My work focuses on the community ecology of symbioses, specifically of fungal endophytes and their hosts. This thesis describes how plant defense compounds and a seed endophyte influence community structure of maize fungal endophytes. Maize produces benzoxazinoids (BXs), compounds toxic to microbes and insects. I assessed the influence of three factors on endophyte communities: host BX production, host neighbor identity and presence of a BX-detoxifying endophyte, Fusarium verticillioides (FV). To determine the influence of BXs on communities, two BX-producing (BX+) and one BX-nonproducing (BX–) genotype were planted in Ridgetown and Harrow, Ontario (triculture). Fungi were isolated and tested for tolerance to 2-benzoxazolinone (BOA), a toxic BX byproduct. Species and functional diversity (community distribution of BOA tolerance levels) was calculated. In seedling roots and mature leaves, the community proportion with low BOA tolerance was greater in BX– than BX+ plants. Fusarium abundance was up to 35 times higher in mature leaves of BX+ than BX– plants. Next, to assess the effect of host neighbor identity on communities, BX– monocultures were planted, and communities from BX– plants in monoculture and triculture compared. Monoculture root communities had higher species diversity than those in triculture. In vitro experiments were conducted to evaluate the influence of BOA on endophyte species interactions. FV facilitated species with lower BOA tolerance in the presence of BOA. Finally, fields were planted with a BX+ and BX– genotype in Ontario, Canada and Georgia, USA. Seed was inoculated with FV (FV+) or sterilized (FV–). FV abundance was highest in BX+FV+ plants, and Fusarium abundance was greater in BX+ than BX– plants in mature leaves. In Georgia, BX+FV+ communities in below ground tissue had lower abundance of BOA sensitive species than BX+FV–. Overall, results suggest that BXs are a habitat filter that increased colonization by horizontally transmitted and seed-born Fusarium species. This invokes the hypothesis that selective breeding for enhanced BX concentrations increased abundance of Fusarium species in maize. The in vitro study indicated that FV could facilitate other species. In contrast, field results suggest that FV interacts competitively with community members, a trait enhanced in the presence of BXs.

My work focuses on the community ecology of symbioses, specifically of fungal endophytes and their hosts. This thesis describes how plant defense compounds and a seed endophyte influence community structure of maize fungal endophytes. Maize produces benzoxazinoids (BXs), compounds toxic to microbes and insects. I assessed the influence of three factors on endophyte communities: host BX production, host neighbor identity and presence of a BX-detoxifying endophyte, Fusarium verticillioides (FV). To determine the influence of BXs on communities, two BX-producing (BX+) and one BX-nonproducing (BX–) genotype were planted in Ridgetown and Harrow, Ontario (triculture). Fungi were isolated and tested for tolerance to 2-benzoxazolinone (BOA), a toxic BX byproduct. Species and functional diversity (community distribution of BOA tolerance levels) was calculated. In seedling roots and mature leaves, the community proportion with low BOA tolerance was greater in BX– than BX+ plants. Fusarium abundance was up to 35 times higher in mature leaves of BX+ than BX– plants. Next, to assess the effect of host neighbor identity on communities, BX– monocultures were planted, and communities from BX– plants in monoculture and triculture compared. Monoculture root communities had higher species diversity than those in triculture. In vitro experiments were conducted to evaluate the influence of BOA on endophyte species interactions. FV facilitated species with lower BOA tolerance in the presence of BOA. Finally, fields were planted with a BX+ and BX– genotype in Ontario, Canada and Georgia, USA. Seed was inoculated with FV (FV+) or sterilized (FV–). FV abundance was highest in BX+FV+ plants, and Fusarium abundance was greater in BX+ than BX– plants in mature leaves. In Georgia, BX+FV+ communities in below ground tissue had lower abundance of BOA sensitive species than BX+FV–. Overall, results suggest that BXs are a habitat filter that increased colonization by horizontally transmitted and seed-born Fusarium species. This invokes the hypothesis that selective breeding for enhanced BX concentrations increased abundance of Fusarium species in maize. The in vitro study indicated that FV could facilitate other species. In contrast, field results suggest that FV interacts competitively with community members, a trait enhanced in the presence of BXs.

Fungal endophytes can improve plant tolerance to abiotic stresses such as heat and drought. I hypothesized that the six endophytic fungi SMCD 2204, 2206, 2208, 2210, 2214 and 2215 would promote heat and drought tolerance in wheat during both seed germination and at later developmental stages. The Vujanovic and Germida laboratories originally discovered these fungi from the roots of Saskatchewan grown wheat (Triticum turgidum L.). I assessed mycomediated enhancement of seed germination (mycovitality) including seedling performance, in vitro in terms of percent germination, seedling fresh weight, energy of germination (EG) and hydrothermal time (HTT) of germination. Endophytes SMCD 2206, 2210 and 2215 improved seedling heat or drought resistance, while SMCD 2204, 2208 and 2214 did not. In the greenhouse and phytotron, I evaluated the ability of the same six endophytes to enhance wheat tolerance for heat or drought stress by measuring photosynthetic stress (PS), carbon isotopic discrimination (∆), average seed weight (ASW), total seed weight (TSW) and the EG and percent germination of the F1 seeds produced. SMCD 2206, 2201 and 2215 increased performance of pot-grown wheat under heat and drought. Epigenetic modifications frequently involve changes in DNA methylation. Methyl-sensitive amplified polymorphism (MSAP) revealed that drought stressed wheat seedlings colonized with SMCD 2206 had DNA methylation patterns more similar to those of unstressed plants (with or without the endophyte) than to uncolonized drought stressed plants. Plant DNA sequences – similar to a cytochrome p450 EST and three transposable elements (TEs) – were differentially methylated between endophyte-free and endophyte colonized drought stressed plants. I tested the hypothesis that the endophyte-free progeny of SMCD 2206 colonized wheat grown in the phytotron or greenhouse under heat or drought stress would have heightened resistance for the same abiotic stressors to which their parents were exposed, compared to uninoculated first generation plants. Data on PS, ASW, TSW and ∆ showed that F2 plants incompletely inherited stress tolerance. This research demonstrated that fungal endophytes SMCD 2206, 2210 and 2215 improve wheat tolerance for heat and drought both in vitro and in pot studies. If field trials produce similar results, these isolates could be agriculturally important.

This work describes progress toward developing a model system to investigate <i>in plantae</i> suppression of human pathogens by <i>Stemphylium</i>-like fungal endophyte strains.

Plant microbiomes are increasingly appreciated as major drivers of plant health and ecosystem services, and are of ever-greater interest for their potential in human applications. However, plant-associated microorganisms often live in complex associations in nature. Here, I characterize one of these microbial associations: the symbiosis between foliar fungal endophytes and their bacterial endosymbionts (endohyphal bacteria, EHB). EHB influence fungal phenotypes and can shape the outcomes of plant-fungal interactions. EHB are thought to form facultative associations with many foliar fungi in the species-rich Ascomycota, but little is known about how these symbioses are initiated and maintained, or how EHB shape the ecology of their fungal hosts. In this study, I assessed factors mediating the relationships between two foliar fungi (Microdiplodia sp., Dothideomycetes; Pestalotiopsis sp. Sordariomycetes) and their EHB. I first established methods for introducing EHB into axenic mycelia of their fungal hosts, providing an important step forward for understanding the establishment of EHB associations and a critical tool for experimental tests of the effects of EHB on fungal phenotypes. Through experiments in vitro, I found that both the identity of the fungal host and the conditions under which fungi and bacteria are grown influence the establishment of EHB/fungal associations. Moreover, I showed EHB of foliar fungi can be transferred across fungal classes, thus creating experimental strains that could be used for the first time to examine the contribution of each symbiont to important fungal traits. Using these strains I evaluated how EHB influence the capacity of foliar fungi to degrade plant material as saprotrophs. I found that the presence and identity of EHB significantly influenced fungal growth on particular media, cellulase and ligninase activity, and mass loss from senescent tissue of their native host plant species in a partnership-specific manner. Because EHB can be acquired horizontally, they may help shape plant-fungal interactions, resultant ecosystem services, and the functional diversification of plant-associated fungi along the saprotroph-endophyte continuum. By manipulating EHB/fungal interactions in new ways, we can potentially influence fungal phenotypes for diverse human applications.

Plants synthesize a diverse array of phytochemicals in response to interactions with herbivores, pathogens, and commensal microbes. These phytochemicals may simultaneously enhance crop defense and quality, representing a potential pest management strategy. However, plant chemical responses to different types and levels of biotic interactions remain unclear, particularly in fruit tissues, and the feasibility of inducing these defenses through elicitor application in field environments also requires further examination. Thus, apples were used to 1) examine the impact of distinct communities of biotic interactions among plants, insects, and microbes on fruit phenolic chemistry, and 2) examine the impact of the phytohormones jasmonic acid (JA), salicylic acid (SA), and melatonin (M) on fruit phenolic chemistry and resistance against pests and pathogens. Ultimately, phenolic defenses were induced by fungal damage primarily in ripe pulp tissues, where there was also a positive relationship between fungal endophyte and phenolic diversity, supporting a broad hypothesis that chemical diversity may increase with biotic diversity. Additionally, two compounds were upregulated in response to fungal damage: chlorogenic acid and an unidentified benzoic acid. Elicitor applications did not affect phenolic chemistry, but the combined application of JA-SA analogues had some chemical or physical effect, as this treatment reduced emergence of the insect Rhagoletis pomonella. Thus, fruit induced defenses may be tissue-specific and subject to temporal, environmental, or genotypic variation. Overall, these chapters examined the relationship between biotic interactions and induced fruit chemistry, with the goal of improving understanding of plant-microbe-insect interactions and incorporating these interactions into more sustainable agricultural practices. / Master of Science / Plants may produce a diverse array of defensive phytochemical compounds in response to interactions with herbivores, pathogens, and the microorganisms that reside within plant tissues. These phytochemicals may simultaneously improve crop defenses and quality, representing a potential agricultural management strategy. However, plant chemical responses to different types and levels of biotic interactions are not well-understood, particularly in fruit tissues, and the feasibility of activating these defenses in fruits through the application of phytohormones that regulate defense pathways as a potential management strategy also requires further examination. Thus, apples were used to 1) examine the impact of distinct communities of biotic interactions among plants, insects, and microbes on fruit chemistry, focusing on phenolics, an important class of phytochemical compounds, and 2) examine the impact of the defense-activating phytohormones jasmonic acid (JA), salicylic acid (SA), and melatonin (M) on fruit phenolic chemistry and resistance against pests and pathogens. Ultimately, phenolic defenses were activated by fungal damage primarily in ripe pulp tissues, where there was also a positive relationship between fungal endophyte and phenolic diversity, supporting a broad hypothesis that chemical diversity may increase with biotic diversity. Additionally, two compounds were produced in response to fungal damage: chlorogenic acid and an unidentified benzoic acid. Phytohormone applications did not affect phenolic chemistry, but the application of the combined JA-SA analogues had some chemical or physical effect, as this treatment reduced emergence of the insect Rhagoletis pomonella. Overall, the phytochemical defenses activated by biotic interactions in fruits may occur primarily in certain tissue types, and may also vary due to environmental conditions, time of year, or plant species. These chapters examined the relationship between fruit chemistry and biotic interactions with the goal of improving understanding of plant-microbe-insect interactions and incorporating these interactions into more sustainable agricultural practices.

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Microsystems are a broad category of engineered technologies in the micro and nano scale that have a diverse range of applications. They are emerging as a powerful tool in the field of biomedical research, drug discovery, as well as clinical diagnostics and prognostics, especially with regards to cancer. One of the major challenges in precision and personalized medicine in cancer lies in the technical difficulties of ex-vivo cell culture and propagation of the limited number of primary cells derived from patients. Therefore, our aims are to 1. Develop a biologically relevant platform for culturing cancer cells and characterize how it influences the cell growth and phenotype compared to conventional 2-dimensional(2D) cell culturing techniques, 2. Isolate secondary metabolites from endophytic fungi and screen them on the platform for potential anticancer properties in a preliminary drug discovery pipeline, 3. Design and develop biosensors for quantifying cell responses in real-time within these systems. Several biomaterial scaffolds with microscale architectures have been utilized for engineering the tumor extracellular matrix, but very few studies have thoroughly characterized the phenotypic changes in their cell models, which is critical for translational applications of biomaterial systems. The overall objective of these studies is to engineer a biomimetic platform for the culture of breast cancer cells in vitro and to quantify and profile their phenotypic changes. In order to do this, we first evaluated a blank-slate matrix consisting of thiolated collagen, hyaluronic acid and heparin, cross-linked chemically via Michael addition reaction using diacrylate functionalized poly (ethylene glycol). The hydrogel network was used with triple-negative breast cancer cells and showed significant changes in characteristics, with cells self-assembling to form a 3D spheroid morphology, with higher viability, and exhibiting significantly lower cell death upon chemotherapy treatment, as well as had a decrease in proliferation. Furthemore, the transcriptomic changes quantified using RNA-Seq and Next-Gen Sequencing showed the dramatic changes in some of the commonly targeted pathways in cancer therapy. Furthermore, we were able to show the importance of our biomimetic platform in the process of drug discovery using fungal endophytes and their secondary metabolites as the source for potential anticancer molecules. Additionally, we developed gold nanoparticle and antibody-based (ICAM1 and CD11b) sensors to quantify cell responses spatiotemporally on our platform. We were able to show quenching of the green fluorescent fluorophores due to the Förster Resonance Energy Transfer mechanism between the fluorophore and the gold nanometal surface. We also observed antigen-dependent recovery of fluorescence and inhibition of energy transfer upon the antibody binding to the cell-surface receptors. Future efforts are directed towards incorporating the hydrogel system with antigen-dependent sensors in a conceptually-designed microfluidic platform to spatiotemporally quantify the expression of surface proteins in various cells of the tumor stroma. This includes the migration,infiltration, and polarization of specific immune cells. This approach will provide further insight into the heterogeneity of cells at the single-cell resolution in defined spaces within the 3D microfluidic platform. / Doctor of Philosophy / Microsystems are a broad category of engineered technologies in the micro and nano scale that have a diverse range of applications. They are emerging as a powerful tool in the field of biomedical research, drug discovery, as well as clinical diagnostics and prognostics, especially with regards to cancer. However, a major challenge in being able to offer personalized medicine to cancer patients comes from the difficulty of growing cells from the patient's tumor biopsy in a laboratory for further screening and analysis. There are also limited resources available for real-time expression of proteins on cell-surfaces, that could be potential biomarkers and targets for treatment. Various natural and synthetic polymers are biocompatible and have been used widely in engineering the tumor extracellular matrix. However, the effect of hydrogels derived from these polymers on the specific tumor cells are not always well characterized. Our studies explore the influence of a biohybrid hydrogel on breast cancer cells and our results show that the microscale architecture of the hydrogel platform works as a suitable scaffold for recapitulating the 3-dimensional(3D) breast tumor microenvironment, and can also be employed in the drug discovery process. Additionally, we developed a nano-scale biosensor to enable the quantification of specific cell-surface proteins in real-time. Ongoing and future efforts are focused on designing and fabricating a microfluidic device with precise control over the design of space and special chambers for cell culture. These will be used for studying interactions of various cells in the tumor microenvironment that influence cancer progression. Integrating these micro-scale systems, including sensors will allow researchers to quantify cell behavior in response to the variable factors they are exposed to, as well as provide insight to answer fundamental questions about cancer biology that are limited by the conventional 2D cell culture systems.

No description available.

No description available.