JUSTIN Y. CHAN Towards a mechanistic understanding of fungal life history strategies: Dispersal and competition as critical components of saprotrophic fungal ecology A THESIS IN FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY SCHOOL OF BIOLOGICAL, EARTH & ENVIRONMENTAL SCIENCES FACULTY OF SCIENCE FEB 2021 1 Abstract Saprotrophic fungi perform the vital role of cycling nutrients and carbon back into the environment through the decomposition of organic matter. But in a rapidly changing global environment, we do not fully understand how these environmental changes will affect the process of decomposition by saprotrophic fungi. To understand decomposition and carbon cycling at a global scale, we must first begin to identify the life history strategies that saprotrophic fungi employ. For saprotrophic fungi, resources are arrayed in patches in the environment, much like an archipelago of islands. On these resource islands, interspecific competition is intense and available resources are continually depleted as a consequence of fungal metabolism. Here, airborne dispersal is a key factor that allows fungi to avoid being restricted to an island experiencing total resource patch collapse and to persist within the environment. In this thesis, I take an experimental approach and explore how living in finite resource patches shapes allocation to dispersal in fungi, and how a resource patch can alter the course of interspecific competition. In Chapters 2 and 3, I tracked allocation to dispersal in saprotrophic fungi using Phacidium lacerum, a novel model species. In Chapter 2, I ran a Petri-dish experiment varying resource island size (Petri-dish size) and nutrient concentration to test how environmental quality influenced allocation to dispersal. In Chapter 3, I included both interspecific and intraspecific competitors to see how negative interactions changed patterns of allocation to dispersal. In Chapters 4 and 5, I focused on competition between saprotrophic fungi. In Chapter 4, I explored how the strength of competition varied across simple and complex substrates, and in Chapter 5, I tracked how wood decay was influenced by interspecific competition in a paired wood block experiment. Altogether, these studies highlight the importance of considering dispersal and competition in saprotrophic fungi, especially in the context of finite resource patches as islands. 2 Contents Abstract 2 Acknowledgements 7 List of Figures 9 List of Tables 11 List of Published Works 12 Chapter 1: Introduction: Investigating the strategies for life of wood decay fungi 1.1 Fungi 14 1.2 The global importance of wood decomposition 15 1.3 Wood as both habitat and resource for fungi 17 1.4 Life history theory and fungi 18 1.5 Resource patches as islands and fungal meta-populations 19 1.6 Dispersal and fungal life history 20 1.7 Colonisation, competition, and fungal combat 22 1.8 Community assembly and interactions 24 1.9 Understanding competition and dispersal in saprotrophic fungi 26 1.10 Competition in saprotrophic fungi 28 1.11 An experimental approach: Thesis outline 29 1.12 References 32 Chapter 2: Environmental cues for dispersal in a filamentous fungus in simulated islands 2.1 Abstract 41 2.2 Introduction 42 2.3 Methods 46 2.3.1 Species isolation and identification 46 2.3.2 Experimental Design 46 3 2.3.3 Image Analysis 47 2.3.4 Statistical Analysis 48 2.4 Results 49 2.4.1 Colony growth rate and patch edge detection 49 2.4.2 Effect of resource level on pycnidia production 50 2.4.3 Patterns of allocation to growth and dispersal across different islands 54 2.5 Discussion 54 2.5.1 Cues for dispersal 54 2.5.2 Patterns in dispersal allocation between island sizes 55 2.5.3 A two-cue model for dispersal in fungi 57 2.5.4 Conclusion 60 2.6 References 62 2.7 Supplementary Material 67 Chapter 3: When to cut your losses: Dispersal allocation in an asexual filamentous fungus in response to competition 3.1 Abstract 73 3.2 Introduction 74 3.3 Materials and methods 76 3.3.1 Study Species 76 3.3.2 Isolating Competitors 77 3.3.3 Experimental Design 77 3.3.4 Image Analysis 78 3.3.5 Statistical Analysis 79 3.4 Results 80 3.4.1 Colony growth and contact with competitors 80 3.4.2 Allocation to dispersal as a response to competition 82 3.4.3 Trade-offs in allocation 84 4 3.5 Discussion 87 3.5.1 Trade-offs in allocation 87 3.6 Conclusion 90 3.7 References 91 3.8 Supplementary Material 96 Chapter 4: Complex environments alter competitive dynamics in fungi 4.1 Abstract 98 4.2 Introduction 99 4.3 Methods 102 4.3.1 Species selection 102 4.3.2 Microbial respiration assay 103 4.3.3 Experimental design 104 4.3.4 Establishment of simple competitive environments 104 4.3.5 Establishment of wood block interactions 105 4.3.6 Statistical analysis 106 4.4 Results 107 4.4.1 Respiration rate and growth rate 107 4.4.2 Patterns of competition between fungi on agar and wood 108 4.4.3 Competitive hierarchies on agar and wood 111 4.5 Discussion 115 4.5.1 Patterns of competition across simple and complex substrates 115 4.5.2 Metabolic rate and competitive ability 117 4.5.3 Conclusion 118 4.6 References 120 4.7 Supplementary Material 126 5 Chapter 5: The effect of fungal dynamics on early wood decomposition: insights from a laboratory experiment 5.1 Abstract 129 5.2 Introduction 130 5.3 Methods 133 5.3.1 Species selection 133 5.3.2 Ability to respire cellulose and lignin 134 5.3.3 Establishing wood block interactions 135 5.3.4 Statistical analysis 137 5.4 Results 138 5.4.1 Lag in early wood decay 138 5.4.2 The effect of competition on mass change in wood blocks during early wood decay 138 5.4.3 Biomass import in early wood decay 139 5.5 Discussion 142 5.5.1 Lag in early wood decay 142 5.5.2 The effect of fungal competition on wood decay 143 5.5.3 Priority effects and implications on early wood decay 144 5.5.4 Conclusion 145 5.6 References 147 5.7 Supplementary Material 152 Chapter 6: General Conclusions 6.1 Fungal life history in the context of declining resource patches 160 6.2 The need to disperse 161 6.3 Fungus eat fungus world 163 6.4 An archipelago of ephemeral resource islands? 166 6.5 A need for theory 168 6.6 References 170 6 Acknowledgements This work has been the culmination of my academic journey thus far. I remember looking up to all the postgraduate students ahead of me, inspired by their experiments and their presentations. When I had finally started my honours year, I knew I would take the path of the PhD. The PhD has been the most intellectually rigorous and at times, was a vertical learning curve. During this process, I remember trying so hard to be what I thought the model fungal ecology researcher. The first year was challenging – learning how to make agar, use an autoclave (I am still terrified of that machine), run PCRs, and a whole gamut of microbiological lab skills. Later, I would relax from that personal mission, and I learnt to enjoy the PhD as a process. This journey has taught me many things, of which I would learn that giving presentations weren’t so scary, and that it would become one of my favourite things to do. Suffice to say, my PhD has been the biggest learning opportunity I have undertaken, and in this endeavour, I owe an enormous debt of gratitude to all the people that have made it possible. My primary supervisor, Will, has been a pillar for my PhD journey. Forever patient, his mentorship and guidance has been a driving force for me even when experiments go awry. I am eternally grateful for his wisdom and advice throughout this entire process, and I cannot thank him enough. Stephen, whom I’ve worked with since my undergraduate days, has been a constant presence in my academic journey. Always ready for a chinwag, he has always given me time when I knock on his door unannounced. His mentorship will always be appreciated. Jeff - my last supervisor. My first year was made possible because of your generosity. And Jess, thank you for bearing with me when I asked basic questions about microbiological lab technique. You are a superstar. To Lynne and the Boddy Lab, thank you for allowing me to visit your lab. Thank you, Melanie, for providing me the guides, the how-to’s, and instructions for the experimental set-ups, this process would’ve taken me far longer if it weren’t for your generosity. 7 Thank you to the Australian Research Council (DP160103765), whose granted funded the studies in this thesis. And I acknowledge the support by the government through the Australian Government Research Training Program Scholarship. Thanks to Jono, for saving my hide more times than I could count. To Hayley, thank you for all the opportunities you have given me. To MK! Thank you for collaborating with me! To Charlotte, my Bonser lab companion since before we both took this journey. Steph, for inspiring me and pushing me forward. Gina, for being the best cheerleader I could ever ask for. Maya, for all the times I’d roped you into being a research assistant with promise of dumplings, and for being the baddest B since 2008. To my parents, thank you for all the sacrifices you have made to make this possible.