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Temporal Dynamics and Function of Root-Associated Fungi During a Non-Native Plant Invasion

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Temporal Dynamics and Function of Root-Associated Fungi During a Non-Native Plant Invasion i Temporal dynamics and function of root-associated fungi during a non-native plant invasion by Nicola J. Day A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Doctor of Philosophy in Environmental Biology Guelph, Ontario, Canada © Nicola J. Day, January 2015 ii Abstract TEMPORAL DYNAMICS AND FUNCTION OF ROOT-ASSOCIATED FUNGI DURING A NON-NATIVE PLANT INVASION Nicola Jean Day Advisors: University of Guelph, 2015 Associate Professor Pedro M. Antunes Associate Professor Kari E. Dunfield Net effects of root-associated fungal communities on plant growth range from positive to negative due to the combined effects of mutualists and pathogens, and are called plant-soil feedbacks. Exotic invasive plants may benefit more from associating with particular mutualists than with pathogens, resulting in overall positive feedback. Little is known about the identities and functions of root-associated fungal taxa and the time scales over which these communities may change during invasion. The overall aim of this thesis was to investigate temporal dynamics and function of root-associated fungal communities on the invasive plant, Vincetoxicum rossicum (Apocynaceae). A glasshouse study combined with molecular methods showed that V. rossicum was rapidly colonised by many mutualistic arbuscular mycorrhizal (AM) fungal taxa. However, my data suggested that it may take longer than one growing season for this species to exert major changes to the AM fungal community and associations with particular AM fungi can occur in localised areas. A second study using multiple sites representing a timeline over decades of invasion also showed no detectable pattern in total, AM, or pathogenic fungi. A plant-soil feedback study combined with high throughput sequencing showed that V. rossicum forms associations with a broad range of soil fungi that benefit plant growth. Large numbers of fungi that are pathogens on other plant species were detected in the roots but there was no evidence for stronger negative feedbacks or pathogen accumulation at sites of older invasion age. In a third study, plant pathogenicity tests with seven root-associated fungal taxa showed that these fungi had either neutral or positive effects on V. rossicum growth compared to uninoculated controls. Further testing of three of these fungi showed neutral effects on the native species Asclepias syriaca (Apocynaceae), but reduced the growth of Solidago canadensis (Asteraceae). These results suggest that in nature V. rossicum may gain a net benefit from all soil biota in its invasive range and may contribute to V. rossicum’s invasion success. iii Dedication I’d like to dedicate this thesis to the deceased and survivors of the Christchurch earthquake, New Zealand 21 February 2011. I genuinely think of you every day. Your strength through the challenges that you continue to face on a daily basis has often helped me to put my PhD work into perspective. Etu Kahikatea! (and kia kaha). I’m also dedicating this to my Grandad, Robert Charles Fenton, who survived the earthquakes and literally hundreds of aftershocks, as well as many other challenges through his life, but whose funeral I could not attend due to the timely nature of this PhD work. I always admired your courage, honesty, and sense of humour. Arohanui nga whanau nga whakapapa iv Acknowledgements As with all large and long projects, I have many people to thank. I am sincerely grateful to my supervisors, Pedro Antunes and Kari Dunfield, for funding this project and providing great ideas, practical advice, encouragement, and general enthusiasm. I have learned so much from your advice and successes and you have been great role models for me. I hope you consider me to be more mutualistic than pathogenic! I’d also like to thank my committee members, Jonathan Newman and Brandon Schamp for sound advice and feedback when reading this thesis. Greg Boland deserves a special mention for teaching me how to deal with fungi, letting me use his lab, and general chit-chat about life and science as a career. Thank you to the various funding sources that awarded funds to me personally: the Arthur D. Latornell Graduate Scholarship (OAC), Margaret Watling Scholarship (LU), New Zealand Federation of Graduate Women Fellowship, Ontario Federation of Anglers and Hunters, and the University of Guelph International Graduate Scholarship. I also appreciate travel grants from the Ecological Society of America Soil Section Travel Award, Robb Graduate Travel Grant (OAC), Taffy Davison Memorial Research Travel Grant (OAC), and the University of Guelph Travel Grant Award. I want to say that one of the best resources of my graduate career past and present has been the facilities and services provided by the UoG library. The Dissertation bootcamp was one of the best things I have ever done as a grad student. Robin Sakowski felt like my personal librarian at times and helped me track down those obscure references that I confess never made it to the thesis version! I also want to thank the lovely admin staff of both Algoma U and SES, as I’m aware I was often a difficult case with confusing funding but you’ve always been friendly and helpful. Specific people are mentioned for their help in each chapter so I’ll mention general appreciation here. I am truly indebted to Laura Sanderson for helping with many aspects of this thesis, including dealing with administration, talking out ideas about dog strangling vine, lab and field approaches, and beyond. You’re the best! Thanks to the rest of the Antunes and Dunfield labs for comradery and usually helpful solutions. Kamini, Karen, Crystal, and Shawn really helped me get my head round things in the early days, Liz has been a great sounding board for v the 454 work, and Therese, I’m really looking forward to snickerdoodles! Mike Mucci and Tannis Slimmon in the Science Complex Phytotron, and Jeff at Genomics are three of the most amazing and accommodating people I have ever met. I have absolutely loved working at the Phytotron. Also I want to acknowledge Brian Ohsowski and Lizzie Wandrag who have always been keen for statschats. I have had so many undergraduate workstudy students help me with generally repetitive and mundane tasks but we got there in the end and I really appreciate it. I hope that I have managed to impart some enthusiasm to you (and perhaps too much realism at times!). I’m grateful to all the people I have connected with here in Canada, and all the people back home who have never managed to figure out the time difference but have finally realised not to text me after 6pm NZ time! Mum and Dad, thanks for teaching us that we can do anything and always trusting us to make our own decisions. I also need to thank people who have provided financial support in various forms throughout this process and I genuinely wouldn’t be here without you: Mum and Dad, Matthew and Olivia, Nana, Grandma and Grandad, Kris and Mo, Mike and Liz. And of course, thanks to Daisy the dog for ensuring I take frequent breaks for walks and pats, and to Ryan for your infinite love, support, and understanding, and for helping me laugh every day. vi Table of Contents Abstract........................................................................................................................... ii Dedication ....................................................................................................................... iii Acknowledgements .........................................................................................................iv Table of Contents ............................................................................................................vi List of Tables ................................................................................................................ viii List of Figures ................................................................................................................. x Chapter 1. General introduction ............................................................................... 1 1.1. Aim and objectives ................................................................................................. 5 Chapter 2. Temporal effects of an invasive plant on arbuscular mycorrhizal fungal communities ................................................................................ 7 2.1. Abstract .................................................................................................................. 7 2.2. Introduction ............................................................................................................ 8 2.3. Methods ............................................................................................................... 11 2.3.1. Soil and seed collection ........................................................................... 11 2.3.2. Experimental design ................................................................................ 12 2.3.3. Harvest .................................................................................................... 13 2.3.4. DNA extraction from roots ....................................................................... 13 2.3.5. Polymerase Chain Reaction .................................................................... 14 2.3.6. Denaturing Gradient Gel Electrophoresis ................................................ 15 2.3.7. Gel analysis ............................................................................................. 15 2.3.8. Phylogenetic
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