Taxonomic revision of Xanthomonas axonopodis pv. dieffenbachiae strains and pathogenicity on Araceae plants Elena Corina Constantin Promoters Em. Prof. Dr. Paul De Vos Dr. Martine Maes Prof. Dr. Anne Willems Thesis submitted in fulfillment of the requirements for the degree of Doctor (PhD) of Science: Biochemistry and Biotechnology Dutch translation of the title: Taxonomische herziening van Xanthomonas axonopodis pv. dieffenbachiae stammen en pathogeniteit op Araceae planten Please refer to this work as follows: Constantin, EC. (2017). Taxonomic revision of Xanthomonas axonopodis pv. dieffenbachiae strains and pathogenicity on Araceae plants. PhD thesis, Ghent University, Belgium. The author and the promotors give the authorization to consult and to copy parts of this work for personal use only. Every other use is subject to the copyright laws. Permission to reproduce any material contained in this work should be obtained from the author. Acknowledgements No one gets anywhere alone. What little we accomplish in life, we certainly owe it to the people that are around us, the people that raise us, the friends we meet, the colleagues we work with. The work that was developed in the course of this thesis would certainly not have been possible without the support of many people that have helped me on a personal or professional level. To all of them I wish to extend my gratitude, and in particular to: Martine Maes, my PhD supervisor, who gave me the opportunity to carry out the PhD in the Laboratory of Bacteriology at ILVO. Your encouragement, advices and suggestions were invaluable for completing this work. Prof. Paul De Vos and Anne Willems, my PhD supervisors from UGent, thank you very much for taking your time to read my PhD and for your positive feedback. Anne Willems, thank you for being there when I needed the most, in the last months when I could not see the light at the end of this difficult period. All members of the examination committee for their useful suggestions and constructive comments to improve this manuscript. Bart, thank you so much for your direct supervision and encouragement during the whole course of my PhD. Your wide knowledge and scientific input greatly influenced my first steps in the exciting scientific world. Writing the first article is never easy but with your guidance and support it was one of the most important and unforgettable experiences for me. I appreciate your patience, contributions of time and ideas, and seriousness. I am very grateful for our long scientific discussions till late in the evenings while your family was waiting for you. Thank you so much! Dear Johan, thank you for the help provided since I arrived at ILVO, for always listening to me, giving me scientific advice and encouraging me during the tough moments of my PhD. Thank you for making the lab, a pleasant place to work. I should admit that it was always a pleasure to meet your smile and peaceful face which could calm me down at stressful moments. Thank you for everything! My friend Rachid…you were the first person who believed in me before really knowing me. I am very grateful for all the moments we spent together from the saddest to the happiest. Thank you so much for helping me get through the difficult times and for all the unforgettable memories! i Cinzia, we shared not only the office but also a lot of wonderful moments, the long working hours in the greenhouse, my wedding in Romania, and lots of happiness. Thank you for all your help in the lab and for all the weekends you sacrificied to come to wet my plants or to grow a bacteria strain . Anca, Negin, Joanna, Steve, Annelies, Jane, Kris, Pieter, Shana, Mathias, Fran, Caroline, Godfrey, Sanne, both Inge (s), Olivier, Thomas, Brigit, Mireille, Cindy, Nadine, Johan and all the others that I might have forgotten to mention their name here, many thanks for always being so kind and helpful to me. My loving husband, Catalin, who was always my support! Thank you all your love, patience and encouragement. There are no words that can express my gratitude for all you have done for me. I can only say that I am truly blessed. My parents, sister, aunt and uncle for supporting my decision to fly here away from them, who have been so caring and loving. I always knew that you believed in me and wanted the best for me. You helped me shape my career and always guided me at every step in my life. Thank you all for making this possible. Elena May 2017 ii Examination committee Prof. Dr. Savvas Savvides (Chairman) VIB Inflammation Research Center (IRC) Ghent University Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE) Faculty of Sciences, Ghent University, Belgium Em. Prof. Dr. Paul De Vos (Promoter) Laboratory for Microbiology Faculty of Sciences, Ghent University, Belgium Dr. Martine Maes (Promoter) Plant Sciences Unit – Plant Health Flanders research institute for agriculture, fisheries and food (ILVO), Merelbeke, Belgium Prof. Dr. Anne Willems (Promoter) Laboratory for Microbiology Faculty of Sciences, Ghent University, Belgium Prof. Dr. Aurélien Carlier (Secretary) Laboratory for Microbiology Faculty of Sciences, Ghent University, Belgium Prof. Dr. Monica Höfte Laboratory of Phytopathology, Department of Crop Protection Faculty of Bioscience Engineering, Ghent University, Belgium Dr. Danny Vereecke Laboratory of Applied In vitro Plant Biotechnology, Department of Applied Biosciences Faculty of Bioscience Engineering, Ghent University, Belgium Dr. Bart Cottyn Plant Sciences Unit – Plant Health Flanders research institute for agriculture, fisheries and food (ILVO), Merelbeke, Belgium Dr. Joël Pothier Environmental Genomics and Systems Biology Research Group Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland iii Table of Contents Acknowledgements ....................................................................................................................... i Examination committee ............................................................................................................... iii Table of Contents ......................................................................................................................... iv List of abbreviations .................................................................................................................... vii Problem statement and outline .................................................................................................... 1 Summary ..................................................................................................................................... 5 Samenvatting ............................................................................................................................... 9 Chapter 1: General introduction .................................................................................................. 13 1.1 The family Araceae ...................................................................................................................... 15 1.1.1 Introduction .......................................................................................................................... 15 1.1.2 Biology of Araceae plants ..................................................................................................... 15 1.1.3 History and economic importance ....................................................................................... 17 1.1.4 Aroids breeding and cultivation ........................................................................................... 18 1.2 The genus Xanthomonas ............................................................................................................. 20 1.2.1 Introduction .......................................................................................................................... 20 1.2.2 Bacterial taxonomy............................................................................................................... 20 1.2.3 Taxonomy of the genus Xanthomonas ................................................................................. 24 1.3 Bacterial blight of aroids ............................................................................................................. 27 1.3.1 Introduction .......................................................................................................................... 27 1.3.2 Symptoms ............................................................................................................................. 28 1.3.3 Causal Organism ................................................................................................................... 29 1.3.4 Disease cycle and epidemiology ........................................................................................... 30 1.3.5 Geographic distribution ........................................................................................................ 31 1.3.6 Detection and identification ................................................................................................. 32 1.3.7 Control .................................................................................................................................. 33 1.3.8 Economic impact and legislative relevance.......................................................................... 34 1.4 Virulence factors in Xanthomonas .............................................................................................. 35