UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D. Miriam was a driving force behind my love of research and seeking answers to biological questions. I am also deeply indebted to the many faculty members at my undergraduate institution, Northern Kentucky University for providing a solid foundation to build upon. I would like to thank the Oklahoma Biological Survey staff (Trina Steil and Rannell Madding) for the continued support during my time as Ph.D. student. I’m also indebted to my colleagues Huynh Le, Chris Marks, Nate Losey, Lindsey O’Neil, and Brian Harriman, Daniel Jones, Zach Meyers, Jamie Johnson-Duffner for their friendship and collegiate discussions. Also I thank my parents Roger and Sharon Cooper have always been supportive of my adventure into graduate school. I also thank my grandmother Jeanette Cooper, iv who spent hours with me in my earlier years taking me to the Cincinnati Public Library. There I was able to cultivate my quest for knowledge, and explore any topic I became interested in, even if for brief moments. Lastly I would like to thank the Department of Microbiology and Plant Biology for the teaching assistant support granted to me during my time at the University of Oklahoma. Included within this dissertation are already published peer reviewed manuscripts, which represent Chapters 1 and 2. My contribution and the contributions of the other authors are outlined at the beginning of each chapter. v Table of Contents Acknowledgments .......................................................................................................... iv List of Tables ................................................................................................................ viii List of Figure ................................................................................................................... x Abstract ........................................................................................................................ xiii Chapter 1: Analysis of Ammonium, Nitrate, and Urea Uptake by Marine Pelagic Bacteria and Archaea during the Arctic Summer and Winter Seasons via Stable Isotope Probing ............................................................................................................................ 1 Abstract ............................................................................................................... 3 Introduction ......................................................................................................... 4 Material and Methods .......................................................................................... 7 Results ............................................................................................................... 13 Discussion .......................................................................................................... 17 Acknowledgements ........................................................................................... 27 References ......................................................................................................... 28 Chapter 2: Transcriptome Analysis of Scrippsiella trochoidea CCMP 3099 Reveals Physiological Changes Related to Nitrate Depletion .................................................... 41 Abstract .............................................................................................................. 42 Introduction ....................................................................................................... 44 Materials and Methods ...................................................................................... 48 Results .............................................................................................................. 58 Discussion .......................................................................................................... 68 Conclusion ......................................................................................................... 78 Conflict of Interest Statement ............................................................................78 Acknowledgements ........................................................................................... 78 References ......................................................................................................... 80 Chapter 3: Trophic Differences Reflected in the Elemental Stoichiometry from Transcriptomes and Proteomes of Eukaryotic Phytoplankton .....................................108 Abstract ............................................................................................................108 Introduction ..................................................................................................... 110 Methods and Materials .................................................................................... 117 Results ............................................................................................................. 129 Discussion ....................................................................................................... 136 Acknowledgements ......................................................................................... 146 References ....................................................................................................... 147 vi Chapter 4: A Case Study Approach to Teaching Introductory Biology Undergraduates the Application of Genomic Data Analysis in Ecological Studies .............................. 171 Preface ............................................................................................................. 171 Case Teaching Notes ....................................................................................... 174 Introduction ..................................................................................................... 175 Objectives ........................................................................................................ 176 Outcome .......................................................................................................... 176 Competency ..................................................................................................... 177 Misconceptions Addressed .............................................................................. 177 Background ...................................................................................................... 173 Classroom Management/Blocks of Analysis ................................................... 180 Teaching the Case ............................................................................................ 180 Questions ......................................................................................................... 180 Slides ............................................................................................................... 181 Answers to Questions ...................................................................................... 192 References ....................................................................................................... 195 Slide Image Credits ......................................................................................... 197 Appendices and Supplemental Information ................................................................ 205 vii List of Tables Chapter 1: + - Table 1. Concentrations and uptake rates of ammonium (NH4 ), nitrate (NO3 ) and urea in near-shore waters of the Alaskan Arctic during January (winter) and August (summer). Uptake rates were determined with GF/F filters (nominal pore size of 0.7 μm). Where the standard deviation (SD) is noted as not available (N.A.) it implies that n=1 for that measurement .............................................................. 35 Table 2. Percent isotopic labeling of DNA with 15N