Braunschweig, Techn. Universiẗat, Diss., 2004.

Bochum, Universiẗat, Diss., 2001.

Thesis (Ph. D.)--University of Queensland, 2003. / Includes bibliographical references.

Nitrogen oxides are targeted as important gas pollutants to be eliminated. Biological removal of nitrogen oxides, like the use of bio-trickling reactor, is gaining popularity over conventional methods. A bacterium isolated from a bio-trickling reactor showing high performance in removing nitrogen oxides was identified to be Pseudomonas mendocina. The genome of this isolate was sequenced using 454 pyrosequencing technology to a high level of completeness with 33 contigs and N50 contig length of 273 kbp. The genome was annotated by Prokaryotic Genome Automatic Annotaion Pipeline (PGAAP)and the strain was named P. mendocina DLHK. Examination of P. mendocina DLHK genome annotation found nitrate reductase but not nitrite reductase, nitric oxide reductase and nitrous oxide reductase. Novel genes or pathways might be available in P. mendocina DLHK contributingits denitrification function in the bio-trickling reactor. To better understand the evolution of Pseudomonas, a comprehensive comparative study was performed. Genomes of the Pseudomonasgenus were reannotated. Core genes were extracted to construct a phylogenomic tree using supermatrix approach. Effectiveness of using single phylogenetic marker in constructing phylogeny of Pseudomonas was evaluated using rpoB gene marker. Both methods generated phylogenetic trees of very similar topology, suggesting that rpoB gene can be a very effective marker in the rapid construction of Pseudomonas phylogeny.It is surprising to note that Azotobacter vinelandii DJ was included in the large clade of Pseudomonas and have the closest relationship with P. stutzeri in both phylogenetic trees, providing evidence that this species should be reclassified into the genus Pseudomonas. Cluster of Orthologous Groups (COG)category distribution of all pseudomonads were analysed for physiological significance. The large amount of gene categorised into the COG for amino acid metabolism and transcription may imply the importance for these 2 functions on the survival of pseudomonads. It is again surprising to note the COG distribution pattern of A. vinelandii DJ is different from other pseudomonads, especially to its closest phylogenetic neighbour P. stutzeri. Horizontal gene transfer events inpseudomonads were investigated because of its importance in prokaryotic evolution. The high congruence of the phylogemonic tree to most core genes suggests that the phylogenomic tree is a good piece of evidence describing the evolution of pseudomonads. It is a bit surprising to observe that quite a number of core genes may have exhibited horizontal gene transfer which show incongruence of the gene tree to the core genes. The impact of horizontal gene transfer events on the functionality and evolution of pseudomonads remains to be investigated. / published_or_final_version / Biological Sciences / Master / Master of Philosophy

published_or_final_version / Botany / Master / Master of Philosophy

Abstract The ability of several plant-associated bacteria to inhibit the proliferation of root-pathogens has been well established whereas considerably less has been reported about bacterial species inhibiting pathogens on the phylloplane. Sclerotinia sclerotiorum is the fungal causative agent of stem rot and is capable of infecting over 400 plant species, including flowering canola plants. For this reason, there is a need for disease management strategies targeted at preventing sclerotinia infection. Pseudomonas species DF41 was isolated from the canola rhizosphere and found to be an excellent antagonist of sclerotinia stem rot. Therefore, research efforts turned towards elucidating the mechanisms underlying DF41 antifungal (AF) activity. A random transposon mutagenesis approach facilitated the identification of genes essential for DF41 fungal antagonism. One gene that was identified, gacS, encodes the sensor kinase of the Gac two-component signal transduction system. Characterization of the DF41 gacS mutant revealed that this regulator is essential for secondary metabolite production. In other bacteria, the Gac system activates target gene expression by upregulating the transcription of small, untranslated RNA molecules (sRNA). A sRNA molecule called RsmZ was found to act as a downstream regulatory element in the DF41 Gac regulatory cascade. Furthermore, we discovered that DF41 is producing acyl homoserine lactone (AHL) signalling molecules. This prompted us to investigate the effect of quorum sensing (QS) on phenotypes contributing to AF activity. In DF41, AHL- signalling is not important for secondary metabolite production but does influence motility and may indirectly govern gene expression by controlling other regulatory elements Screening of our transposon library led to the identification of a non-ribosomal peptide synthetase gene involved in synthesis of a cyclic lipopeptide (CLP) molecule. High-performance liquid chromatography (HPLC) and mass spectrometry (MS) enabled the identification of an unusual CLP and we propose a preliminary structure containing some unique features. The role of this molecule in Pseudomonas sp. DF41 AF activity was also elucidated. Altogether, this investigation has revealed a number of important findings regarding how DF41 functions as a biocontrol agent. This information will allow us to use DF41 more effectively in the future in managing sclerotinia stem rot on canola plants.

A chitinolytic bacterium of the genus Pseudomonas, isolated from a pond, was grown in liquid culture. Culture filtrates were subjected to purification procedures. The extracellular material was found to contain chitinase and chitobiase activity. The chitinase activity was isolated from contaminating proteins by ammonium sulfate fractionation, affinity chromatography, and molecular weight exclusion chromatography. Overall purification was found to be three-fold, with a recovery of fourteen percent of the `original activity. Polyacrylamide gel electrophoresis showed the presence of two proteins, both exhibiting chitinase activity. / Department of Biology

Abstract The ability of several plant-associated bacteria to inhibit the proliferation of root-pathogens has been well established whereas considerably less has been reported about bacterial species inhibiting pathogens on the phylloplane. Sclerotinia sclerotiorum is the fungal causative agent of stem rot and is capable of infecting over 400 plant species, including flowering canola plants. For this reason, there is a need for disease management strategies targeted at preventing sclerotinia infection. Pseudomonas species DF41 was isolated from the canola rhizosphere and found to be an excellent antagonist of sclerotinia stem rot. Therefore, research efforts turned towards elucidating the mechanisms underlying DF41 antifungal (AF) activity. A random transposon mutagenesis approach facilitated the identification of genes essential for DF41 fungal antagonism. One gene that was identified, gacS, encodes the sensor kinase of the Gac two-component signal transduction system. Characterization of the DF41 gacS mutant revealed that this regulator is essential for secondary metabolite production. In other bacteria, the Gac system activates target gene expression by upregulating the transcription of small, untranslated RNA molecules (sRNA). A sRNA molecule called RsmZ was found to act as a downstream regulatory element in the DF41 Gac regulatory cascade. Furthermore, we discovered that DF41 is producing acyl homoserine lactone (AHL) signalling molecules. This prompted us to investigate the effect of quorum sensing (QS) on phenotypes contributing to AF activity. In DF41, AHL- signalling is not important for secondary metabolite production but does influence motility and may indirectly govern gene expression by controlling other regulatory elements Screening of our transposon library led to the identification of a non-ribosomal peptide synthetase gene involved in synthesis of a cyclic lipopeptide (CLP) molecule. High-performance liquid chromatography (HPLC) and mass spectrometry (MS) enabled the identification of an unusual CLP and we propose a preliminary structure containing some unique features. The role of this molecule in Pseudomonas sp. DF41 AF activity was also elucidated. Altogether, this investigation has revealed a number of important findings regarding how DF41 functions as a biocontrol agent. This information will allow us to use DF41 more effectively in the future in managing sclerotinia stem rot on canola plants.

No description available.

Thesis (M.S.)--University of Hawaii at Manoa, 2006. / Includes bibliographical references (leaves 143-160). / xx, 160 leaves, bound ill. 29 cm