Mechanisms of Invasion and the Microbiome of Introduced Species A Dissertation SUBMITTED TO THE FACULTY OF UNIVERSITY OF MINNESOTA BY Aaron S. David IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Eric Seabloom Georgiana May May 2016 © Aaron S. David 2016 Acknowledgements I have been fortunate to have had incredible guidance, mentorship, and assistance throughout my time as a Ph.D. student at the University of Minnesota. I would like to start by acknowledging and thanking my advisors, Dr. Eric Seabloom and Dr. Georgiana May for providing crucial support, and always engaging me in stimulating discussion. I also thank my committee members, Dr. Peter Kennedy, Dr. Linda Kinkel, and Dr. David Tilman for their guidance and expertise. I am indebted to Dr. Sally Hacker and Dr. Joey Spatafora of Oregon State University for generously welcoming me into their laboratories while I conducted my field work. Dr. Phoebe Zarnetske and Shawn Gerrity showed me the ropes out on the dunes and provided valuable insight along the way. I also have to thank the many undergraduate students who helped me in the field in laboratory. In particular, I need to thank Derek Schmidt, who traveled to Oregon with me and helped make my field work successful. I also thank my other collaborators that made this work possible, especially Dr. Peter Ruggiero and Reuben Biel who contributed to the data collection and analysis in Chapter 1, and Dr. Gina Quiram and Jennie Sirota who contributed to the study design and data collection in Chapter 4. I would also like to thank the amazing faculty, staff, and students of Ecology, Evolution, and Behavior and neighboring departments. Peter Lenz, Dr. Valerie Wong, Dr. Bradford Condon, and Dr. Zewei Song taught me critical laboratory and bioinformatics skills. I thank Dr. Will Pearse, Dr. Eric Lind, and Dr. Yann Hautier who provided guidance for the quantitative analyses. I will forever remember the kindness and i assistance of Johnathon Fankhauser before his untimely death. Thank you to all the other present and former members of the Borer-Seabloom lab group and the May lab group, particularly Dr. Elizabeth Borer, who always provided helpful feedback and ideas. Also, thank you to the EEB Graduate Coordinator Lisa Wiggins, the Directors of Graduate Studies Dr. Andrew Simons, Dr. Sarah Hobbie, and Dr. Jacques Finlay, Department Head Dr. Scott Lanyon, and the EEB front office staff who provided crucial administrative support. This work would not have been possible without funding from the Environmental Protection Agency (EPA/NCER R833836 to E.W. Seabloom, S.D. Hacker, and P. Ruggiero), the NSF Integrative Graduate Education Research and Traineeship (IGERT) Invasive Species and Genotypes program (DGE-0653827), the NSF Graduate Research Fellowship Program (NSF 00039202), the Puget Sound Mycological Society, the Bell Museum of Natural History (Dayton Fellowship), and the Ecology, Evolution, and Behavior graduate program (Florence Rothman Fellowship, EEB Research and Travel Awards). Lastly, I would like to thank my family and friends who supported me along the way. My parents, Amy and Mel, instilled in me a strong work ethic and curiosity about the world. Thank you to the Best Cohort Ever – Kristen Becklund, Jane Cowles, Christine O’Connell, Charlotte Riggs, and Tricia Rubi – for accompanying me through grad school, to the UMN Mycology Club for getting me hooked on fungi, and to the ii rotating menagerie of housemates (human and otherwise) that made these past years so memorable. Last, but certainly not least, thank you to Karen Rice – partner, friend, and willing lab assistant who provided enormous amounts of love and support. iii Dedication For Karen. iv Abstract Invasive species represent a critical threat to ecosystems and ecological communities. Understanding the mechanisms behind their invasion is important for understanding why they invade and the consequences of their invasions. Furthermore, invasive species, like all macroscopic organisms, harbor symbiotic microbes that constitute their microbiomes. Symbionts have been implicated in invasion success of several species, and they also represent an opportunity to learn about community assembly. In this dissertation, I explore the causes and consequences of plant invasion, and the microbiomes that invasive species harbor. In Chapter 1, I explore how two invasive, congeneric beachgrasses (Ammophila arenaria and A. breviligulata) differently alter plant succession in Pacific Northwest, USA dunes. The newer invader, Ammophila breviligulata, occupied a wider distribution across dunes than the established invader, A. arenaria, allowing A. breviligulata to persist longer through successional time. In Chapter 2, I characterize the above- and belowground symbionts of these two Ammophila species and the native Elymus mollis. I found that symbiont communities aboveground are most influenced by host species and geographic distance from one another, while those belowground are most influenced by environmental filtering. In Chapter 3, I conducted two experiments to test the mechanisms by which A. breviligulata invades dunes dominated by A. arenaria. I found that A. breviligulata dominates by tolerating competition from A. arenaria, and that there is some evidence that A. arenaria might limit itself via negative plant-soil feedbacks. Finally, in Chapter 4, I explore the relationship between herbivory and symbiont communities using the invasive wetland v forb Lythrum salicaria. I found positive associations between herbivory and symbiont communities indicative of facilitation. vi Table of Contents Acknowledgements .......................................................................................................... i Dedication ...................................................................................................................... iv Abstract ........................................................................................................................... v Table of Contents .......................................................................................................... vii List of Tables ............................................................................................................... viii List of Figures ................................................................................................................ ix Introduction ..................................................................................................................... 1 Chapter 1 Invasive congeners differ in successional impacts across space and time ......... 6 Chapter 2 Plant host species and geographic distance affect the structure of aboveground fungal symbiont communities, and environmental filtering affects belowground communities in a coastal dune ecosystem ........................................................................ 31 Chapter 3 Tolerance of competition and beneficial plant-soil feedbacks drive beachgrass invasion in coastal dunes .................................................................................................. 68 Chapter 4 Quantifying the associations between fungal endophytes and biocontrol- induced herbivory of invasive purple loosestrife (Lythrum salicaria L.) ......................... 96 References ............................................................................................................... 121 Appendix 1 Supplemental material for Chapter 1 .................................................. 131 Appendix 2 Supplemental material for Chapter 2 .................................................. 140 Appendix 3 Supplemental material for Chapter 3 .................................................. 142 Appendix 4 Supplemental material for Chapter 4 .................................................. 150 vii List of Tables Table 1-1 Results from the decadal study using linear mixed models with independent linear contrasts. ................................................................................................................. 26 Table 2-1 OTU assignments based on alignment-free clustering at the 97 % similarity level. .................................................................................................................................. 57 Table 2-2 Factors influencing quadrat-level endophyte isolation frequency and rarefied richness in leaves and roots based on model averaging .................................................. 58 Table 2-3 Factors influencing site-level endophyte richness in leaves and roots based on model averaging ............................................................................................................... 59 Table 2-4 Results from multiple regression on distance matrices (MRM) analyses for endophyte community composition in leaves and roots as a function of soil properties and geographic distance ................................................................................................... 60 Table 3-1 Results from linear mixed-effects models and model averaging with the dredge() function in the MuMIn R package. .................................................................... 89 Table 3-2 Results from linear models of plant-soil feedback study ................................. 91 Table 4-1 Operational taxonomic units (OTUs) with their overall isolation frequencies and taxonomic assignments. ........................................................................................... 116 Table 4-2 Non-randomness