Characterization of microbiologically influenced corrosion in pipelines by using metagenomics Dissertation by Badoor Ali Nasser In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy King Abdullah University of Science and Technology Thuwal, Kingdom of Saudi Arabia March, 2019 2 EXAMINATION COMMITTEE PAGE The dissertation of Badoor A. Nasser is approved by the examination committee. Committee Chairperson: Prof. Takashi Gojobori Committee Members: Prof. Stefan Arold , Prof. Susana Agusti , Prof. Magdy Mohamed Gad 3 © March, 2019 Badoor Ali Nasser All Rights Reserved 4 ABSTRACT Characterization of microbiologically influenced corrosion in pipelines by using metagenomics Badoor Ali Nasser Corrosion in pipelines and reservoir tanks in oil plants is a serious problem in the energy industries around the world because it causes a huge economic loss due to not only frequent replacements of the parts of pipelines and tanks but also potential damage of the entire fields of crude oil. Previous studies have revealed that corrosions are generated mainly by microbial activities and they are now called as Microbial Influenced Corrosion (MIC) or simply bio-corrosion. Bacterial species actually causing bio-corrosion is crucial for the suppression of the corrosion. To diagnose and give proper treatment to pipelines in industrial plants, it is essential to identify the bacterial species responsible for bio-corrosions. For attaining at this aim, I conducted an analysis of the microbial community at the corrosion sites in pipelines of oil plants, using the comparative metagenomic analysis along with bioinformatics and statistics. In this study, I collected and analyzed various bio-corrosion samples from four different oil fields. First, I collected samples from the seawater pipelines that are essential in the oil fields to maintain seawater injection system (field#1), and then I conducted the metagenomic analysis of these samples. The metagenomes obtained revealed that samples in both sites contain a wide range of bacterial taxa. However, the comparative 5 analysis of the microbial community with statistics in the comparison between sites with corrosion and without corrosion revealed the presence of microorganisms whose abundances were significantly higher in sites with corrosion. Some of these microbes can be sulfate reducers and sulfur oxidizers of which are considered to be casual agents in recent bio-corrosion models. In addition to the seawater pipelines, I also collect samples from corrosion sites in oil pipelines at Field #2 and #3. My metagenomic analysis combined with statistics showed that several microorganisms are speculated to be very active at the corrosion sites in the oil pipeline. Although biological mechanisms of forming bio-corrosion in the oil pipelines still remain unclear, these microbial species are suggested to be some of the responsible bacteria for bio-corrosion in the oil pipelines. Besides seawater injection systems, groundwater injection systems are often used, especially in inland oil fields. Therefore, more detailed understanding of bio- corrosion in the groundwater injection system is also required in oil industries. In the present studies, I then analyzed the microbial communities in pipelines in the oil field where groundwater is used as injection water (field #4). I collected samples from four different facilities in the field #4. Metagenome analysis revealed that microbial community structures were largely different even among samples from the same facility. Treatments such as biocide and demineralization at each location in the pipeline may affect the microbial communities independently. The results indicated that microbial 6 inspection throughout the pipeline network is important to protect industrial plants from bio-corrosions. Identifying the bacterial species responsible to bio-corrosion, this study provides us with information on bacterial indicators that will be available to classify and diagnose bio-corrosions. Furthermore, these species may be available as biomarkers to detect the events of bio-corrosion at an early stage. Then, any appropriate care such as the appropriate choice of biocides can be taken immediately and appropriately. Thus, my study will provide a platform for obtaining microbial information related to bio-corrosion that enables us to obtain a practical approach to protect them from bio-corrosion. 7 DEDICATION This thesis work is for all those who encouraged me to fly toward my dreams, who deserve to write their names beside mine on the thesis cover. Entesar Hamzah and Ali Nasser They have always loved me unconditionally, Been and still my first and neve last remodel, and taught me to work hard for the things that I desire to achieve. Mom and Dad, thank you for believing in me. To the person how live this journey with me and suffered a lot, my husband Abdualziz Alsharani, who has been a constant source of support and encouragement during the challenges of graduate school and life. I am truly thankful for having you in my life. To my little future scientist my joy and my eldest daughter Future Dr. Jude Al-shahrani and to my little baby my youngest Future Dr. Farah Al-shahrani. you bring out the best in me. You will grow up one day and see what Mom went through while taking care of you and let you know that nothing is impossible as long as you work for your dreams. Your smiley face helped me enjoying every single stage of my research. My brother and sisters: Nisreen, Khalid, Wasna, Sara, and Ghida, You all are part of my success, and I feel proud of being your sister. To my role model in profession life my uncles Amin Al-Nasser and my uncial Hesham Al- 8 Nasser Who been giving me the best advice and always support me unconditionally. I hope one day I can be as passionate, dedicated and inspiration person as you now. With much love to all my friends and my extraordinary family who have shaped my life and helped me believe as long as you believe in God then work hard for your dreams you can achieve it. I am truly thankful for having you in my life. 9 ACKNOWLEDGEMENTS Although only my name appears on the cover of this dissertation, many great people have contributed to its production. I owe my gratitude to all those people who have made this dissertation possible and because of whom my graduate experience has been one that I will cherish forever. Any attempt at any level cannot be completed without the support and guidance of learned people. I would like to express my deepest gratitude to my advisors Prof. Takashi Gojobori , His patience and support helped me overcome many crisis situations to finish this dissertation. They have been always there to listen and give advice, to him I say : ありがとう、先生 Besides my advisor, I would like to thank my mentors: Dr. Katsuhiko Mineta, Dr. Yoshimoto Saito, Mr. Mohammed Alarawi, and my mentor from Aramco , Dr. Abdulmohsen Al Humam. Not only that I am deeply grateful for their insightful comments and encouragement, but also for their continuing support and motivation that have helped me to come up with this dissertation. I really appreciate their help, efforts and the time spent with me to complete this project successfully., A great and sincere gratitude for Prof.Wael Al.Muslimany and Prof.Magdy alsaeed whom I learned the basic of Molecular microbiology from and who helped me take the first step in this wonderful path into my science career. to them I will always be thankful . 10 A very special gratitude goes out to Dr. Ashraf Gassaway who supported me when I first moved to KAUST and started my studies and for the academic support he been given me. Moreover, a big thanks to my friend Yasmeen Aldawsari for helping me to formatting this thesis work . And to Aisha, Amjad, Rasha, Halah and Yasmeen again , my friends and my support system in the dark days. To Muhamad Al-Blueshe, I learned from you a lot of things about Biocides treatment , huge thank you for being there in the toughest time. And to all my colleagues at Comparative Genomics and Genetics group, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST) who were always there provide the best help I could ask for. I really happy that I have been part of this wonderful group. Finally, I would like to thanks Research and Development Center(R&DC), Saudi Aramco, my mentor, supervisor, colleagues and upper management and the career development department not only for giving me this chance to get my PhD here in KAUST and funding this project and provide me with all sample I need but also providing continuous help and support. 11 TABLE OF CONTENTS EXAMINATION COMMITTEE PAGE ............................................................................... 2 ABSTRACT .................................................................................................................... 4 DEDICATION ................................................................................................................ 7 ACKNOWLEDGEMENTS ................................................................................................ 9 TABLE OF CONTENTS ................................................................................................. 11 LIST OF ABBREVIATIONS ............................................................................................ 14 LIST OF FIGURES ........................................................................................................ 15 CHAPTER 1 GENERAL INTRODUCTION .......................................................................