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ABSTRACT Microbial Community Gene and Environmental

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ABSTRACT Microbial Community Gene and Environmental ABSTRACT Microbial Community Gene and Environmental Relationships in Phosphorus Biogeochemical Cycling within Streams Erick S. LeBrun, Ph.D. Mentor: Sanghoon Kang, Ph.D. Microbial communities of Bacteria, Archaea, and Fungi are known to play integral roles in phosphorus (P) biogeochemical cycles. P is a vital ecosystem nutrient due to its utilization in many of the biological molecules and processes necessary for life. P is generally considered a limiting nutrient and a sudden influx or overabundance of it can cause drastic ecosystem effects. Stream systems are particularly sensitive to P inputs, primarily anthropogenic inputs, and suffer sever effects such as eutrophication as a result. The enclosed chapters take an in-depth look at microbial communities from all three taxonomic groups within stream and unique wetland environments representing P gradients or potentially unique P environments. We first characterize and investigate the relationships of microbes existing in the open water column to their local environment as well as environmental P. We then build on this foundation using functional metagenomics to explore microbial P cycle gene relationships to each other and then directly to environmental P. Throughout this process, we utilize frontier technologies, methods, and statistics to help elucidate these complex relationships. We further introduce new methods and analyses such as the System Relation Overview of Gene Grouping (SROGG) and compare and contrast some existing methods for investigation like computational functional predictions and functional microarray analyses. Compiled, these studies offer a clearer picture of the quasi-mechanics of environmental microbial P cycling. They also highlight the magnitude of gap that exists relating to this type of study and offers a doorway along with tools for further research into the field. Copyright © 2018 by Erick S. LeBrun All rights reserved TABLE OF CONTENTS LIST OF FIGURES ......................................................................................................... viii LIST OF TABLES ............................................................................................................. xi ACKNOWLEDGMENTS ................................................................................................ xii DEDICATION ................................................................................................................. xiii CHAPTER ONE Introduction ..............................................................................................................1 Background ..................................................................................................1 Project and Chapter Objectives ...................................................................3 Author Contributions ...................................................................................6 Chapter References ......................................................................................6 CHAPTER TWO Microbial Community Structure and Function Decoupling Across a Phosphorus Gradient in Streams................................................................................................10 Abstract ......................................................................................................10 Introduction................................................................................................11 Methods ......................................................................................................13 Results ........................................................................................................20 Discussion ..................................................................................................26 Conclusions ................................................................................................30 Acknowledgements .....................................................................................31 Conflict of Interest .....................................................................................32 Statement of Data Availability ...................................................................32 Chapter References ....................................................................................32 CHAPTER THREE Rivers May Constitute an Overlooked Avenue of Dispersal for Terrestrial Fungi ....................................................................................................................38 Abstract ......................................................................................................38 Introduction................................................................................................38 Methods ......................................................................................................41 Results ........................................................................................................47 Discussion ..................................................................................................52 Conclusions ................................................................................................57 Conflict of Interest .....................................................................................57 Statement of Data Availability ...................................................................57 v Acknowledgements .....................................................................................57 Chapter References ....................................................................................58 CHAPTER FOUR A Metagenome-based Investigation of Gene Relationships for Non-substrate Associated Microbial Phosphorus Cycling in the Water Column of Streams and Rivers ....................................................................................................................65 Abstract ......................................................................................................65 Introduction................................................................................................66 Methods ......................................................................................................68 Results ........................................................................................................73 Discussion ..................................................................................................78 Conclusions ................................................................................................83 Acknowledgements .....................................................................................84 Conflict of Interest .....................................................................................84 Statement of Data Availability ...................................................................84 Chapter References ....................................................................................84 CHAPTER FIVE A Comparison of Computationally Predicted Functional Metagenomes and Microarray Analysis for Microbial P Cycle Genes in a Unique Basalt-soil Forest ....................................................................................................................90 Abstract ......................................................................................................90 Introduction................................................................................................91 Methods ......................................................................................................92 Results and discussion ...............................................................................94 Conclusions ................................................................................................96 Acknowledgements .....................................................................................97 Data availability ........................................................................................97 Competing interests ...................................................................................97 Grant information ......................................................................................97 Chapter references .....................................................................................97 CHAPTER SIX Conclusions ..........................................................................................................101 Summary of Findings and Final Thoughts...............................................101 Chapter References ..................................................................................104 APPENDICES .................................................................................................................105 APPENDIX A Supplementary Figures (Chapter two) ........................................106 APPENDIX B Supplementary Tables (Chapter two) ..........................................116 APPENDIX C Supplementary Results (Chapter two) .........................................118 Importance of Functional Data Resolution .............................................119 Illinois River Effect ..................................................................................120 Appendix C References ............................................................................121 vi APPENDIX D Supplementary Material (Chapter Three) ...................................122 Supplementary Table ...............................................................................123
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