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Thesis Rests with the Author University of Bath PHD Ganoderma stem rot of oil palm (Elaeis guineensis): Mode of infection, epidemiology and biological control Rees, Robert William Award date: 2006 Awarding institution: University of Bath Link to publication Alternative formats If you require this document in an alternative format, please contact: [email protected] General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Download date: 09. Oct. 2021 i Ganoderma Stem Rot of Oil Palm (Elaeis guineensis): Mode of Infection, Epidemiology and Biological Control Submitted by Robert William Rees For the degree of Ph.D. of the University of Bath 2006 Copyright© Attention is drawn to the fact that the copyright of this thesis rests with the author. This copy of the thesis has been supplied on the condition that anyone who consults it is understood to recognise that its copyright rests with the author and that no quotation from the thesis and no information derived from it may be published without prior consent of the author. This thesis may be made available for the consultation within the University library and may be photocopied or lent to other libraries for the purpose of consultation. f a * UMI Number: U223403 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. Dissertation Publishing UMI U223403 Published by ProQuest LLC 2013. Copyright in the Dissertation held by the Author. Microform Edition © ProQuest LLC. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 ERSITY OF BATH LIBRARY 2 7 JUL 2007 ii Acknowledgements I would like to express my gratitude to my supervisors Dr Richard Cooper and Dr Julie Flood for their endless help and advice during this project. I’d especially like to thank Richard for his thorough and rapid editing of this manuscript. If this thesis is readable, he is due a large portion of the credit. I owe a huge debt of thanks to Julie for keeping me focused on the important issues relating to the project, for giving me moral support when I needed it and for being so extremely supportive of my career development, thank you very much. I’d also like to acknowledge the great help extended to me by Dr Rob Jackson, who was a great source of advice regarding molecular strategies during the project. This Ph.D. was conducted in association with LONSUM and many experiments were carried out at Bah Lias research station (BLRS). I would like to pay special thanks to Dr Hugh Foster for supporting this project, for extending me help and for being such a good breakfast/lunch/dinner companion during my visits. I am also extremely grateful to Yonnes Hasan for his invaluable assistance with logistics and practical implementation of field trials; without his help my work at Bah Lias would have been impossible. In addition, Oslan deserves tremendous credit for helping me implement the often complicated trials and for monitoring trials with incredible efficiency, I will always be very grateful. I would also like to thank Dr Steven Nelson for his help, advice and discussions on all things oil palm. I am also very appreciative of the bacon butties, roast beef lunches and the occasional beer with him and Adrine during the visits. Also, Ganoderma is a troubling beast to work with and I would like to extend my thanks to Dr Frederick Breton for our mutual Ganoderma griping sessions, his good humour and friendship. Ursula Potter was incredibly helpful for the electron microscopy studies during this project. I would also like to acknowledge the valuable contributions made to this project by Francis Briscoe, Alex Barker, Sarah Norman and Benjamin N. Short. I’d like to express my deep gratitude to Ben. Alongside his excellent work on microscopy of infected oil palm roots, which was invaluable as the basis for further ultrastructure studies of oil palm infection, I’d like to thank him for being such a good friend; an absolute legend. During my time at Bath the department was a terrific place to be and numerous people can accept culpability for this; A1 Garfunkle, ‘The General’ aka Ben Short, Tommy Gun, Hilton Macmhaoinigh, Emmsy, Rob Jacko Jackson, Jess Pollitt, Kate Hanrott, Saara Nuutinen, Jane Dickinson, Gaffer Paul Whitley, Dave Clark 5, Pete Millichap, Shifaan, the always serious Chris and Carolyn, Liz Harrison, Iaonnis, Cath Haigh, Mark Hornsey, Amelia Preedy, Ben Heath, Vicky Fleming, Reto Bazzani, Richard Parker, Shazia and all the members of lab 1.52 and write-up room 1.55. iv Abbreviations AFLP Amplified fragment length polymorphism AIR Alcohol insoluble residue (plant cell walls) ANOVA Analysis of variance BCA Biological control agent BLRS Bah Lias research station BSR Basal stem rot CABI Centre for Agriculture and Biosciences International CAGE Cellulose acetate gel electrophoresis CBH Cellobiohydrolase CBL Column barrier layer CODIT Compartmentalisation of decay in trees CPO Crude palm oil CTAB Cetylmethylammonium bromide CWDE Cell wall degrading enzymes 2,4-DAPG 2,4-diacetylphloroglucinol DMSO Dimethyl sulphoxide ED50 Effective Dose 50 EDTA Ethylenediaminetetraacetic acid EG Endo-glucanase ELISA Enzyme-linked immunosorbent assay FD Frond debris FFB Fresh fruit bunch FP Fallen palms GFP Green fluorescent protein GM Gunung Malayo estate GSM Ganoderma selective medium IM P Integrated management practice ITS Intergenic transcribed spacer Lac Laccase LiP Lignin peroxidase MES 2-N-morpholino ethanesulphonic acid MLST Multilocus sequence typing M nP Manganese peroxidase MtDNA Mitochondrial DNA NMR Nuclear magnetic resonance PAGE Polyacrylamide gel electrophoresis PCA Phenazine-1 -carboxamide PCR Polymerase chain reaction PDA Potato dextrose agar PEG Polyethylene glycol PG Endo-polygalacturonase PGL Polygalacturonide lyase PGPR Plant growth promoting rhizobacteria PKO Palm kernel oil PNG Papua New Guinea PR Pathogenesis-related proteins PyAW Pyridine: acetic acid: water RAMS Randomly amplified microsatellites RAPD Randomly amplified polymorphic DNA RBB Remazol brilliant blue rDNA Ribosomal DNA RFLP Restriction fragment length polymorphism RH Relative humidity RISR Rhizobacteria-induced systemic resistance RVU Relative viscometric units SAR Systemic acquired resistance SBJ Sonneibijangkar estate SDW Sterile distilled water SEM Scanning electron microscopy SIG Somatic incompatibility group TAD Take-all decline TE Tris EDTA TEM Transmission electron microscopy TSM Trichoderma selective medium UPGMA Unweighted pairgroup method with arithmetic USR Upper stem rot UV Ultra violet vi Ganoderma Stem Rot of Oil Palm (Elaeis guineensis): Mode o f Infection, Epidemiology and Biological Control Stem rot of oil palm, caused by Ganoderma boninense, a white-rot basidiomycete, is the main threat to oil palm production in South East Asia. Indonesia and Malaysia produce 80% of the world’s palm oil, but losses can reach 50% by the time palms reach 15 years. G. boninense can infect both roots and lower stems where it is called basal stem rot (BSR) or upper stems when it is referred to as upper stem rot (USR). Reproducible root infection was obtained using small, infested wood blocks as inoculum and revealed that intimate association of palm roots with the inoculum source was a prerequisite. This method of infection also showed variation in pathogen aggressiveness and has potential for resistance screening. Under field conditions, temperatures of exposed field soil exceeded 40°C, but Ganoderma is inhibited above 35 °C; shading markedly enhanced infection and may explain late disease appearance when canopy closure creates shade. Ultrastructure combined with biochemistry revealed that G. boninense rapidly degraded starch, lignin and cellulose and caused extensive breakdown of root cortical cell walls. Subsequent enzyme analysis showed production of all major enzyme groups, which are potential pathogenicity factors. Randomly amplified microsatellites (RAMS) were used to study epidemiology. High genetic variation of isolates was observed within fallen palms and some BSR infected trees contained several isolates of Ganoderma, whereas all isolates within USR infected trees were clonal, thus BSR and USR infections appear distinct. Basidiospores may be important for USR infections and were detected in very high numbers ( ca . 2,000 - 10,000/m3) in plantation air samples. Scanning electron microscopy (SEM) revealed that these spores have the potential to germinate on various wounded palm surfaces. Biocontrol is a possible means of disease control and several
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