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published_or_final_version / Ecology and Biodiversity / Master / Master of Philosophy

Thesis (M.S.)--University of Tennessee, Knoxville, 2008. / Title from title page screen (viewed on Mar. 20, 2009). Thesis advisor: John C. Waller. Vita. Includes bibliographical references.

Thesis (Ph. D.)--University of Hawaii at Manoa, 2003. / Includes bibliographical references (leaves 130-141). Also available via World Wide Web.

Thesis (M. Phil.)--University of Hong Kong, 2002. / Includes bibliographical references (leaves 100-117).

Thesis (PhD.(Plant Pathology))--University of Pretoria, 2006. / Includes bibliographical references. Available on the Internet via the World Wide Web.

>Magister Scientiae - MSc / In this study, the diversity of endophytic bacteria associated with food crops, sorghum (Sorghum bicolor L. Moench), pearl millet (Pennisetum glaucum L.) and groundnut (Arachis villosulicarpa) is investigated using culture-independent techniques: terminal retriction fragment length polymorphism (t- RFLP) and next generation sequencing (NGS). The first objective of this study was to investigate the effect of different DNA extraction protocols on mDNA yield and quality, as well as the diversity of endophytic bacteria retrieved from root and stem tissues (0.1g or 0.3g) of sorghum, pearl millet and groundnut. Protocols used include two classical methods (CTAB- and SDS-based) and five commercial kits: MoBio PowerPlant Pro® DNA Isolation Kit, Qiagen DNeasyR Plant Mini Kit, Fermentas GeneJET Plant Genomic DNA Purification Kit, MoBio PowerSoilTM DNA Purification Kit and MoBio UltraClean® Soil DNA Isolation Kit. Eletrophoresis and the Nanodrop were used to determine DNA yield and purity

The total number of viable bacteria found in Solanum tuberosum stems and tubers was found to vary from less than 1 x 10³ to 4.7 x 10⁷ cells per cm³ in stems and from 0 to 1.6 x 10⁴ cells per cm³ in tubers. About 75% of both stems and tubers had populations at the lower end of the range but there was no significant correlation between bacterial counts in stems and tubers of the same plant. Bacteria found in potato tubers included species of Micrococcus, Pseudomonas, Bacillus, Flavobacterium, Agrobacterium, and Xanthomonas. Also present were coryneforms and some others which were not identified to genus but were gram negative. Some of the coryneforms were morphologically indistinguishable from the bacterial ring rot organism (Corynebacterium sepedonicum) but non-pathogenic and biochemically different from it. About 5% of stem smears of healthy plants showed more than 30 gram positive rods per microscope field. All the Bacillus spp., one Pseudomonas sp. and three unidentified species were found to inhibit C. sepedonicum in vitro. An antibiotic was partially purified from the Bacillus sp. showing the greatest amount of inhibition. This species was also antagonistic toward the following potato pathogens: Pseudomonas solanacearum, Erwinia atroseptica, E. carotovora, Alternaria solani, and Phytophthora infestans. Physical and chemical tests showed that both a lipid and a peptide antibiotic were involved in the antagonistic effect. / Land and Food Systems, Faculty of / Graduate

published_or_final_version / Ecology and Biodiversity / Doctoral / Doctor of Philosophy

Fungi have been an important source of many structurally diverse and biologically active secondary natural products. These secondary metabolites have found applications in pharmaceutical and agriculture industry. Fungi are estimated to be second only to insects in species diversity. It is estimated that there are at least 3.5 million species of fungi of which a less than 5% have so far been explored. Fungi are known to produce many secondary natural metabolites, however their role has still not been clearly understood. However it is possible that fungi which often thrive in competitive environments would experience evolutionary pressure to produce such metabolites for defensive or offensive functions. Our research focusses on isolation and structure elucidation of secondary metabolites from endophytic and mycoparasitic/fungicolous fungi. Mycoparasitic and fungicolous fungi are those that colonize other fungi, and could be potential sources of antifungal agents because of the negative effects exerted on their hosts due to this colonization. Endophytic fungi are those that colonize the inner tissues of plants in a symbiotic or a non-symbiotic manner. They may or may not be necessary for the growth, defense and survival of the host. They may protect the plants from attack by other pathogens by producing secondary metabolites that inhibit the growth of other pathogenic organisms. Many biologically active secondary metabolites have been isolated from various members of these two classes of fungi. During the course of this research fourteen new and several known compounds representing various biosynthetic classes including peptides, polyketides, terpenoids, and compounds with mixed biogenetic origins have been isolated and characterized using various tools such as NMR and MS. Details of the isolation, structure elucidation, and biological activity of these new compounds are presented in this thesis. Structure elucidation was performed mainly by analysis of various MS and NMR data, along with chemical derivatization reactions and/or X-ray diffraction analysis data. Absolute configuration assignments were made using, X-ray crystallography, and/or by ECD spectral analysis in combination with computational analysis.