University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2016 Ecology of Organohalide-Respiring Dehalococcoides mccartyi: Corrinoid Cofactor-Related Community Interactions and Controls over Strain Selection Burcu Şimşir University of Tennessee, Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Civil and Environmental Engineering Commons, and the Environmental Microbiology and Microbial Ecology Commons Recommended Citation Şimşir, Burcu, "Ecology of Organohalide-Respiring Dehalococcoides mccartyi: Corrinoid Cofactor-Related Community Interactions and Controls over Strain Selection. " PhD diss., University of Tennessee, 2016. https://trace.tennessee.edu/utk_graddiss/4111 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Burcu Şimşir entitled "Ecology of Organohalide-Respiring Dehalococcoides mccartyi: Corrinoid Cofactor-Related Community Interactions and Controls over Strain Selection." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, with a major in Environmental Engineering. Frank E. Löffler, Major Professor We have read this dissertation and recommend its acceptance: Terry Hazen, Qiang He, Gary Sayler Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Ecology of Organohalide-Respiring Dehalococcoides mccartyi: Corrinoid Cofactor-Related Community Interactions and Controls over Strain Selection A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Burcu Şimşir December 2016 by Burcu Şimşir, 2016 All Rights Reserved. ii To my angels of my life, my Grandmother Ayşe and my Mom Figen for the unconditional love and support iii “Rise to the challenge, to live your own life. Success is not something that can be measured or worn on a watch or hung on a wall… [It] is the certain knowledge that you have become yourself, the person you were meant to be from all time.” George Sheehan iv Acknowledgements This dissertation could not have been completed without great support and encouragement that I have received from so many people over the years. The PhD journey has not been easy but when I look back over the years at the end, I only find great experiences, successes, people, friendships, lessons and beautiful memories, which have made me grow in to the person who I am now. I would like to offer my most heartfelt thanks to the people who have touched my life during this journey. I would first and foremost like to thank my advisor, Dr. Frank Löffler. Thank you for giving me the opportunity to meet and explore the “Microbe Life”, which amazes me every single day. You have motivated me and gave me countless opportunities to explore and learn the subject with interesting discussions, freedom, guidance and support, for which I am very grateful. Part of my success is related to your contagious enthusiasm for science. Thank you! Dr. Jun Yan, my “Uncle Jun” deserves special recognition for being a great guiding spirit during this hard work. I owe much gratitude to you for all the guidance and support. I learned so much from our interesting discussions and fruitful collaboration. You are an amazing teacher, research mate, and uncle! I am so happy that we worked so well with each other; the work described in this dissertation could not be done without your guidance. Thank you! I would also like to thank my dissertation committee, Dr. Terry Hazen, Dr. Qiang He and Dr. Kostas Konstantinidis and Dr. Gary Sayler. Thank you for your guidance, expertise and kind support over the course of this degree. v Many thanks are to supportive and great current and former lab mates in the Löffler’s Lab. Special thanks to Yi Yang, Jeongdae Im, Jay Lee, Steve Higgins and Jenny Onley, you all are amazing friends and coworkers. Kirsti Ritalahti, Gillian Walshe Langford, Kathleen Cusick and Silke Nissen, thank you all for everything you have taught me, and great memories we shared. I would like to acknowledge Dan Williams, thank you Dan for our interesting discussions, and your kind help. I would also like to thank other faculty, staff and students I have met at University of Tennessee for all help and support. I also owe much gratitude to Dr. Göksel Demirer, my undergraduate degree-advisor. Thank you for giving me the opportunity to work on your project during the last two years of my undergraduate degree, which opened the doors of science journey. I learned so much from you as an amazing scientist and a teacher but also a great person. I am so grateful for all the inspiration and support, which encouraged me to pursue a graduate degree. I would also like to thank other faculty, staff and student from Middle East Technical University for all encouragement and support. I would also like to acknowledge Dr. Duane Graves. I am glad that I got to work with you on Third Creek project, which taught me about the practitioners’ perspectives in the field. Thank you for the interesting discussions and the great support. I also benefited greatly from my interactions with Dr. Kostas Konstantinidis. Thank you for giving me the opportunities to visit Konstantinidis’s Lab at Georgia Tech to learn bioinformatics tools. Special thanks to Despina Tsemenzti and Miguel Rodríguez for everything you taught me, and kind help. I would also like to thank Dr. Gina Austin, thank you for the endless support and motivating me to go through the most difficult year of this journey. You are an amazing teacher and a friend. I have learned so much about life from the discussions we had, which all will guide my future journeys. Most importantly, I like to give very special thanks to my family and friends, who always were there for me and cheered me during these challenging years. vi I owe much gratitude firstly to my Mom Figen Şimşir, thank you for the endless love and support; this dissertation could not have been completed without your encouragement and help. I would also like to thank my grandparents Ayşe and Faruk İşler, my father Murat Şimşir, my brothers Buğra and Burkay Şimşir, my uncle Metin İşler, my aunt Gamze Öztürk, aunt-in-law and uncle-in-law Yeliz Şimşir and Berat Öztürk, and my beloved cousin Doğukan İşler for always being there for me, for the unconditional love, support, and the many prayers you sent my way, which were always felt. I also like to thank my little angels Hira and Ada for warming my heart all the time even from so far away. I am so blessed to have you all. I also like to thank my spiritual sister, Ezgi Köker- Thank you for always being there and the unconditional love. I also owe much gratitude to my beloved fiancé Gökhan Sarıalp. It has not been easy for us being so far away from each other, thank you for being patient during these challenging years. I am so grateful for your constant encouragement, belief that I can accomplish anything, your constant love and endless support. Now it is time for our journey, I love you! I would also like to thank Gökhan’s parents Gül, and Orhan Sarıalp for their love and prayers. Many thanks are to my Knoxville family for making Knoxville my home. To Duygu and Elçin- Thank you for being always with me through lots of laughter and tears. To my Greek-dominated gang, Kostas, Loukas, Panos, Marissa, and Grace- You are all amazing people, thanks for all the support, the motivation trips, and the Greek dinners. To my Knoxville-Turkish crew, Levent, Kübra, Yasemin, Mehmet and Ogün- I am so thankful for your friendship and support. You all helped me to make Knoxville, my home and all the years in PhD life so special for me. Thank you all! vii Abstract Organohalides such as tetrachloroethene (PCE) and trichloroethene (TCE) are among the most prevalent toxic groundwater contaminants. Remediation of organohalide- contaminated sites has high priority, and efficient and cost-effective remedies are needed to prevent environment and human exposure through contaminated water. Bacterial organohalide-respiration plays a major role in organohalide detoxification. Dehalococcoides mccartyi (Dhc) are key mediators in bioremediation, since only Dhc strains have been documented in complete detoxification of chlorinated ethenes to benign ethene. Dhc depends on other microorganisms in the environment for essential growth requirements (e.g., hydrogen and vitamins). For successful implementation of the reductive dechlorination to remediate contaminated sites, microbial interactions controlling Dhc reductive dechlorination must be elucidated. The overall objective of this research was to address the key gaps in the scientific understanding of the controls over Dhc reductive dechlorination activity, including Dhc corrinoid-related interactions with other microorganisms. Detailed hydrogeological and microbial characterization of mixed chlorinated solvent contaminated Third Creek site (Knoxville, TN) attributed an important role to the creek sediment, where organohalide-respiring bacteria (e.g., Dhc and Dehalobacter) co-exist, for detoxification of contaminants. Different chlorinated solvent-amendments affected Dhc strain selection and non-dechlorinating microbial composition in enrichment cultures derived from Third Creek sediment. Corrinoid- auxotroph Dhc require corrinoid cofactor for the reductive dehalogenase enzyme systems. Microorganisms including Acetobacterium, Clostridium, Geobacter, and methanogens were identified as corrinoid-producers in the enrichment cultures. 5,6- dimethyl-benzimidazole cobamide (DMB-Cba) was the most abundant corrinoid in enrichment cultures to support Dhc reductive dechlorination.