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Cover_Njira.pdf 1 5/12/16 09:51 Possibilities of endophytic fungi from Kenya for growth promotion rice (Oryza sativa L.) and defense against nematodes C M Y CM MY CY CMY K Possibilities of endophytic fungi from Kenya for growth promotion of rice (Oryza sativa L.) and defense against nematodes Njira Njira Pili Njira Pili ISBN 978-9-0598995-1-3 2016 9 789059 899513 Progress is made by trial and failure; the failures are generally a hundred times more numerous than the successes; yet they are usually left unchronicled. William Ramsay, 1852 to 1916. i Promotors: Prof. Dr. Godelieve Gheysen Department of Molecular Biotechnology, Coupure Links 653, 9000 Gent. Faculty of Bioscience Engineering, Ghent University. Prof. Dr. Richard Kiprono Mibey Moi University, P.O Box 3900-30100, Eldoret, Kenya. Prof. Dr. ir. Monica Höfte Department of Crop Protection, Coupure Links 653, 9000 Gent. Faculty of Bioscience Engineering, Ghent University Dean: Prof. Dr. ir. Marc Van Meirvenne. Rector: Prof. Dr. Anne De Paepe. ii Possibilities of endophytic fungi from Kenya for growth promotion of rice (Oryza sativa L.) and defense against nematodes Njira Njira Pili Thesis submitted in fulfilment of the requirements for the degree of Doctor (PhD) in Applied Biological Sciences iii Dutch translation of the title: Mogelijkheden van endofytische schimmels uit Kenia voor groeibevordering in rijst (Oryza sativa L.) en verdediging tegen nematoden. Cover illustration Front: An upland rice field in Kenya. Pili, N.N. (2016). Possibilities of endophytic fungi from Kenya for growth promotion of rice (Oryza sativa L.) and defense against nematodes. PhD thesis, Ghent University, Ghent, Belgium. ISBN-Number: 978-90-5989-951-3 This research was supported by grants from the Special Research Fund of Ghent University (GOA 01GB3013), BOF (01W02411), the MU-K VLIR-UOS program, Moi University and COST Action FA1103. The author and the promotors give the authorisation to consult and to copy parts of this work for personal use only. Any other use is subject to the copyright laws. Permission to reproduce any material contained in this work should be obtained from the author. Promotors Author Prof. Dr. Godelieve Gheysen Njira Njira Pili Prof. Dr. ir. Monica Höfte Prof. Dr. Richard K. Mibey iv Member of examination committee Prof. Dr. ir. Patrick Van Damme (Chairman) Department of Plant Production, Coupure Links 653, B-9000, Ghent Faculty of Bioscience Engineering, Ghent University Prof. Dr. ir. Geert Haesaert (Secretary) Department of Applied Bioscience, Ghent University, Valentyn Vaerwyckweg, 1, Schoonmeersen-gebouw C, B-9000, Ghent. Prof. Dr. Godelieve Gheysen (Promotor) Department of Molecular Biotechnology, Coupure Links 653, B-9000, Ghent. Faculty of Bioscience Engineering, Ghent University. Prof. Dr. Richard Kiprono Mibey (Promotor) Moi University, P.O Box 3900-30100, Eldoret, Kenya. Prof. Dr. ir. Monica Höfte (Promotor) Department of Crop Protection, Coupure Links 653, B-9000, Ghent. Faculty of Bioscience Engineering, Ghent University. Prof. Dr. Sofie Goormachtig VIB/ Ghent University, Department of Plant Systems Biology, Technologiepark 927, B-9052, Ghent, Belgium. Prof. Dr. Dirk De Waele Laboratory of Tropical Crop improvement, Division of Crop Biotechnics, Willem de Croylaan 42-box 2455, 3001 K.U. Leuven. Faculty of Bioscience Engineering. Prof. Dr. ir. Tina Kyndt Department of Molecular Biotechnology, Coupure Links 653, B-9000, Ghent, Faculty of Bioscience Engineering, Ghent University. Prof. Dr. ir. Annemie Elsen Soil Service of Belgium, W. de Croylaan 48, 3001 Heverlee, Belgium/ Department of Biology, Nematology Unit, K.L. Ledeganckstraat 35, B-9000 Ghent, Faculty of Science, Ghent University. v Acknowledgements My experience at the Department of Molecular Biotechnology, Ghent University, is a memory worth remembering. I have felt at home since my first day at the department. The entire Mobi- group is marvellous and more so the Nema-group led by Prof. Dr. Godelieve Gheysen -my promotor. Lieve, you are not only caring, inspirational and motivating, but also an excellent, dedicated and patient mentor. Your guidance has helped me all through my research, I appreciate you so much and I thank you abundantly. Special thanks also go to Prof. Dr. Richard K. Mibey -my co-promotor, for his continuous support, valuable comments and suggestions during my PhD study and related research. His immense knowledge about fungi has motivated me a lot and I have made it one of my dream future research disciplines. Prof. Dr. ir. Monica Höfte -my other co-promotor, I thank you for your patience, motivation, valuable suggestions, comments and immense knowledge about fungi. Prof. Dr. ir. Tina Kyndt, thank you for your insightful comments and encouragement and also for the hard questions which incented me to widen my research from various perspectives. All members of the Department of Molecular Biotechnology (Ghent University) are highly acknowledged; particularly Sofie De Schynkel, Fien De Block, Geert Meesen, Isabel Verbeke, Isabel Tilmant, Lien De Smet, Shakhina Khanam, Lander Bauters, Kennedy Pkania, Lore Eggermont, Sofie Van Holle, Zobaida Lahari, Henry Mwaka, Diana Naalden, Yasinta Nzogela, Dora Quispe, Eliud Rugut, Henok Zemene Yimer, Mohammad Reza Atighi, Ruben Verbeek, Richard Singh and many others, for their support and encouragement in various academic and social issues. Dr. Soraya C. França, thank you for all the support and encouragement, especially during the write-up of my first article on fungi. All members of the Phytopathology group (Ghent University) are highly acknowledged for their individual and collective contributions towards the successful completion of this PhD thesis. My sincere thanks also go to Prof. Dr. Alexander Schouten, Prof. Dr. Florian Grundler and the entire MPM group (Bonn University) who provided me with opportunity to join their team as an exchange student, and who gave access to the laboratory and research facilities. In particular, I am grateful to Prof. Alexander for his constant guidance in setting up experiments, data collection and general supervision of my thesis abroad. Catherine Wanja Bogner and Thomas Bogner, you made our stay at Bonn really enjoyable. Big thank to you and may the Almighty GOD bless you abundantly. I am also indebted to other members of the examination committee: Prof. Dr. ir. Patrick Van Damme (Chairman), Prof. Dr. ir. Geert Haesaert (Secretary), Prof. Dr. Sofie Goormachtig (member), Prof. Dr. ir. Annemie Elsen (member) and Prof. Dr. Dirk De Waele (member) for a friendly interaction during the examination period. Their valuable comments, suggestions, critics and professional advice on the thesis are highly appreciated and have been seriously considered in improving the text. vi I am very grateful to the staff of BeCA-hub in Nairobi, particularly Dr. Robert Skilton, Dr. Francesca Stomeo and Mr. Bramwel Wanjala for their contribution toward realisation of the objectives of this thesis, especially chapter four. The farmers in Siaya, Busia, Ahero, Mwea and Kwale are highly appreciated for allowing me to collect enough samples for the lab analyses, knowing that any loss of a single plant through the destructive sampling I applied contributed to a loss of yield and/ or profit. Bravo to you farmers! The financial support offered by BOF-UGent, VLIR-UOS, Moi University, The Commissie Wetenschappelijk Onderzoek (CWO), Faculty of Bioscience Engineering, Ghent University and COST Action FA1103 is highly appreciated. To Dr. Rolf-Ferdinand Gehre and the family, thank you for the support that you have given us. You made our stay in Germany more comfortable. We appreciate a lot, and pray to the Almighty GOD to bless you abundantly. To my parents, thank you for the sacrifice you made to see me through the academic ladder. I will always remember your effort. Finally, I express my very profound gratitude to my wife Lisanza Nasiali Bonciana (Kadzo) for providing me with unfailing support and continuous encouragement throughout my years of study and through the process of researching and writing of this thesis. Njira Njira Pili vii viii Table of Contents Acknowledgements ..................................................................................................................... vi List of Abbreviations .................................................................................................................... xi Chapter 1: ....................................................................................................................................... 1 1.0 Problem statement ................................................................................................................. 1 1.1 Thesis outline ......................................................................................................................... 3 Chapter 2: ....................................................................................................................................... 5 2.0 General introduction ............................................................................................................... 5 2.1 The root-knot nematode Meloidogyne graminicola .......................................................... 10 2.2 The root-lesion nematode Pratylenchus zeae ................................................................. 12 2.3 Management practices of rice nematodes ....................................................................... 13 2.4 Endophytic fungi ..............................................................................................................
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