UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE DEVELOPMENT OF HIGH-THROUGHPUT EXPERIMENTAL AND COMPUTATIONAL TECHNOLOGIES FOR ANALYZING MICROBIAL FUNCTIONS AND INTERACTIONS IN ENVIRONMENTAL METAGENOMES A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By ZHOU SHI Norman, Oklahoma 2017 DEVELOPMENT OF HIGH-THROUGHPUT EXPERIMENTAL AND COMPUTATIONAL TECHNOLOGIES FOR ANALYZING MICROBIAL FUNCTIONS AND INTERACTIONS IN ENVIRONMENTAL METAGENOMES A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Lee Krumholz, Chair ______________________________ Dr. Meijun Zhu ______________________________ Dr. Sridhar Radhakrishnan ______________________________ Dr. Yiqi Luo ______________________________ Dr. Jizhong Zhou © Copyright by ZHOU SHI 2017 All Rights Reserved. Dedication I dedicate this dissertation to my wife, Mengting Yuan, whom I met and married during the time period of this work and whose love, faith and support is the greatest gift that I can ever imagine in my life; to my son, Andrew Shi, who is always curious, energetic and wonderful, and is my lasting source of enlightenment and true happiness; to my parents, Yiping Shi and Aiping Zeng, whose selfless love and care transcended the distance and time, and carried me whenever I need; to my aunt, Cindy Shi, whose unwavering support and encouragement instilled in me the spirit of striving for excellence; to my friend, Su Xu, who boarded on the same plane with me to the U.S. seven years ago and then has witnessed all parts of this work as my best friend, and Dian Zou, who passed away in an accident during the time period of this work and is a friend I will forever miss. Acknowledgement Pursuing the degree in this program is such a unique and transformative journey to me. As the end of my journey draws near, I would like to take this special opportunity to thank all the people who lifted me up through the past seven years. Without their help and support, I would have been still struggling in the middle of nowhere. First and foremost, I would like to express my immeasurable gratitude to my advisor, Dr. Jizhong Zhou, for providing me the precious opportunity to start my journey in the first place, and thereafter tremendous support and guidance throughout my entire study and research. The diverse training and research experience I received during this work under his supervision will benefit my future career undoubtedly and persistently. Also, I am deeply grateful that my advisory committee has been always greatly supportive and beneficial. I wished to thank Dr. Lee Krumholz, my advisory committee chair, for his help in improving my knowledge in a broad range of topics in molecular biology and microbial ecology, and for his guidance and suggestion in scientific writing and academic career development; Dr. Meijun Zhu, for his expert knowledge in validating and improving the mathematical parts of this work and his advice on my professional career from computational perspective; Dr. Yiqi Luo, for his lectures and insights that inspired me to see microbes as a part of the earth system and taught me the essentials in predictive research based on the paradigm of modeling; and Dr. Sridhar Radhakrishnan, for his expertise in computer science and data science, and his humorous and inspiring encouragement on this work and my professional career. I also wish to express my sincerest appreciation to many of my colleagues at IEG and project collaborators, who provided their kind help and cooperation in every single iv project in which I was involved. Their patience in explaining basic knowledge in biology and willingness to answer my absurd questions helped me speed up my adaptation to interdisciplinary research in this program and gain the confidence and experience in the accomplishing this work, especially when I just started it. v Table of contents Dedication ......................................................................................................................... 4 Acknowledgement ........................................................................................................... iv Table of contents ............................................................................................................. vi List of Tables ................................................................................................................... xi List of Figures ................................................................................................................ xiii Abstract ........................................................................................................................... xx : Introduction .................................................................................................... 1 1.1 Limitations of culture-dependent methods in microbial ecology research ............ 1 1.2 Overview of high-throughput metagenomic technologies ..................................... 2 1.3 High-throughput sequencing and challenges .......................................................... 4 1.4 High-throughput DNA microarray and challenges ................................................ 6 1.5 Inference of microbial association networks .......................................................... 7 1.6 Objectives of this study .......................................................................................... 9 : Development of a Functional Gene Array to Characterize Plant Growth Promoting Microorganisms Beneficial to Plants ............................................................ 13 2.1 Abstract ................................................................................................................. 13 2.2 Introduction .......................................................................................................... 15 2.3 Materials and methods .......................................................................................... 18 2.3.1 Designing and selecting oligonucleotide probes for the PABMC ................. 18 vi 2.3.2 Sample collection, DNA preparation, and microarray hybridization ............ 19 2.3.3 Microarray data pre-processing ..................................................................... 20 2.3.4 Statistical analysis ......................................................................................... 21 2.4 Results .................................................................................................................. 22 2.4.1 Summary of PABMC probe design ............................................................... 22 2.4.2 Selected functional genes for PABMC .......................................................... 23 2.4.3 Computational evaluation of specificity ........................................................ 26 2.4.4 Application of the PABMC to characterize PGPM communities under exotic plant invasion .......................................................................................................... 28 2.5 Discussion ............................................................................................................. 32 : Ultra-sensitive and -quantitative Detection of Microbial Populations in complex communities with New Functional Gene Arrays ............................................. 39 3.1 Abstract ................................................................................................................. 39 3.2 Introduction .......................................................................................................... 41 3.3 Materials and methods .......................................................................................... 44 3.3.1 Sequence retrieval and probe design ............................................................. 44 3.3.2 Microarray construction ................................................................................ 45 3.3.3 DNA extraction, purification, and quantification. ......................................... 45 3.3.4 Target DNA preparation, amplification and labeling .................................... 46 3.3.5 GeoChip hybridization .................................................................................. 47 vii 3.3.6 Microarray imaging and signal processing .................................................... 48 3.3.7 Statistical analysis ......................................................................................... 49 3.4 Results .................................................................................................................. 50 3.4.1 Selection of gene families and categories for array fabrications ................... 50 3.4.2 GeoChip 5.0 design and overall features ....................................................... 54 3.4.3 Optimization of hybridization conditions ...................................................... 56 3.4.4 Specificity of designed arrays ....................................................................... 57 3.4.5 Sensitivity of the designed arrays .................................................................. 60 3.4.6 Quantitation of the designed arrays ............................................................... 63 3.4.7 Application of GeoChip 5.0 to analysis of contaminated groundwater microbial communities ........................................................................................... 64 3.5 Discussion ............................................................................................................