PHYLOGENETIC ANALYSES OF SPECIES-SPECIFIC MACERGENS IN SOUTH AFRICAN EXPORTABLE VEGETABLES L NWu ~ L!J.f!B_ARV BY BUKOLA RHODA AREMU A Thesis Submitted in Fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY (BIOLOGY) LIBRARY r,JIJ\Fl!H:1 JG CAMPUS CALL NO.: 2019 -07- 1 5 ACC. "1O .: : i'.&ORTH!-W IEST UNIVERSITY DEPARTMENT OF BIOLOGICAL SCIENCES FACULTY OF SCIENCE, AGRICULTURE AND TECHNOLOGY, NORTH-WEST UNIVERSITY, MAFIKENG CAMPUS, SOUTH AFRICA Supervisor: Professor Olubukola 0. Babalola 2015 NORTH-WEST UNIVERSITY • I YUNIBESITI YA BOKONE -BOPHIRIMA NOORDWES-UNIVERS ITEIT It all starts here '" DECLARATION I, the undersigned, declare that this thesis submitted to the North-West University for the degree of Doctor of Philosophy in Biology in the Faculty of Science, Agriculture and Technology, School of Environmental and Health Sciences, and the work contained herein is my original work with exception of the citations and that this work has not been submitted at any other University in part or entirety for the award of any degree. Student AREMU, Bukola Rhoda S1gnature. ::..:::~ .AJA...... ... .. Date ..<:2--q/oL?(. .. ... .. .... ... .lb.. ... .... .... .... Supervisor BABALOLA, 0.0. (Professor) Date ... '+1/ O.tf I(&. ....... II NWU· ~ · lueRARY_ DEDICATION Thi s thesis is dedicated to six indispensabl e people of my li fe ; my lovely husband O luwole Samuel Aremu, three j ewels Favour, Mercy and Grace, my dearest daddy Amos A lade Amoa and late mummy Dorcas Mosunmola Amoa. Ill ACKNOWLEDGEMENTS I would like to express my gratitude to those who assisted me. First, my supervisor Prof. Olubukola Oluranti Babalola for her support, care, directions and timely advice to ensure that this project is brought to completion. May God continue to take you from glory unto glory. I acknowledge extends to North-West University for offering me North-West Postgraduate and North-West Institutional bursary awards to pursue the PhD degree. Heartfelt gratitude also goes to Prof. 0. Rudvidzo, the head of the Department of Biological Sciences for his valuable advice and encouragement throughout my studies. Many thanks also go to all academic and support staff of the Department of Biological Sciences for their love and assistance during this work, as well as all faculty and staff members of the School of Environmental and Health Sciences, North-West University, for their valuable co­ operation. My sincere appreciation is extends to Dr. M.F. Adegboye, Dr. E.T. Alori, Dr. S.P. Banakar, Dr. C.N. Wose Kinge, Dr. H. Tak, Dr. L. Ngoma, Ms. R. Huyser and Mr. E.W. Bumunang for help rendered in the techniques or part of my research at one stage or the other, I can never thank you enough for all your troubles and patience. I would also like to thank all my colleagues in the Microbial Biotechnology Research Group for the good working relationship in the laboratory and their help. I appreciate the time spent with you all. My special thanks go to the Nigerian community at the North-West University. I am also indebted to all my friends including Mrs. M.O. Fashola, Ms. A.R. Adebayo, Mrs. A. Akindolire, Mrs. C.O. Ajilogba, Mr. and Mrs. E. Megbowon, Dr. and Mr. E.O. Fayemi, Mrs. IV I NWU LIBRARYJ A.T. Adesetan, Dr. and Mrs. A. Ayeleso, Dr. and Mrs. Akingba, Dr. M. Ogunlaran, Mrs. 0 . Fadiji, Sis. Bisi, Ms. M.A. Egbuta, Mr. and Mrs. Omotayo, Mr. R.J.N. Aka, Mr. and Mrs. Mayo, Florence Ayandokun, Sis. Ifeoma for their invaluable support. I appreciate all the members of Molopo Christian Church and Global World Distributor Ministry for all their love, assistance and prayers. I am very grateful to my father Dr. A.A. Amoa for being there for me through thick and thin. May he live long to eat the fruit of his labour. I would also like to thank my mother, mother-in-law, siblings, brother and sister-in­ law, niece, nephew and cousins. They have given me their unequivocal support. Thanks to my husband, Dr. O.S. Aremu for his spiritual, financial and moral support. He always stood by me through the good times and bad with great patience at all times, and also my children Favour, Mercy and Grace Aremu for their prayers, understanding and cooperation during the course of this programme. Thank you with all my heart! Finally, I thank all those who have helped me directly or indirectly in the successful completion of my thesis. Anyone missed in this acknowledgement is also thanked. Above all, I give all the glory to God of I am that I am, the all sufficient God who showed me the path of life, if not for Him that shed upon me His Favour, Mercy and Grace I would not have finished this work. To Him be all glory and honour forevermore. Amen V TABLE OF CONTENTS DECLARA TION ..................................................................................................................... II DEDICATION ....................................................................................................................... III ACKNOWLEDGEMENTS ................................................................................................. IV TABLE OF CONTENTS ..................................................................................................... VI LIST OF TABLES .................................................................................................................. X LIST OF FIGURES .............................................................................................................. XI GENERAL ABSTRACT ................................................................................................... XIII CHAPTER 1 ............................................................................................................................. 1 GENERAL INTRODUCTION ............................................................................................... ! 1.1 Background and Rationale ....................................................................................... I 1.2 Research Problem ..................................................................................................... 3 1.3 The Significance of the Study ................................................................................... 4 1.4 Purpose and Objectives of the Study ....................................................................... 4 1.4.1 Purpose ................................................................................................................ 4 1.4.2 Objectives of the Study ...................................................................................... 4 LIST OF PUBLICATIONS .................................................................................................... 6 CHAPTER2 ............................................................................................................................. 8 CLASSIFICATION AND TAXONOMY OF VEGETABLE MACERGENS ................... 8 Abstract ................................................................................................................................. 8 2.1 Introduction ............................................................................................................... 9 2.2 Types of Microorganisms on Vegetables ............................................................ 13 2.3 Taxonomy of Macergens ......................................................................................... 13 2.3.1 Genus Erwinia .................................................................................................. 13 2.3.2 Nomenclature of Erwinia ................................................................................. 15 2.3.3 Genus Pseudomonas ........................................................................................ 20 2.3.4 Nomenclature of Pseudomonas ....................................................................... 22 2.3.5 Genus Xanthomonas ......................................................................................... 25 VI 2.3.6 Nomenclature of Xanthomonas ....................................................................... 25 2.4 Conclusion ................................................................................................................ 28 CHAPTER 3 ........................................................................................................................... 30 METHODS FOR THE DETECTION AND QUANTIFICATION OF VEGETABLE MACER GENS .................................................................................................................... 30 Abstract ............................................................................................................................... 30 3.1 Introduction ............................................................................................................. 30 3.2 Vegetables ................................................................................................................ 32 3.3 Disease causing microorganisms in some vegetables ........................................... 33 3.4 Vegetable macergens ............................................................................................... 34 3.4.1 Primary macergens .......................................................................................... 34 3.4.2 Opportunistic macergens ................................................................................ 34 3.5 Mechanism of infection ........................................................................................... 34 3.6 Identification Methods ...........................................................................................