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Doctoral Dissertation Template UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE METAGENOMIC INSIGHTS INTO MICROBIAL COMMUNITY RESPONSES TO LONG-TERM ELEVATED CO2 A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By QICHAO TU Norman, Oklahoma 2014 METAGENOMIC INSIGHTS INTO MICROBIAL COMMUNITY RESPONSES TO LONG-TERM ELEVATED CO2 A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Jizhong Zhou, Chair ______________________________ Dr. Meijun Zhu ______________________________ Dr. Fengxia (Felicia) Qi ______________________________ Dr. Michael McInerney ______________________________ Dr. Bradley Stevenson © Copyright by QICHAO TU 2014 All Rights Reserved. Acknowledgements At this special moment approaching the last stage for this degree, I would like to express my gratitude to all the people who encouraged me and helped me out through the past years. Dr. Jizhong Zhou, my advisor, is no doubt the most influential and helpful person in pursuing my academic goals. In addition to continuous financial support for the past six years, he is the person who led me into the field of environmental microbiology, from a background of bioinformatics and plant molecular biology. I really appreciated the vast training I received from the many interesting projects I got involved in, without which I would hardly develop my broad experienced background from pure culture microbial genomics to complex metagenomics. Dr. Zhili He, who played a role as my second advisor, is also the person I would like to thank most. Without his help, I could be still struggling working on those manuscripts lying in my hard drive. I definitely learned a lot from him in organizing massed results into logical scientific work—skills that will benefit me for life. I also owe great thanks to my committee members—Dr. Meijun Zhu, Dr. Felicia Qi, Dr. Michael McInerney, and Dr. Bradley Steven for serving as my committee members for this long time. As a graduate student trying to develop his own background in a multidisciplinary area, I deeply appreciated their guidance throughout this whole degree period, by providing valuable suggestions for every step in pursuing this degree. The different angles they look at questions greatly benefitted me to analyze problems comprehensively. My special thanks to Dr. Felicia Qi from OU Health iv Sciences Center since every time it cost her additional hours to attend my committee meetings driving from and back to OKC. Also many thanks to many people for their help during my research, especially Dr. Joy Van Nostrand, Dr. James Voordeckers, Dr. Christopher Hemme, Dr. Liyou Wu and Dr. Ye Deng from IEG, Dr. Patrick Chain and Dr. Gary Xie from Los Alamos National Laboratory, Dr. Peter Reich and Dr. Sarah Hobbie from the University of Minnesota. The data analysis methods and scientific writing skills I learned from them would also benefit me for life. My final sincerest gratitude belongs to my maternal grandparents, my parents and my wife, for their continuous encouragements and support in my whole life. I can imagine the happiness and proudness on his wrinkled face if my grandfather were still alive, when sitting at the riverside in the twilight and talking to his old friends about his young grandson. My wife is the most beautiful, smart and hardworking lady I have ever met. Nothing could compensate the great efforts and sacrifice she has made for this new family. v Table of Contents Acknowledgements ......................................................................................................... iv Table of Contents ............................................................................................................ vi List of Tables ................................................................................................................... xi List of Figures ................................................................................................................. xii Abstract .......................................................................................................................... xvi Chapter 1: Introduction ..................................................................................................... 1 1.1 Atmospheric CO2: the background ....................................................................... 1 1.2 Effects of elevated atmospheric CO2 on macroecosystems ................................. 1 1.3 Effects of elevated atmospheric CO2 on soil microbial communities .................. 3 1.4 Microbial biodiversity and current challenges ..................................................... 6 1.5 Foci of this study .................................................................................................. 9 Chapter 2: Strain/Species Identification in Metagenomes Using Genome-Specific Markers ............................................................................................................... 13 2.1 Abstract ............................................................................................................... 13 2.2 Introduction ........................................................................................................ 15 2.3 Materials and Methods ....................................................................................... 18 2.3.1 Data resources ........................................................................................... 18 2.3.2 Selection of genome-specific markers (GSMs) ......................................... 19 2.3.3 Specificity evaluation of GSMs ................................................................. 21 2.3.4 Determining the detection limit and true positive thresholds .................... 22 2.3.5 Profiling T2D-/obesity-associated microbial strains ................................. 22 2.4 Results ................................................................................................................ 23 vi 2.4.1 Selection of strain/species-specific GSMs ................................................ 23 2.4.2 Specificity evaluation with mock community metagenomes .................... 26 2.4.3 Specificity evaluation against recently sequenced genomes and body site specific metagenomes ............................................................................. 27 2.4.4 Determining the detection limit and true positive calling thresholds for microbial identification using GSMs ...................................................... 30 2.4.5 Comparison with other approaches ........................................................... 31 2.4.6 Metagenomic profiling of type 2 diabete (T2D)-associated microbial strains/species ......................................................................................... 32 2.4.7 Metagenomic profiling of obesity-associated microbial strains/species ... 35 2.5 Discussion ........................................................................................................... 38 Chapter 3: Long-term Elevated CO2 Decreases Microbial Biodiversity by Functional Convergence ....................................................................................................... 45 3.1 Abstract ............................................................................................................... 45 3.2 Introduction ........................................................................................................ 46 3.3 Results and discussion ........................................................................................ 48 3.4 Materials and Methods ....................................................................................... 59 3.4.1 Site description and sample collection ...................................................... 59 3.4.2 Plant and soil property measurements ....................................................... 60 3.4.3 DNA extraction, purification and quantification ....................................... 61 3.4.4 Shotgun metagenome sequencing and 16S rRNA gene amplicon sequencing .............................................................................................. 61 3.4.5 Shotgun data preprocessing, gene prediction and annotation ................... 62 vii 3.4.6 16S amplicon data processing and OTU identification ............................. 63 3.4.7 Biodiversity definition and calculation ..................................................... 63 Chapter 4: Fungal Communities Respond to Long-term Elevated CO2 by Community Reassembly ......................................................................................................... 66 4.1 Abstract ............................................................................................................... 66 4.2 Introduction ........................................................................................................ 68 4.3 Materials and Methods ....................................................................................... 71 4.3.1 Site description and sample collection ...................................................... 71 4.3.2 DNA extraction, purification and quantification ....................................... 71 4.3.3 PCR amplification and 454 pyrosequencing ............................................. 71 4.3.4 Data analysis .............................................................................................. 72 4.3.5 Co-occurrence ecological network construction and analysis ................... 73 4.3.6
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