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Diversity of Root Nodule Bacteria Associated with Phaseolus Coccineus and Phaseolus Vulgaris Species in South Africa

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Diversity of Root Nodule Bacteria Associated with Phaseolus Coccineus and Phaseolus Vulgaris Species in South Africa University of Pretoria etd, Lindeque M I (2006) Diversity of root nodule bacteria associated with Phaseolus coccineus and Phaseolus vulgaris species in South Africa by Michelle Irene Lindeque Submitted in partial fulfilment of the requirements for the degree Magister Scientiae in the Department of Microbiology and Plant Pathology Faculty of Natural and Agricultural Sciences University of Pretoria Pretoria Supervisor: Dr J.B. Jaftha July 2005 1 University of Pretoria etd, Lindeque M I (2006) ACKNOWLEDGEMENTS I would like to thank the following people for their contributions: Ian Law from the ARC- Plant Protection Research Institute for the collection of bacterial isolates. Julian Jaftha for his advice, guidance and unlimited patience. Jaco le Roux, Bridgitta Steyn and Marinda Oosthuizen for their assistance and advice with the SDS-PAGE gels. Marleen Kock for her help and advice, in addition to the Burkholderia isolate Fanus Venter for giving me a place to hang my lab coat. The University of Pretoria and the National Research Foundation for the financial assistance during my studies. All the students with whom I have shared a lab; there are too many to mention, but thank-you for all the help, entertainment and friendship. A special word of thanks: Gayle for helping with the graphics. You helped to make my life so much easier and I am so grateful. My friends who helped me stay sane. Thank-you for your kindness and encouragement. My family, thank-you for your faith in me and all the love and support you have shown me. I am blessed to have a family that cares so much. 2 University of Pretoria etd, Lindeque M I (2006) CONTENTS SUMMARY i LIST OF ABBREVIATIONS iii LIST OF TABLES v LIST OF FIGURES vi CHAPTER 1: INTRODUCTION 1 CHAPTER 2: LITERATURE REVIEW 2.1 Introduction 3 2.2 Biological Nitrogen Fixation (BNF) 4 2.3 The root nodule 6 2.3.1 Plant signals 7 (i) Flavonoids 8 2.3.2 Bacterial signals 8 (i) The nodulation genes 8 (ii) Nod factors 9 2.3.3 Control of nodule development 9 2.3.4 Nodulation of Phaseolus species 10 2.4 Host specificity 10 2.5 Inoculation 11 2.6 The rhizobia-legume symbiosis 12 2.6.1 Plant symbionts: legumes 13 2.6.1.1 The family Fabaceae 13 3 University of Pretoria etd, Lindeque M I (2006) 2.6.1.2 The genus Phaseolus 14 2.6.2 Microbial symbionts: The rhizobia 15 2.6.3 The current taxonomy of the root-nodulating bacteria 16 (i) The genus Rhizobium 21 (ii) The genus Bradyrhizobium 22 (iii) The genus Azorhizobium 23 (iv) The genus Sinorhizobium 23 (v) The genus Mesorhizobium 24 (vi) The genus Allorhizobium 24 2.6.4 Bean symbionts 24 (i) Rhizobium tropici 25 (ii) Rhizobium etli 25 (iii) Rhizobium gallicum 25 (iv) Rhizobium giardinnii 26 2.6.5 Proposed reclassification of the rhizobia 26 2.6.6 Novel root-nodulating species 27 (i) Burkholderia species 27 (ii) Methylobacterium nodulans 28 (iii) Devosia neptuniae 28 (iv) Ralstonia taiwanensis 28 (v) Blastobacter denitrificans 28 2.7 Methods used for the characterisation of bacteria 29 2.7.1 Protein electrophoresis 29 (i) SDS-PAGE 30 (ii) Multi-locus enzyme electrophoresis (MLEE) 31 2.7.1.1 Comparison of protein electrophoretic techniques 32 2.7.2 DNA fingerprinting techniques 33 2.7.2.1 Locus-specific DNA fingerprinting techniques 34 (i) PCR-based locus-specific RFLP 34 (ii) Amplified rDNA restriction analysis (ARDRA) 34 4 University of Pretoria etd, Lindeque M I (2006) 2.7.2.2 DNA fingerprinting techniques utilizing the whole genome 35 (i) Randomly amplified DNA fingerprinting (AP-PCR, RAPD, DAF) 35 (ii) Pulsed-field gel electrophoresis (PFGE) 36 (iii) Amplified fragment length polymorphism (AFLP) 36 (iv) Repetitive sequence-based PCR (rep-PCR) 37 2.7.2.3 Comparison of the DNA fingerprinting techniques 39 2.8 DNA sequencing in bacterial systematics 40 (i) Sequencing of the16S rRNA gene 41 CHAPTER 3: CHARACTERISATION OF PUTATIVE RHIZOBIAL ISOLATES WITH SDS-PAGE AND PARTIAL 16S rDNA SEQUENCING 3.1 Introduction 42 3.2 Materials and Methods 43 3.2.1 Bacterial strains used and maintenance 43 3.2.2 Rhizosphere soil properties 46 3.2.3 SDS-PAGE of whole-cell proteins 47 (i) Bacterial strains and references used 47 (ii) Preparation of whole-cell protein extracts 48 (iii) Polyacrylamide gel electrophoresis 49 (iv) Analysis of the protein profiles 49 3.2.4 Partial 16S rDNA sequencing of selected putative rhizobial strains 50 (i) Bacterial strains used 50 (ii) Extraction of genomic DNA 50 (iii) Amplification of the 16S rRNA gene 51 (iv) Partial 16S rDNA sequencing 52 (v) Phylogenetic analysis of the 16S rRNA gene 52 3.3 Results 54 3.3.1 Rhizosphere soil properties 55 3.3.2 SDS-PAGE of whole cell proteins 56 3.3.3 16S rDNA amplification and partial 16S rDNA sequencing 64 3.3.4 Phylogenetic analysis of the partial 16S rDNA sequences 66 3.4 Discussion 69 5 University of Pretoria etd, Lindeque M I (2006) 3.4.1 Comparison of soil properties 69 3.4.2 SDS-PAGE of whole-cell proteins 71 3.4.3 The clustering of isolates in relation to host plant species and geographic location 72 3.4.4 Phylogenetic analysis 73 3.5 Conclusion 75 CHAPTER 4: GENOMIC DNA FINGERPRINTING OF PUTATIVE RHIZOBIA USING rep-PCR AMPLIFICATION 4.1 Introduction 76 4.2 Materials and Methods 78 4.2.1 Bacterial strains used and maintenance 78 4.2.2 Extraction of genomic DNA 79 4.2.3 rep-PCR amplification 80 (i) Analyses of the rep-PCR DNA fingerprints 81 (ii) Comparison of SDS-PAGE data and combined rep-PCR data 82 4.2.4 Amplification and sequencing of the nodA gene 82 4.3 Results 83 4.3.1 rep-PCR amplification 83 4.3.2 Analyses of the rep-PCR DNA fingerprints 84 4.3.3 Amplification and sequencing of the nodA gene 95 4.4 Discussion 95 4.4.1 Analyses of the rep-PCR product 95 4.4.2 The clustering of isolates in relation to host plant species and geographic location 98 4.4.3 Correlation between SDS-PAGE and rep-PCR 100 4.4.4 Sequencing of the nodA gene 102 4.5 Conclusion 103 CHAPTER 5: CONCLUDING REMARKS 104 CHAPTER 6: REFERENCES 107 6 University of Pretoria etd, Lindeque M I (2006) Diversity of root nodule bacteria associated with Phaseolus coccineus and Phaseolus vulgaris species in South Africa by Michelle Irene Lindeque PROMOTER: Dr J.B. Jaftha DEPARTMENT: Microbiology and Plant Pathology DEGREE: MSc (Microbiology) SUMMARY The association between root-nodulating bacteria and leguminous plants is advantageous due to their ability to alter atmospheric nitrogen into a useful form in a process known as biological nitrogen fixation (BNF). Research has shown that BNF is the most efficient way to supply the large amounts of nitrogen needed by plants to produce high-yielding crops. As a result, there have been numerous studies into the diversity and identity of the associated nitrogen-fixing bacterial symbionts. Recent advances in molecular microbiology together with the isolation of rhizobia from previously uninvestigated legumes have led to major revisions of rhizobial taxonomy, most notably the inclusion of bacteria from the ß-Proteobacteria in the genera Burkholderia and Ralstonia. In this study, the diversity of root nodule bacteria associated with Phaseolus coccineus and Phaseolus vulgaris species in South Africa was investigated. A selection of rhizobial isolates were characterised by SDS-PAGE of whole cell proteins and rep-PCR DNA fingerprint analyses. These results were supplemented by partial 16S rDNA sequencing of a select number of isolates to confirm their identity. Where isolates displayed unexpected genus associations, partial nodA i University of Pretoria etd, Lindeque M I (2006) sequencing was performed to determine whether these were incidental contaminants or true nodulators. Based on 16S rDNA sequence analysis, the majority of isolates investigated were fast-growers belonging to the genus Rhizobium. A few isolates showed close relationship to species of the ß- Proteobacteria genus, Burkholderia. Both the SDS-PAGE analyses and the combined rep-PCR analyses were able to resolve isolates down to strain level, but the comparison of the SDS-PAGE and 16S rDNA sequencing data confirmed that bacterial discrimination using SDS-PAGE is not useful at the genus level and higher, as isolates showing affinity to Burkholderia were mingled with isolates showing similarity to Rhizobium. These isolates were separate from the Rhizobium isolates in the combined rep-PCR dendrogram. While there were discrepancies between results obtained from SDS-PAGE and rep-PCR analyses, results from the combined rep-PCR analysis correlated with many of the results obtained in the SDS-PAGE analysis. Both geographic location and host plant species appear to have affected the grouping of isolates. Many clusters consisted of isolates from the same location or the same host plant species in both the SDS- PAGE dendrogram as well as the combined rep-PCR dendrogram. The nodA sequencing demonstrated that the majority of isolates tested contain the nodA gene indicating that they are capable of nodulation. There was a large strain diversity observed for the isolates of this study and a number of the root-nodulating bacteria of the Phaseolus spp. appear to constitute several novel nodulating genotypes. ii University of Pretoria etd, Lindeque M I (2006) LIST OF ABBREVIATIONS AP-PCR arbitrarily primed-PCR ARC Agricultural Research Council ARDRA amplified ribosomal DNA restriction analysis AFLP amplified fragment length polymorphism BNF biological nitrogen fixation bp base pairs bv. biovar ClustalX cluster analysis version X DAF DNA amplification fingerprinting °C degrees Celsius DNA deoxyribonucleic acid dNTP deoxyribonucleoside-5′-triphosphate EDTA
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