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1 Diversity and Activities of Phagotrophic 1 DIVERSITY AND ACTIVITIES OF PHAGOTROPHIC MICRO-EUKARYOTES IN BOILING SPRINGS LAKE, LASSEN VOLCANIC NATIONAL PARK ________________ A Thesis Presented to the Faculty of California State University, Chico ________________ In Partial Fulfillment of the Requirements for the Degree Master of Science in Biological Science ________________ by William Henry Harrison Reeder IV Fall 2011 2 DIVERSITY AND ACTIVITIES OF PHAGOTROPHIC MICRO-EUKARYOTES IN BOILING SPRINGS LAKE, LASSEN VOLCANIC NATIONAL PARK A Thesis by William Henry Harrison Reeder IV Fall 2011 APPROVED BY THE DEAN OF GRADUATE STUDIES AND VICE PROVOST FOR RESEARCH: _____________________________________________ Eun K. Park, Ph.D. APPROVED BY THE GRADUATE ADVISORY COMMITTEE: _____________________________________________ Gordon V. Wolfe, Ph.D., Chair ____________________________________________ Larry F. Hanne, Ph.D. _____________________________________________ Andrea K. White, Ph.D. iii ACKNOWLEDGMENTS This thesis would not have come to fruition without the help and guidance of many people. I would initially like to thank Dr. Gordon Wolfe, my advisor, for his attention and assistance through my journey. His insight, support, and direction were indispensible for the completion of this work. Without the opportunity provided to me, I would have never achieved these goals, and learned as much as I have. I want to give a special thanks to Jessica Sanck, whose assistance was mandatory for much of the early work, primarily her work with flagellates and distinct eye for the organisms. I am grateful for the financial support for this project, provided by the National Science Foundation grant MCB-0702069, which has allowed me and many other students gain knowledge and insight into the complexities of our world. I would like to thank my committee, Dr. Larry Hanne and Dr. Andrea White, for their advice and expertise with my research, and microbiology as a science. They were always there to answer any questions I had. Additionally, I am grateful to Rick Giberson. His assistance with preparation, and technical knowledge of electron microscopy was invaluable. Dr. Russell Shapiro for his help with geological questions and GPS mapping of the lake. Dr. Kenneth Stedman from Portland State University, and Drs. Mark Wilson and Patty Siering from Humboldt State University were all instrumental in launching the iii iv study, and providing a wealth of knowledge. Without their assistance I never would have been able to complete this work. Friendships and understanding eased the challenges associated with my graduate studies. Without the friendship and understanding of fellow graduate students Akira Iwami, Juan Araujo-Sarinana, Lindsey Wallace and Alena Chin-Curtis, I would not have been able to maintain sanity through this process, and specifically Sarah Hoddick for reading my thesis countless times. Finally, I would like to thank my parents, Susan and William Reeder, for their belief, and support for everything I chose to do. If it wasn’t for them, none of this would have been possible. iv v TABLE OF CONTENTS PAGE Acknowledgments .......................................................................................................................... iii List of Tables ..................................................................................................................................... viii List of Figures ................................................................................................................................... ix Abstract .............................................................................................................................................. xiii CHAPTER I. Introduction ............................................................................................................... 1 Boiling Springs Lake: Microbial Food Webs in Extreme Environments ........................................................................................ 1 Microbial Food Webs ................................................................................. 3 Microbial Eukaryote Diversity In Geothermal and Acidic Environments ........................................................................................ 4 Geothermal Environments ...................................................................... 5 Acid Mine Drainage Sites ......................................................................... 8 Coal mining sites ......................................................................................... 10 Microbial Food Webs in Geothermal and Acidic Environments ........................................................................................ 11 Geothermal Environments ...................................................................... 11 AMD Sites ....................................................................................................... 12 Coal Mining Sites ......................................................................................... 13 Objectives, Questions, and Gypotheses ............................................. 14 II. Materials & Methods ................................................................................................ 15 Study Site and Sampling ........................................................................... 15 Media Creation: Enrichments and Isolations .................................. 17 Culturing: Food Stocks and Feeding .................................................... 18 Feeding in Liquid and Solid Media ....................................................... 19 v vi CHAPTER PAGE Isolation of T. thermacidophilus: Attempts at Monoxenic Cultures ............................................................................ 19 pH and Temperature Tolerance ............................................................ 20 Environmental Distribution of T. thermacidophilus Cysts ......... 21 Microscopy: General Observation Techniques ............................... 22 Genetics: Extraction and Analysis ....................................................... 22 Clone Libraries ............................................................................................. 23 DGGE ................................................................................................................ 24 Group-specific Primers ............................................................................. 24 Sequencing and Bioinformatics ............................................................. 25 Feeding Observations via TEM and Acridine Orange Staining .................................................................................... 26 TEM................................................................................................................... 26 Acridine Orange Staining ......................................................................... 28 III. Results ........................................................................................................................... 29 Enrichment Cultures 2008 ...................................................................... 29 Genetic Characterization of Diversity - DGGE ................................. 32 Isolation Efforts ........................................................................................... 33 Enrichment Cultures 2009 ...................................................................... 42 Isolation Efforts ........................................................................................... 42 Genetic Characterization of Diversity: Clone Libraries ............... 46 Genetic Characterization of Diversity: DGGE .................................. 47 Genetic Characterization of Diversity: Group-specific PCR Primers..................................................................................................... 49 Characterization of Grazers .................................................................... 55 Screening for Viral Symbionts................................................................ 58 Summer 2010 Enrichments .................................................................... 63 IV. Discussion ............................................................................................................. 67 Major Findings ............................................................................................. 67 Vahlkampfiid Amoebae: Key Grazers ................................................. 68 T. thermacidophilus: Kamchatka and Italy ....................................... 69 Other Amoebae Associated with BSL’s Geothermal Features .. 71 Lobose Amoebae ......................................................................................... 72 Kinetoplastid Flagellates .......................................................................... 73 Other Potential Members of the Grazing Community ................. 74 Comparison to Other Sites ....................................................................... 75 Biogeography of Acidothermophilic Protists .................................. 78 vi vii CHAPTER PAGE Grazing Impact of Protists in Extreme Environments ................. 80 Suggestions for Future Work.................................................................. 82 Conclusions ................................................................................................... 85 Literature Cited ........................................................................................................................ 87 vii viii LIST OF TABLES TABLE PAGE
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