An investigation of the possibility of developing a differential medium for isolation of soil bacteria in the family Rhizobiaceaa was conducted. Although the observation was made that pure cultures of I Rhizobium were able to grow on the rose bengal agar of Smith and Dawson, bacteria in the family Rhizobiaceae did not develop when soil was used as the inoculum, The predominate groups of bacteria which developed on this medium from soil were in the families Achromobacteriaceas and Pseudomonadaceae, Organisms chosen to represent the groups of bacteria in the families Achromobacteriaceae and Pseudomonadaceae were identified tentatively in the genera Flavobactgerium and Pseudomonas, respectively. / Master of Science

Thesis (Ph. D.)--University of Missouri-Columbia, 2003. / Typescript. Vita. Includes bibliographical references (leaves 222-247). Also available on the Internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 2003. / Typescript. Vita. Includes bibliographical references (leaves 222-247). Also available on the Internet.

With the high rate of human population growth in Africa, it is imperative that food production be increased through improving yields and bringing more land under cultivation. Nitrogen is a key element required for plant growth and with the low input of fertilizers into African farming-systems, it is necessary to harness biological nitrogen fixation (BNF) to its fullest extent. To maximize nitrogen fixation in crop and pasture legumes under various conditions and cropping systems requires intensified research. In this study the diversity of root nodule bacteria associated with Lotononis species in South Africa was investigated. To our knowledge, no past attempts have been made to investigate the diversity of rootnodule-bacteria associated with the genus Lotonollis. Eighty nodulated plants representing thirty-two Lotononis spp. were collected from all the main geographical and climatological regions in South Africa. Isolates obtained from rootnodules were purified and characterized with sodium dodecyl-sulphate gel polyacrylamide gel electrophoresis (SDS-PAGE), supplemented at the genomic level with 16S rDNA sequence data of selected strains. Initial screening (SDS-PAGE) showed that most isolates obtained from the same plant species, grouped into various clusters within the dendrogram. A few of the isolates from similar host plants seemed to cluster with high similarity. It is thus reasonable to conclude that host specificity in the symbiotic interaction is less applicable for most species of Lotononis. When considering the geographical origins of the isolates, their diverse nature was clearly illustrated. It was showed that isolates from similar geographical regions were evenly distributed throughout the dendrogram. Some of the isolates obtained from arid environments formed closely related electrophoretic groups. It was subsequently shown that root-nodule bacteria associated with Lotononis species are not restricted to a particular rhizobial genus, but that heterogeneity is evident. Some of the isolates were also related to genera outside the Rhizobiaceae, namely Methylobacterium and Burkholderia. / Dissertation (MSc (Microbiology))--University of Pretoria, 2006. / Microbiology and Plant Pathology / unrestricted

The advantageous association between rhizobia and leguminous plants has motivated numerous studies into the diversity and identity of the associated bacterial symbionts. This, as well as developments in molecular microbiology, has led to major revisions of rhizobial taxonomy. Previous investigations of the rhizobia, associated with various leguminous plants from South Africa, concluded that most of the indigenous strains were related to the genus Bradyrhizobium (Dagutat, 1995; Kruger, 1998). The other rhizobial genera represented, albeit to a lesser extent, were Rhizobium, Sinorhizobium and Mesorhizobium. The major shortcoming of these investigations was the lack of sufficient genotypic characterisation. Since the completion of these initial investigations, a new rhizobial genus and several new species have been described. These developments and the additional isolation of rhizobia, from previously uninvestigated legumes, necessitated a more detailed analysis of the indigenous rhizobia. The aim of this study was therefore to study the diversity of the indigenous strains, focusing particularly on genotypic traits. A selection of indigenous rhizobia was characterised by partial 16S rDNA sequencing, restriction fragment length polymorphism (RFLP) of the 16S-23S intergenic spacer (IGS) region, partial nifH sequencing and nodC RFLP. Based on 16S rDNA sequencing, most of the isolates could be assigned to a specific genus, most being related to the genus Bradyrhizobium. A group of isolates was also related to the genus Methylobacyterium. The IGS- RFLP analyses were sufficiently discriminatory to indicate additional variation among isolates which showed little or no 16S rDNA sequence variation. The nifH phylogenetic groupings correlated well with those obtained by 16S rDNA sequencing. However, nodC RFLP indicated that the indigenous rhizobia carry diverse range nodC genotypes, with only a few showing host-specific associations. In the absence of sequence data of these nodC genotypes, their origin and correspondence to known nodC genes of other rhizibial genera, remain uncertain. Considering the results obtained here and the phenotypic characteristics determined previously, several novel Bradyrhizobium and Mesorhizobium strains were identified, however, their specific status should be validated by DNA homology studies. / Thesis (PhD (Microbiology))--University of Pretoria, 2002. / Microbiology and Plant Pathology / unrestricted

Includes two journal articles with contributions by the author Bibliography: leaves 145-154

Includes two journal articles with contributions by the author / Bibliography: leaves 145-154 / vii, 164 leaves : ill ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Plant Pathology, 1988

Les bactéries du genre Agrobacterium forment un ensemble taxonomiquement diversifié composé de nombreuses espèces, présent dans la plupart des sols et des rhizosphère. Les agrobactéries sont le plus souvent anodines voire stimulatrices de la croissance des plantes. Par contre, celles qui hébergent un plasmide Ti induisent la maladie de la galle du collet à de nombreuses plantes d'intérêt agronomique. Dans ce contexte, nous avons d'une part donné l'état actuel des connaissances sur la taxonomie du genre Agrobacterium, et nous avons fait une revue des méthodes d'isolement et de typage de ces bactéries. D'autre part, nous avons cherché à mettre au point des méthodes d'identification rapides et fiables des différentes espèces d'agrobactérie. La méthode de MALDI-TOF MS a permis d'identifier les espèces mais elle n'était pas assez résolutive pour typer des souches et encore moins la présence de plasmides Ti dans les isolats. Nous avons alors développé des amorces de PCR spécifiques de 17 espèces, du genre Agrobacterium et de la famille Rhizobiaceae. Ces amorces se sont révélées efficaces pour identifier les bactéries cultivées et aussi pour détecter leur présence dans des communautés microbiennes. Nous avons utilisé ces outils pour étudier la répartition des agrobactéries à l'échelle d'un pays, d'une station et entre sols nus et sols rhizosphériques en utilisant soit des isolats soit des ADN extraits des différents environnements. Enfin, nous avons montré que le clonage-séquençage ou le séquençage à haut débit d'amplicons obtenus à partir d’ADN de communautés microbiennes nous permettaient de connaître la diversité des populations d'agrobactéries / Agrobacterium are Alphaproteobacteria common in most soils that closely interact with plants in two respects. Firstly, they are rhizospheric bacteria saprophytically living in the rhizosphere of numerous plants and they are likely beneficial to plants. Secondly, when they harbor a dispensable Ti plasmid (i.e. tumor inducing plasmid), agrobacteria are plant pathogens able to cause the crown gall disease to most dicots and gymnosperms and some monocots. An epidemiological survey of crown gall thus also requires expert determination of the Agrobacterium taxonomy. In this thesis we evaluated the usefulness of MALDI-TOF MS technique as a high throughput tool to determine and classify agrobacteria. Then we set up a recA-based PCR method to accurately and exhaustively assess agrobacterial diversity either of isolated agrobacteria or directly in various biotopes. We applied standard biochemical, recA-based and Ti plasmid-based identification methods to study the prevalence of pathogenic and non-pathogenic agrobacteria at the country and local scales. Finally, we tested whether analyzing the internal composition of recA amplicons could be a way to directly assess the micro-diversity of agrobacterial populations using cloning sequencing or pyrosequencing approaches. The later methodology was applied to establish the actual field diversity of Agrobacterium and to evaluate whether plant genotypes differentially select agrobacteria in their root systems, providing first data upon biotic factors shaping the population structure of agrobacteria

Agrobacterium are Alphaproteobacteria common in most soils that closely interact with plants in two respects. Firstly, they are rhizospheric bacteria saprophytically living in the rhizosphere of numerous plants and they are likely beneficial to plants. Secondly, when they harbor a dispensable Ti plasmid (i.e. tumor inducing plasmid), agrobacteria are plant pathogens able to cause the crown gall disease to most dicots and gymnosperms and some monocots. An epidemiological survey of crown gall thus also requires expert determination of the Agrobacterium taxonomy. In this thesis we evaluated the usefulness of MALDI-TOF MS technique as a high throughput tool to determine and classify agrobacteria. Then we set up a recA-based PCR method to accurately and exhaustively assess agrobacterial diversity either of isolated agrobacteria or directly in various biotopes. We applied standard biochemical, recA-based and Ti plasmid-based identification methods to study the prevalence of pathogenic and non-pathogenic agrobacteria at the country and local scales. Finally, we tested whether analyzing the internal composition of recA amplicons could be a way to directly assess the micro-diversity of agrobacterial populations using cloning sequencing or pyrosequencing approaches. The later methodology was applied to establish the actual field diversity of Agrobacterium and to evaluate whether plant genotypes differentially select agrobacteria in their root systems, providing first data upon biotic factors shaping the population structure of agrobacteria