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A Test of Host-Taxon, Environment, and Distance Effects on Leaf Fungal Endophytes in Metrosideros on the Island of O'ahu a Th

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A TEST OF HOST-TAXON, ENVIRONMENT, AND DISTANCE EFFECTS ON LEAF FUNGAL ENDOPHYTES IN METROSIDEROS ON THE ISLAND OF O‘AHU A THESIS SUBMITTED TO THE GRADUATE DIVISION OF THE UNIVERSITY OF HAWAI‘I AT HILO IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE IN TROPICAL CONSERVATION BIOLOGY AND ENVIRONMENTAL SCIENCE DECEMBER 2019 By Gary L. Sur Thesis Committee: Dr. Rebecca Ostertag, Chairperson Dr. Jolene Sutton, Primary Advisor Dr. Scott Geib Dr. Elizabeth Stacy Acknowledgments First and foremost, I want to thank my primary advisor, Dr. Elizabeth Stacy, for her steadfast guidance, inspiration, and support throughout the course of this project. Her tireless efforts helped me overcome many seemingly insurmountable challenges, and encouraged me to become a better researcher. Additionally, I thank the members of my thesis committee Dr. Rebecca Ostertag, Dr. Jolene Sutton, and Dr. Scott Geib for their contributions in developing this project, providing lab supplies, equipment, and recommendations that were vital for this project. I thank the National Science Foundation CREST (Centers of Research Excellence in Science and Technology) grant and University of Hawai‘i at Hilo for funding this project. I also thank Doreen Koizumi for her assistance in procuring supplies, reagents, and sequencing services. Special thanks are owed to Dr. Stacy, Jennifer Johansen, and Tomoko Sakishima for collecting and storing all Metrosideros leaf samples from O‘ahu and to Anne Veillet, Renee Corpuz, and Tomoko Sakishima for their invaluable help towards completing my DNA extractions, PCRs, and library preparation. I am grateful to Audra McKinzie of ThermoFisher Scientific, and DC3 Therapeutics LLC for their Ion Torrent sequencing service. Demultiplexing and filtering of the DNA sequences and bioinformatic analyses would not have been possible without the significant efforts and patience of Dr. Geoffrey Zahn, to whom I am extremely grateful. Thanks are also owed to Dr. Naupaka Zimmerman, Dr. Karla McDermid, Deborah Beirne, Erin Datlof, Blaine Luiz, Chris Yakym, and Ron Kittle for their helpful advice with lab methods or bioinformatics and to Dr. Anthony Amend for his correspondence on factors that can influence leaf fungal communities. Finally, I thank the TCBES program, the UH Hilo Core Genetics Facility, and the U.S. Pacific Basin Agricultural Research Center for providing resources and equipment for this project. i Abstract Tree fungal endophyte (FE) communities may be influenced not only by abiotic environmental conditions, but also by varying degrees of affinity to their host plants. The landscape-dominant woody genus Metrosideros (Myrtaceae) comprises many morphologically distinct taxa that occupy different habitats throughout the Hawaiian Islands. This study used Metrosideros on O‘ahu to test the relative importance of environment versus host taxon on FE composition and diversity. Variation in FE communities due to geographic distance (across and within sites) was also examined. From each of four elevation gradients (sites), leaves were collected from four Metrosideros taxa, two sympatric taxa occurring at high elevations, representing a wetter and slightly cooler environment, and two sympatric taxa occurring at lower elevations, representing a drier and slightly warmer environment (11 trees/taxon/gradient, n = 176 trees). DNA was extracted from surface-sterilized leaf samples. Fungal DNA was amplified using barcoded internal transcribed spacer (ITS) forward and reverse primers, and the barcoded amplicons underwent next-generation sequencing (IonTorrent). The sequences were filtered in R, using RStudio and bioinformatically processed with the vegan and dada2 packages. The remaining samples (n = 113 trees) yielded 1,637 unique ESVs (exact sequence variants). Permutation tests, diversity indices, and Akaike information criterion models revealed that variation in FE diversity was significantly explained by Metrosideros taxon, site, and geographic distance. Non-metric multidimensional scaling (NMDS) plots showed considerable overlap in FE communities among host taxa and among sites, however, and evidence for host-specificity of leaf FEs was weak and restricted to 700-1,000 m above sea level. FE communities did not vary with elevation (environment); however, the elevation ranges examined may be too narrow for the detection of elevation/environmental effects. Lastly, a significant pattern of isolation by distance on FE ii community composition was detected across the island as well as within each of the four sites. These results suggest that within O‘ahu Metrosideros, leaf FE communities vary in diversity and composition across space, some of this variation is associated with host taxonomic effects and distance, and very little is associated with environmental variation across the island`s elevation gradients. iii Table of Contents Acknowledgements ..................................................................................................................... i Abstract ....................................................................................................................................... ii List of Tables ............................................................................................................................ vii List of Figures .......................................................................................................................... viii INTRODUCTION ...................................................................................................................... 1 Host-Specificity .................................................................................................................... 3 Leaf Pubescence and Fungal Communities ........................................................................ 4 Environmental Effects on Leaf FEs .................................................................................... 5 Isolation by Distance in FE Communities ......................................................................... 7 DNA Barcoding of FEs ......................................................................................................... 7 Shift to Exact Sequence Variants ....................................................................................... 8 Tree Genus Metrosideros ................................................................................................... 10 Hawaiian Metrosideros ....................................................................................................... 10 Leaf FEs in Hawaiian Metrosideros .................................................................................. 12 HYPOTHESES ........................................................................................................................ 15 METHODS ............................................................................................................................... 17 Study System ...................................................................................................................... 17 Sample Collection ............................................................................................................... 17 Surface Sterilization ........................................................................................................... 18 DNA Extraction .................................................................................................................. 19 Amplification and Sequencing .......................................................................................... 19 Polymerase Chain Reaction (PCR) ................................................................................ 20 iv PCR Purification and Dilution ....................................................................................... 20 Library Synthesis and Sequencing ................................................................................. 21 Bioinformatics .................................................................................................................... 22 Raw Sequence Demultiplexing ...................................................................................... 22 ITSxpress ....................................................................................................................... 22 ESV Filtering and Statistical Analyses .......................................................................... 23 FE Richness and Relative Abundance (H1A, H1B, H3) ................................................... 24 FE Community Dissimilarity (H1A, H2, H3) ................................................................... 25 Isolation by Distance (H3) .............................................................................................. 25 Shannon Diversity (H1A, H1B, H2, H3) ........................................................................... 26 Host-Specificity (H1A) ................................................................................................... 26 RESULTS ................................................................................................................................ 28 Amplification and Sequencing .......................................................................................... 28 Bioinformatics .................................................................................................................... 29 Taxonomy and Richness of FEs .......................................................................................
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