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Isolation, Characterization, and Applications of Rhizobiophages

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Isolation, Characterization, and Applications of Rhizobiophages University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2014-10-02 Isolation, characterization, and applications of rhizobiophages Halmillawewa, Anupama Halmillawewa, A. (2014). Isolation, characterization, and applications of rhizobiophages (Unpublished doctoral thesis). University of Calgary, Calgary, AB. doi:10.11575/PRISM/26680 http://hdl.handle.net/11023/1912 doctoral thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Isolation, characterization, and applications of rhizobiophages by Anupama P. Halmillawewa A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF BIOLOGICAL SCIENCES CALGARY, ALBERTA AUGUST, 2014 © Anupama Halmillawewa 2014 Abstract Rhizobiophages are the group of bacteriophages that infect rhizobia. The rhizobia constitute a bacterial group that includes members of several different genera and are capable of nodulating legume plant roots, and providing a source of fixed nitrogen for the plant. Rhizobiophages can play a vital role in the Rhizobium-legume symbiosis by altering the population dynamics of the rhizobia present in the rhizosphere, which can be used in agriculture to improve the efficacy of commercial Rhizobium inoculants and mitigate the Rhizobium competition problem. As a prerequisite for the application of such technology, a thorough understanding of rhizobiophage biology is required. Isolation of rhizobiophages from soil samples obtained from Alberta, Saskatchewan, Ontario and British Columbia was performed using several different strains of rhizobia as trapping hosts. The isolated phages were characterized using host range, transmission electron microscopy, protein profiles and genomic characterization. All phage isolates were characterized as tailed phages belonging to the Order Caudovirales, while further classification allowed us to place them in families Siphoviridae, Myoviridae and Podoviridae. Depending on the host range, morphotype and trapping host, several phages were selected and detailed genome characterization was performed using whole genome sequencing. Five rhizobiophage genomes were sequenced to finished state (vB_RleM_P10VF, vB_RglS_P106B, vB_RleM_PPF1, vB_MloP_Lo5R7ANS, and vB_MloP_Cp1R7ANS-C2) and annotated. The complete genome sequences of vB_RglS_P106B (KF977490), vB_RleM_PPF1 (KJ746502), vB_RleM_P10VF (KM199770) and vB_MloP_Lo5R7ANS (KM199771) are publically available at the database of National Center of Biological Information (NCBI). The genome of ii vB_MloP_Cp1R7ANS-C2 will be submitted to the NCBI in the near future. The integration of temperate phage vB_RleM_PPF1 into its bacterial host R. leguminosarum F1 was also studied. The site-specific recombination system of the phage targets an integration site that lies within a putative tRNA-Pro (CGG) gene in R. leguminosarum F1. Upon integration, the phage is capable of restoring the disrupted tRNA gene, owing to the 50 bp homologous sequence (att core region) it shares with its rhizobial host. To develop a phage-based inoculant technology, the phages of Rhizobium leguminosarum with broadest possible host range were selected and tested in nodulation competition assays. The presence of phages altered the nodule occupancy by phage-sensitive and phage-resistant strains of rhizobia, increasing the efficacy of nodulation by phage- resistant rhizobia under controlled environmental conditions. iii Acknowledgements Firstly, I am extremely grateful to my supervisor, Dr. Michael Hynes for believing in me enough to give me an opportunity to work in his lab. I am indebted to him for resurrecting my own faith and rescuing my carrier in science, at a time when I was reconsidering my decision to pursue a doctoral degree and doubting my abilities after being at the receiving end of series of rejections by various graduate schools. All his advices, mentorship and constant support during my time in the lab helped me in becoming a better scientist. I am also indebted to Dr. Christopher Yost, who has been a co-supervisor than a committee member to me, for all his guidance, support and encouragements. His endless excitement and enthusiasm over anything related to science was contagious and always motivated me to give my best into everything I did. I am thankful to Dr. Kenneth Sanderson for providing helpful suggestions and feedbacks on my research over the years. I am also grateful to Dr. Tao Dong and Dr. Antonet Svircev for serving in my thesis defense and providing valuable inputs on my thesis manuscript. I would also like to extend my gratitude to Dr. Raymond Turner for taking time out from his busy schedule to teach me techniques related to ‘proteomics’. I greatly appreciate all the support provided by the University of Kelaniya, especially by the members of the Department of Microbiology, including Dr. D. L. Jayaratne and Mr. M.M. Gunawardena. I owe a big ‘thank you’ to Dr. Indrika Abeygunawardena for all her kind advices and encouragements during my struggle to get a placement to do my Ph.D. iv I consider myself as fortunate, to be a part of the Hynes lab when four wonderful scientists were around. I am thankful to Dr. Hao Ding for his scientific inputs and help for my research. I also need to thank Dr. Cynthia Yip for all her suggestions during our ‘little-scientific-coffee chats’ and her friendship. I’ve found one of the most kind-hearted, loving and caring friend and also a great researcher who never fails to inspire me in Dr. Dinah Tambalo. My work in the lab wouldn’t have been such a pleasure without the help and friendship of Marcela Restrepo. I sincerely appreciate the friendships of Dinah and Marcela, which made me feel comfortable and secure during my early days in Calgary. I am grateful to Suriakarthiga Ganesan and Rémy Gavard, two project students who worked under my supervision, for their contributions to my research. Finally, I am very thankful to all my family and friends. I wouldn’t have achieved anything in my life without the never wavering support and unconditional love of my dearest parents. Thank you very much for always being the guiding light in my world and encouraging me to chase my own dreams. And I am blessed to have my baby sister and her little encouraging and loving words in my life. v Dedication This work is dedicated to my loving parents; my father, Nihal Halmillawewa and my mother, Ranjani Halmillawewa for being there with me and making me what I am today. vi Table of Contents Abstract ............................................................................................................................... ii Acknowledgements ............................................................................................................ iv Dedication .......................................................................................................................... vi Table of Contents .............................................................................................................. vii List of Tables .................................................................................................................... xii List of Figures and Illustrations ....................................................................................... xiv List of Symbols, Abbreviations and Nomenclature ........................................................ xvii CHAPTER ONE: Introduction ............................................................................................1 1.1 Bacteriophages ...........................................................................................................1 1.1.1 Bacteriophage abundance and distribution ........................................................2 1.1.2 The general infection process of a bacteriophage: the lytic life cycle ..............3 1.1.3 Lysogeny and its consequences .........................................................................5 1.1.4 Phages as agents of horizontal gene transfer agents ..........................................8 1.1.4.1 Generalized Transduction ........................................................................8 1.1.4.2 Specialized Transduction .......................................................................10 1.1.5 Classification of bacteriophages ......................................................................10 1.1.6 Bacteriophage genomics ..................................................................................13 1.1.6.1 Diversity of phage populations ..............................................................15 1.1.6.2 Bacteriophage genome mosaicism .........................................................15 1.1.6.3 Phage genome architecture ...................................................................18 1.1.6.4 Prophages and prophage-like elements .................................................18 1.1.6.5 Phage metagenomics .............................................................................20 1.1.7 Bacteriophages and their applications .............................................................20 1.1.7.1
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