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University of Florida Thesis Or Dissertation Formatting Template SPATIO-TEMPORAL ANALYSIS AND MODELING OF THE SPREAD OF BANANA XANTHOMONAS WILT (BXW) AND CITRUS HUANGLONGBING (HLB): IMPLICATIONS FOR DISEASE CONTROL By MPOKI SHIMWELA A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2016 © 2016 Mpoki Shimwela To my lovely wife Luth Magnus Haule ACKNOWLEDGMENTS I would like to thank my committee members, Prof. Dr. Ariena H.C van Bruggen, Prof. Dr. Jeffrey B. Jones, Prof. Dr. Randy C. Ploetz, Prof. Dr. Wonsuk Lee and Dr. Fen Beed for their support, constructive criticism and guidance through the entire research project and preparation of this manuscript. I especially appreciate Ariena van Bruggen’s goodwill, and loyalty that she showed in the time of need. Thank you for inspiring me with your knowledge in areas beyond plant diseases epidemiology. This work was made possible by the generous support of the American people through the United States Agency for International Development (USAID)- funded Innovative Agricultural Research Initiative project (iAGRI) (Award No. CA-621-A-00- 11-00009-00). Funding from Esther B. O’Keeffe Foundation facilitated part of this research. Thanks to the IAGRI team in Morogoro, Tanzania and The Ohio State University, United States. Special thanks to IAGRI director in Tanzania Dr. David Kraybill, deputy director Dr. Isaack Minde and training specialist Dr. Emmanuel Rwambali for their support. Special thanks to IFAS Global Director Walter Bowen for facilitation of the funding and for his general guidance. Special thanks to the director of the Emerging Pathogens Institute (EPI) at the University of Florida, Prof. Dr. Glenn J. Morris, for his hospitality and giving me permission to work at the institute. Special thanks to the permanent secretary ministry of agriculture, food and cooperative (MAFCS), United Republic of Tanzania for granting me a study leave. To all my colleagues at ARI-Maruku, who assisted in one way or the other during enumeration of questionnaires. Special thanks to Dr. Jackson Nkuba, Mr. Innocent Ndyetabura, Mr. Shaban Mkulila, Mr. Sayi Bulili, Mr. Leornard Mukandala, and Mr. Byabachwezi Mgenzi for their support. Special thanks to Dr. George Mahuku, Mr. Haruni Murithi, Mr. Emmanuel Koyano and Mr. Rudolph Shirima for their professional guidance at the Pathology laboratory at the International Institute of Tropical Agriculture (IITA), Dar es Salaam. Special thanks to Prof Dr. Theodore Msogoya and Mr. 4 Deogratius Massawe for their professional guidance at the Pathology laboratory at Sokoine University of Agriculture. Special thanks to Debra Jones and Dr. Susan Halbert at Florida Department of Agriculture and Consumer Services (FDACS), Division of Plant Industry (DPI) for their support. Special thanks to my former laboratory members, Ellen Dickstein, Hong Ling Er, Shankar Shakya, Dr. Kalpana Sharma, and Dr. Weishou Shen for their help with disease scoring and leaf sampling in Citra. Thanks to Dr. Hossain A. Narouei-Khandan for his help and technical advice on species distribution modelling. Many thanks to my lovely wife Luth Magnus Haule, for love, patience, support and encouragement during the whole period of my study. To my children Gwakisa-Meschack, Debora, and Nichrous. Special thanks to my parents for instilling in me a vision for the thirst of education at an early age. I would like to specifically thank my Lucy Shimwela and Neema Shimwela and her husband Deus Shio for their support and encouragement. Special thanks to CMC church family at Alabama for your prayers. Finally, I thank Almighty God for the free gift of life, strength and wisdom for the achievement. 5 TABLE OF CONTENTS page ACKNOWLEDGMENTS ...............................................................................................................4 LIST OF TABLES ...........................................................................................................................9 LIST OF FIGURES .......................................................................................................................11 ABSTRACT ...................................................................................................................................14 CHAPTER 1 GENERAL INTRODUCTION ..............................................................................................16 Banana Xanthomonas Wilt .....................................................................................................16 Citrus Huanglongbing .............................................................................................................21 Objectives ...............................................................................................................................26 Structure of the Dissertation ...................................................................................................26 2 LOCAL AND REGIONAL SPREAD OF BANANA XANTHOMONAS WILT (BXW) IN SPACE AND OVER TIME IN KAGERA, TANZANIA .................................................30 Introduction .............................................................................................................................30 Methodology ...........................................................................................................................34 BXW Outbreak Data Acquisition ....................................................................................34 BXW Data Pre-processing ..............................................................................................35 Temporal Development of BXW ....................................................................................35 Spatial Analysis of BXW Cases in Kagera Region Landscape .......................................36 Ripley’s K Function Analysis .........................................................................................36 Getis and Ord 푮풊 ∗ (풅) ....................................................................................................38 Environmental Effects .....................................................................................................39 Ecological Niche Modelling ............................................................................................40 Regression Modeling. ......................................................................................................41 Results.....................................................................................................................................43 Temporal Progress of BXW ............................................................................................43 BXW Cluster Analysis in Kagera Region .......................................................................43 Environmental Effects .....................................................................................................44 Modeling Potential Geographic Distribution of BXW in Tanzania ................................44 Discussion ...............................................................................................................................45 3 SURVEY OF MANAGEMENT PRACTICES AND SPATIO-TEMPORAL DISTRIBUTION OF BANANA XANTHOMONAS WILT IN KAGERA REGION, TANZANIA ............................................................................................................................62 Introduction .............................................................................................................................62 Materials and Methods ...........................................................................................................65 6 Description of the Study Area .........................................................................................65 Data Collection ................................................................................................................65 Space-Time Analysis of Banana Plant Removal Records. ..............................................67 Statistical Analysis of Survey Data .................................................................................68 Results.....................................................................................................................................69 Discussion ...............................................................................................................................73 4 FIRST OCCURRENCE OF DIAPHORINA CITRI IN EAST AFRICA, CHARACTERIZATION OF THE CA. LIBERIBACTER SPECIES CAUSING HUANGLONGBING (HLB) IN TANZANIA, AND POTENTIAL FURTHER SPREAD OF D. CITRI AND HLB IN AFRICA AND EUROPE. ........................................91 Introduction .............................................................................................................................91 Materials and Methods ...........................................................................................................95 Surveys and Sample Collection in Tanzania ...................................................................95 Psyllid Identification .......................................................................................................96 DNA Extraction from Leaf Samples ...............................................................................96 DNA Extraction from Psyllid Samples ...........................................................................97 PCR Detection of Ca. L. africanus and Ca. L. asiaticus in Leaf Extracts .......................97
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