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Multi-Dimensional Mycelia Interactions Multi-dimensional mycelia interactions A thesis submitted to Cardiff University for the degree of Doctor of Philosophy By Jade O’Leary, B.Sc (Hons) February 2018 DECLARATION This work has not been submitted in substance for any other degree or award at this or any other university or place of learning, nor is being submitted concurrently in candidature for any degree or other award. Signed ………………………………………… (candidate) Date ………………………… STATEMENT 1 This thesis is being submitted in partial fulfilment of the requirements for the degree of PhD. Signed ………………………………………… (candidate) Date ………………………… STATEMENT 2 This thesis is the result of my own independent work/investigation, except where otherwise stated. Other sources are acknowledged by explicit references. The views expressed are my own. Signed ………………………………………… (candidate) Date ………………………… STATEMENT 3 I hereby give consent for my thesis, if accepted, to be available for photocopying and for inter- library loan, and for the title and summary to be made available to outside organisations. Signed ………………………………………… (candidate) Date ………………………… STATEMENT 4: PREVIOUSLY APPROVED BAR ON ACCESS I hereby give consent for my thesis, if accepted, to be available for photocopying and for inter- library loans after expiry of a bar on access previously approved by the Academic Standards & Quality Committee. Signed ………………………………………… (candidate) Date ………………………… i Acknowledgements I would like to thank my supervisors, Dr Carsten Müller and Professor Dan Eastwood for all their time and advice, and especially Professor Lynne Boddy for her tireless dedication and infectious enthusiasm. Thanks to the Natural Environment Research Council (NERC) for studentship NE/L00243/1 and for funding UHPLC-MS analyses at the NERC Biomolecular Analysis Facility, Birmingham (NBAF-B). Many thanks also to all the technical staff, bioinformaticians and statisticians at NBAF-B: Professor Mark Viant, Dr Ulf Sommer, Dr Clement Heude, Dr Jasper Engle and Kas Houthujis, for all their hard work and for teaching me that MS data needn’t be scary. I will always be grateful to the fungal ecology group: Dr Jen Hiscox, Dr Mel Savoury, Sarah Johnston, Emma Gilmartin, Marta Misiak and Yu Fukasawa, for all their assistance, teachings and advice, and to Katie Journeaux for being a brilliant project student. Huge thanks go to 6th floor office friends: Fred Windsor, Hisham Razi, Ifan Jâms, Willow Smallbone, Rhidian Thomas, Katie Dunkley and Mike Reynolds, for many laughs over the last three years. Thank you to all my non-science friends, especially Fi, Lizzie, Stew and Dave, for always providing me with an adventure buddy when times have gotten hard, and massive thanks to Pat, who has never failed to put a smile on my face. Finally, I’d like to thank my brothers, Rhys and Sam, for always humbling me with their own ridiculous achievements, and of course, Mum and Dad, for their life time of support and encouragement. ii Statement of contributions The contributions of colleagues and students to the work presented in this thesis are explicitly detailed below: Chapter 3: Dr Jen Hiscox and Dr Mel Savoury collaborated on experimental set up, field work and harvesting procedures. Andrew Langley and Stewart McDowell assisted Dr Jen Hiscox with enzyme assays. Chapter 7: Katie Journeaux collaborated on practical lab work and bioinformatics. Chapter 8: Professor Mark Viant provided invaluable advice on experimental design. Dr Ulf Sommer ran UHPLC-MS analyses and conducted bioinformatics and metabolome annotation. Dr Jasper Engle and Kas Houthuijs collaborated on statistical analysis. iii Table of contents Acknowledgements ................................................................................................................... ii Statement of contributions ...................................................................................................... iii Table of contents ...................................................................................................................... iv Summary ................................................................................................................................... ix List of figures ............................................................................................................................ xi List of tables ............................................................................................................................ xiii List of abbreviations ............................................................................................................... xiv List of publications .................................................................................................................. xvii Chapter 1. General introduction ................................................................................................... 1 1.1 Temperate forest ecosystems and the accumulation of dead wood .................................. 1 1.2 Wood decomposers – drivers of the carbon cycle .............................................................. 2 1.3 Thesis aims........................................................................................................................... 2 Chapter 2. Wood decay basidiomycetes: their interactions and metabolism .............................. 6 2.1 Abstract ............................................................................................................................... 6 2.2 Introduction ......................................................................................................................... 7 2.3 Interspecific fungal interactions .......................................................................................... 7 2.3.1 Mechanisms of combat ................................................................................................ 8 2.3.2 Multispecies interactions ........................................................................................... 11 2.4 Fungal secondary metabolism and enzymatic decay ........................................................ 12 2.4.1 Wood, and the role of extracellular enzymes in lignocellulose decomposition ........ 13 2.4.2 Lignin modifying enzymes (LMEs) .............................................................................. 15 2.4.3 Non-ligninolytic enzymes ........................................................................................... 18 2.5 Fungal secondary metabolism: volatile organic compounds ............................................ 19 2.6 Metabolomics .................................................................................................................... 22 2.7 Conclusions ........................................................................................................................ 24 Chapter 3. Abiotic conditions alter metabolic processes during the competitive interactions of wood decay fungi: Extracellular enzyme production .................................................................. 25 3.1 Abstract ............................................................................................................................. 25 3.2 Introduction ....................................................................................................................... 26 3.3 Methods ............................................................................................................................ 28 3.3.1 Colonisation of wood blocks ....................................................................................... 28 iv 3.3.2 Interactions set up ..................................................................................................... 28 3.3.3 Harvest and re-isolation procedures ......................................................................... 31 3.3.4 Enzyme extraction and assays ................................................................................... 31 3.3.5 Statistical analysis ...................................................................................................... 34 3.4 Results ............................................................................................................................... 34 3.4.1 Interaction outcomes change under different abiotic conditions ............................. 34 3.4.2 Pre-colonisation time alters combative abilities ....................................................... 35 3.4.3 Competition affects enzyme activity during interactions in wood at 15 C and in the field ..................................................................................................................................... 37 3.4.4 Enzyme activity reflects changes to interaction outcome caused by abiotic condition ............................................................................................................................................ 39 3.4.5 Enzyme production can be tracked throughout the interaction between T. versicolor and H. fasciculare over 84 days .......................................................................................... 42 3.4.6 Rate of decay is slower during interactions than monocultures ............................... 43 3.5 Discussion .......................................................................................................................... 46 3.5.1 Reversal of outcomes at different temperatures is reflected in enzyme activity ..... 46 3.5.2 Terminal hydrolase enzyme activity is greatest during deadlock, but reactive
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