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Phenotypic and Genetic Diversity of Pseudomonads

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Phenotypic and Genetic Diversity of Pseudomonads PHENOTYPIC AND GENETIC DIVERSITY OF PSEUDOMONADS ASSOCIATED WITH THE ROOTS OF FIELD-GROWN CANOLA A Thesis Submitted to the College of Graduate Studies and Research In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy In the Department of Applied Microbiology and Food Science University of Saskatchewan Saskatoon By Danielle Lynn Marie Hirkala © Copyright Danielle Lynn Marie Hirkala, November 2006. All rights reserved. PERMISSION TO USE In presenting this thesis in partial fulfilment of the requirements for a Postgraduate degree from the University of Saskatchewan, I agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for copying of this thesis in any manner, in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work or, in their absence, by the Head of the Department or the Dean of the College in which my thesis work was done. It is understood that any copying or publication or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use which may be made of any material in my thesis. Requests for permission to copy or to make other use of material in this thesis in whole or part should be addressed to: Head of the Department of Applied Microbiology and Food Science University of Saskatchewan Saskatoon, Saskatchewan, S7N 5A8 i ABSTRACT Pseudomonads, particularly the fluorescent pseudomonads, are common rhizosphere bacteria accounting for a significant portion of the culturable rhizosphere bacteria. The presence and diversity of Pseudomonas spp. in the rhizosphere is important because of their ability to influence plant and soil health. Diversity is generated as the result of mutation, the rearrangement of genes within the genome and the acquisition of genes by horizontal transfer systems, e.g. plasmids, bacteriophages, transposons or integrons. The purpose of this study was to examine the phenotypic and genotypic diversity of a subset of pseudomonads (N=133) isolated from the rhizosphere and root- interior of four cultivars of field-grown canola. Pseudomonads were analyzed according to their 16S rRNA and cpn60 gene sequences and selected phenotypic properties (fatty acid methyl ester (FAME) profiles, antibiotic resistance, extracellular enzyme production and carbon substrate utilization). On the basis of 16S rRNA and cpn60 gene sequences, two major clusters were observed, the Pseudomonas fluorescens complex and the P. putida complex. Phylogenetic analysis of the partial gene sequences suggested that the phylogeny of root-associated pseudomonads had no effect on their associations with different cultivars or root zones (i.e. rhizosphere and root interior). Principal component analysis (PCA) of their phenotypic properties revealed little variation among the pseudomonads associated with different canola cultivars. Importantly, while little difference was observed in isolates from different cultivars significant phenotypic ii variation was observed in isolates from different root zones. Cluster analysis of their phenotypic properties exhibited little correlation with their phylogenetic relationships. In the majority of situations, the isolates grouped into a phylogenetic cluster had less than 75-80% similarity among their phenotypic traits despite a close evolutionary relationship as determined by 16S rRNA and cpn60 gene sequencing. The results indicated that the genotype of the rhizosphere pseudomonads was not accurately reflected in their phenotype. Analysis of the mobile genetic elements (MGEs) associated with a randomly selected subset of the pseudomonad isolates (N=66) revealed that 58% (N=38) contained plasmids, 50% (N=33) contained inducible prophages, 24% (N=16) contained integrons and 23% (N=15) contained transposons. Examination of the MGEs associated with a subset of rhizosphere pseudomonads revealed that MGEs were present in the isolates independent of the degree of similarity between their phenotypic and phylogenetic relationships. Therefore, mutation and genomic rearrangement appear to be the major influences in the observed incongruence between the phylogenetic and the phenotypic relationships of the bacteria examined. iii ACKNOWLEDGEMENTS I wish to acknowledge and thank Professor James J. Germida for the contributions that he has made to my Ph.D. I also wish to thank the members of my committee; Drs. H.D. Deneer, L.M. Nelson, S.D. Siciliano, G.G. Khatchatourians and D.R. Korber for their advice and support. My gratitude is extended to Dr. Lyle Whyte for serving as my external examiner. My sincere thanks to Arlette Seib and to all the soil microbiology 343 students whom I have taught for providing their friendship and inspiration. The financial support of the Natural Science and Engineering Research Council of Canada and the College of Graduate Studies and Research is gratefully acknowledged. Finally, thanks and love to my husband, Cris, who has provided invaluable support through my Ph.D. iv TABLE OF CONTENTS PERMISSION TO USE....................................................................................................... i ABSTRACT........................................................................................................................ ii ACKNOWLEDGMENTS ................................................................................................. iv TABLE OF CONTENTS.....................................................................................................v LIST OF TABLES........................................................................................................... viii LIST OF FIGURES ........................................................................................................... ix LIST OF ABBREVIATIONS............................................................................................ xi 1.0 INTRODUCTION ......................................................................................................1 2.0 LITERATURE REVIEW...........................................................................................5 2.1 Introduction - The rhizosphere................................................................................ 5 2.1.1 Rhizosphere microbial biodiversity..................................................................6 2.2 Pseudomonas .......................................................................................................... 7 2.2.1 General characteristics.....................................................................................9 2.2.2 Classification and taxonomy ..........................................................................10 2.3 Phenotypic classification and characterization of bacteria ................................... 12 2.3.1 Fatty acid methyl ester (FAME) profiles .......................................................17 2.3.2 Carbon substrate utilization............................................................................18 2.3.3 Extracellular enzyme production....................................................................19 2.3.4 Antibiotic resistance.......................................................................................20 2.4 Phylogenetic classification and characterization of bacteria ................................ 20 2.4.1 16S rRNA gene ..............................................................................................25 2.4.2 cpn60 gene......................................................................................................26 2.5 Diversity among pseudomonads........................................................................... 27 2.5.1 Mutation .........................................................................................................28 2.5.2 Recombination................................................................................................29 2.5.2.1 Mobile genetic elements (MGEs).....................................................30 2.5.2.1.1 Plasmids ................................................................................30 2.5.2.1.2 Transposons..........................................................................34 2.5.2.1.3 Integrons................................................................................36 2.5.2.1.4 Bacteriophages......................................................................37 v 2.6 Lateral gene transfer of genetic material in the rhizosphere................................. 39 2.6.1 Conjugation ....................................................................................................40 2.6.2 Transformation ...............................................................................................43 2.6.3 Transduction...................................................................................................46 2.6.4 Transposition..................................................................................................47 3.0 Taxonomic diversity of root-associated pseudomonads...........................................49 3.1 Introduction........................................................................................................... 49 3.2 Materials and Methods.......................................................................................... 51 3.2.1 Pseudomonas isolates.....................................................................................51
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