thesis and Dissertation Repository

Impact craters represent excellent astrobiological targets for planetary exploration missions to Mars. The impact of an asteroid or comet into a crystalline, H₂O-bearing target may result in development of a hydrothermal system and increase the habitability of the substrate for the colonization of endolithic microorganisms. Given that Mars’ surface is covered by cratered basaltic rock, this study investigated target rocks and impact breccias from Vargeão Dome and Vista Alegre impact structures that formed in basalt in the Paraná Basin of Brazil.

Utilizing petrography and micro-X-ray diffraction (μXRD), the degree of shock metamorphism in plagioclase was quantitively determined. Measuring …

Investigating The Impact Of Environmentally Relevant Imidazole Concentrations On The Antifungal Susceptibility And Community Composition Of Soil Fungi, Farhaan Kanji

Electronic Thesis and Dissertation Repository

Miconazole and clotrimazole are environmentally-persistent drugs that are entrained into crop soils through the application of biosolids. There is concern that environmental exposure to such azole antifungals, which inhibit fungal growth by disrupting the production of the fungal cell membrane component ergosterol, promotes resistance in clinically or agriculturally relevant fungi. Thus, either environmentally-relevant or excessive levels of these drugs were applied to microplots over ten years and compared with drug-free plots. Overall, ergosterol quantification, plates counts, and identification of >250 fungal isolates showed lower fungal counts and species richness in plots receiving excessive drug amounts. In addition, fungi from treated …

Characterizing The Diversity Of The Eukaryotic Microbiome In Marine Crustacean Zooplankton., Rose-Lynne Savage

Electronic Thesis and Dissertation Repository

Understanding zooplankton productivity is critical for modeling marine food web function, of which one poorly known factor is the influence of zooplankton symbionts. Zooplankton protist symbiont diversity is underestimated due to the limited surveys and techniques previously used. Using 18S V4 metabarcoding, I characterized the eukaryotic microbiomes associated with crustacean zooplankton from the northern Strait of Georgia, BC. Apostome ciliates were most abundant in all hosts except for cyclopoid copepods, which were dominated by Syndiniales. Most symbiont lineages were more abundant in one or two hosts, suggesting some degree of host preference. Microbiome data also provided information on diet, confirming …

Contraction Analysis Of Functional Competitive Lotka-Volterra Systems: Understanding Competition Between Modified Bacteria And Plasmodium Within Mosquitoes., Nickolas Goncharenko

Electronic Thesis and Dissertation Repository

We propose and analyze an extension to the classic Competitive Lotka-Volterra (CLV) model. The goal is to model competition between species, with a response from the environment. This response is a function of the population of all species and can represent numerous physical phenomena including resource limitation and immune response of a host due to infection. We name this new system a Functional Competitive Lotka-Volterra (FCLV) model. We mainly use the construction of contraction metrics, to determine global properties of the model. We use this result to analyze the competition between Plasmodium sp. and genetically engineered bacteria within the midgut …

Nutritional Regulation Of Sulfonamide Antibiotic Biodegradation By Microbacterium Sp. Strain C448, Tonya Malcolm

Electronic Thesis and Dissertation Repository

Sulfonamide antibiotics are frequently released into the environment due to their widespread use in livestock production, imposing a potential selection pressure for the development and dissemination of sulfonamide resistance. Recently, a sulfonamide-degrading bacterium Microbacterium sp. Strain C448 was discovered, whose activity has the potential to be used as a sulfonamide removal strategy from agricultural soils. This research gains insight into the sulfonamide biodegradation pathway by 1) evaluating the nutritional regulation of sulfamethazine biodegradation and 2) undertaking a comparative proteomic analysis of cells grown in the presence and in the absence of sulfamethazine. The nutritional analyses revealed that increasing amounts of …

Urea As An Effective Nitrogen Source For Cyanobacteria, Kevin J. Erratt

Electronic Thesis and Dissertation Repository

Urea use has grown substantially in the past half-century, with urea now accounting for > 50% of nitrogen fertilizer applications worldwide. The shift from inorganic nitrogen fertilizers to urea-based sources has coincided with the reappearance of cyanobacteria blooms in freshwaters. Here, we examined urea as a nitrogen source for three bloom-forming cyanobacteria species. We found that (1) urea was consumed more rapidly relative to inorganic nitrogen substrates, suggesting that cyanobacteria exhibit a preference for urea; (2) urea was consumed in excess of cellular requirements; and (3) urea may offer cyanobacteria a competitive edge over eukaryotic algae by enhancing light absorption capabilities. …

Disturbance And The Community Composition Of Arbuscular Mycorrhizal Fungi In Ontario Tallgrass Prairies, Sarah N. Allan

Electronic Thesis and Dissertation Repository

Arbuscular mycorrhizal fungi (Glomeromycota) form beneficial symbiotic relationships with the majority of land plants, especially in grasslands. Tallgrass prairies in Ontario are an endangered plant community currently being restored on former agricultural land. The objectives of my study were to determine if there were differences in the communities of Glomeromycota between disturbed and undisturbed tallgrass prairies in Ontario and if there were any potential indicator taxa for the ends of the disturbance spectrum. A molecular approach using DNA derived from soil samples was used to compare species composition between disturbed and undisturbed tallgrass prairies. A total of 177 operational taxonomic …

Microbial Repopulation Following In Situ Star Remediation, Gavin Overbeeke

Electronic Thesis and Dissertation Repository

In situ STAR (Self-sustaining Treatment for Active Remediation) is an emerging remediation technology which uses smouldering combustion to destroy nonaqueous phase liquid (NAPL) contamination in the subsurface. Since STAR smouldering travels through contaminated soils slowly (~0.5 to 5 m/day) and subjects them to high temperatures (400–1000°C), it is expected that this technology will thoroughly dry and sterilize the zones which it treats. Further, soils surrounding the treatment zone which are not smouldered will be heated, although not smouldered, by virtue of their proximity to STAR, impacting microbial communities within them. Therefore, the objectives of this work are to quantify the …

Field Scale Application Of Nanoscale Zero Valent Iron: Mobility, Contaminant Degradation, And Impact On Microbial Communities, Chris M.D. Kocur

Electronic Thesis and Dissertation Repository

This thesis began by verifying that nanoscale zero valent iron (nZVI) synthesis methods could be scaled up and implemented at the field scale in a safe manner. This led to successful demonstration of nZVI injection and mobility under constant head gravity injection into a contaminated utility corridor in Sarnia, Ontario. Where field studies have fallen short in the past was linking the somewhat qualitative field geochemical parameters to other evidence of nZVI transport. Definitive nZVI detection was elusive in previous field studies due to the highly reactive nature of the particles caused by their high surface area. nZVI was detected …

Clinical And Mechanistic Insights Into Novel Probiotic Functions And Formulations, Jordan Bisanz

Electronic Thesis and Dissertation Repository

Using a combination of hypothesis and discovery based approaches, the goal of this thesis was to better describe novel probiotic functions and their mechanisms while striving to better understand the effect of formulation on Bifidobacterium animalis subsp. lactis, Lactobacillus paracasei and L. rhamnosus.

Using RNA-Seq, a bacterial metatranscriptome analysis of a commonly consumed probiotic yogurt showed that the organisms adapted to storage time and flavor additions. This led to the discovery that in addition to the probiotic health benefits, members of the L. casei group (L. rhamnosus and L. paracasei) produce volatile sulfur compounds mediated by a novel …

Response Of Soil Nitrification To The Veterinary Pharmaceuticals Monensin, Ivermectin And Zinc Bacitracin, Magda A. Konopka

Electronic Thesis and Dissertation Repository

Pharmaceutical residues can reach agricultural land through amendment with animal or human waste. Since 2010, a series of replicated plots received annual applications of ivermectin, monensin and zinc bacitracin, either singly or in a mixture, at 0.1 mg/kg and 10 mg/kg concentrations. I collected soil samples before and after the fourth annual application of pharmaceuticals and assayed them for functional changes and amoA gene abundance, a gene needed for ammonia oxidation. In 2013, I exposed the soils to 100 mg/kg in a laboratory experiment which resulted in acceleration of nitrification. Under 10 mg/kg treatments in the field the abundance of …

Characterizing The Human Vaginal Microbiome Using High-Throughput Sequencing, Jean Megan E. Macklaim

Electronic Thesis and Dissertation Repository

The human vaginal microbiome undoubtedly has a significant role in reproductive health and for protection from infectious organisms. Recent efforts to characterize the bacterial species of the vagina using molecular techniques have uncovered an unexpected diversity. Using high-throughput sequencing I sought to describe the structure and function of the vaginal microbiome under different physiological states including healthy, bacterial vaginosis (BV), post-menopausal vaginal atrophy, and acute vulvovaginal candidiasis (VVC).

Partial 16S rRNA gene sequencing revealed that healthy, asymptomatic women most often have vaginal biotas dominated by Lactobacillus iners or L. crispatus. In contrast, BV is a heterogeneous, highly diversified condition …

Effects Of Biodiesel Concentration On Microbial Deterioration Of Polyethylene In A Simulated Fuel Storage Tank, Juan Manuel Restrepo-Florez

Electronic Thesis and Dissertation Repository

In this study a simulated fuel storage tank was used to investigate the effect of biodiesel concentration on biodegradation of polyethylene. This research is relevant in the field of fuel storage. The simulated storage system consisted of a number of identical conical flasks. Each flask was comprised of two layers, an upper one consisting of a fuel blend of diesel with biodiesel in concentrations ranging from 0 to 100% of biodiesel and the bottom layer containing an aqueous mineral media inoculated with a community obtained from a real fuel storage facility. Polyethylene slabs cut to a specific size were immersed …

Iron-Regulated Cyanobacterial Predominance And Siderophore Production In Oligotrophic Freshwater Lakes, Ryan J. Sorichetti

Electronic Thesis and Dissertation Repository

The frequency and intensity of cyanobacterial blooms (cyanoblooms) is increasing globally. Contrary to existing phosphorus (P) and nitrogen (N) paradigms describing cyanobloom proliferation in eutrophic (nutrient-rich) freshwater lakes, many of the recent cyanobloom reports pertain to oligotrophic (nutrient-poor) freshwater lakes with no prior history of cyanobloom occurrence. There exists a critical research need to re-visit existing conceptual models, identify regulating factors currently unaccounted for and improve our ability to effectively detect and measure cyanobacterial toxins (cyanotoxins) in lakes. Iron (Fe) is required in nearly all pathways of cyanobacterial macronutrient use, though its direct role in regulating cyanobacterial biomass is not …

An Investigation Of Plant-Microbe Interactions Under Cadmium Stress In Agar-Based Medium, Hydroponics, And Soil Studies, Melanie P. Columbus

Electronic Thesis and Dissertation Repository

This thesis investigated plant-microbe-metal interactions at two scales: a single plant-microbe system and an agricultural rhizobacterial community. The first objective was to investigate the effectiveness of a plant growth-promoting rhizobacterium (PGPR) on mediating cadmium stress in a plant model system. Arabidopsis thaliana Col-0 was inoculated with Pseudomonas putida UW4, which in its wild type form has been reported to reduce plant stress by simultaneously metabolizing the ethylene precursor 1-aminocyclopropane-1-carboxylate (ACC) with the enzyme ACC deaminase and stimulating plant growth through the production of indole-3-acetic acid (IAA). A mutant strain that lacks ACC deaminase and a no bacteria treatment were used …

Sequesteration Of Lead, Cadmium And Arsenic By Lactobacillus Species And Detoxication Potential, Marc A. Monachese

Electronic Thesis and Dissertation Repository

Toxic metals are a class of elements with no biological role but with extreme toxicity. On average only 50% of ingested toxins are absorbed into the human body, for reasons still unknown. It was hypothesized that the gut microbiota plays a role in reducing toxin absorbance. The aim of this study was to determine if constituents of the gut, namely Lactobacillus species, are able to sequester arsenic, lead and cadmium from the environment. Lactobacilli were incubated with the metals, both in vitro and with a Caco-2 cell line. Analysis of metal concentrations was conducted to determine if these were reduced …

Colonization Of Zea Mays By The Nitrogen Fixing Bacterium Gluconacetobacter Diazotrophicus, Nikita Eskin

Electronic Thesis and Dissertation Repository

To achieve high yields, corn fields are supplemented with nitrogen fertilizers. Nitrogen fertilizers account for a significant portion of production costs, and are harmful to the environment. Gluconacetobacter diazotrophicus, an endophytic nitrogen-fixing bacterium supplies its natural host sugarcane with a significant amount of nitrogen. This study investigated the colonization of G. diazotrophicus in seven different corn genotypes consisting of sweet and grain corn via three different methods of inoculation: soil drench, root dip, and aseptic inoculation. Sucrose content of the corn genotypes and nitrogenase activity were also analysed. Colonization was confirmed by PCR analysis. G. diazotrophicus colonization was detected using …