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Investigation of Dehalobacter-Containing Cultures That Reductively Dechlorinate Chloroform and 1,1,1-Trichloroethane

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Investigation of Dehalobacter-Containing Cultures That Reductively Dechlorinate Chloroform and 1,1,1-Trichloroethane INVESTIGATION OF DEHALOBACTER-CONTAINING CULTURES THAT REDUCTIVELY DECHLORINATE CHLOROFORM AND 1,1,1-TRICHLOROETHANE by Shuiquan Tang A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Chemical Engineering and Applied Chemistry University of Toronto © Copyright by Shuiquan Tang 2014 INVESTIGATION OF DEHALOBACTER-CONTAINING CULTURES THAT REDUCTIVELY DECHLORINATE CHLOROFORM AND 1,1,1-TRICHLOROETHANE Shuiquan Tang Doctor of Philosophy Chemical Engineering and Applied Chemistry University of Toronto 2014 Abstract ACT-3 is an enrichment culture derived from aquifer material collected from a contaminated site in the northeastern United States. ACT-3 is currently used as a bioaugmentation culture to detoxify groundwater at sites contaminated by 1,1,1-trichloroethane (1,1,1-TCA) and chloroform (CF). This thesis aims to improve the understanding of this culture and its dominant dechlorinating organisms, Dehalobacter spp., which are commonly involved in organohalide respiration but thus far poorly understood. This research contributes to the expanding application of bioremediation for site remediation. ACT-3 can dechlorinate 1,1,1-TCA to monochloroethane (CA) via 1,1-dichloroethane (1,1-DCA), and CF to dichloromethane (DCM). By partially separating reductive dehalogenases (RDases) using blue native polyacrylamide gel electrophoresis, followed by enzymatic assays for dechlorination and peptide sequencing with liquid chromatography tandem mass spectrometry, two novel RDases were found coexpressed in ACT-3: CfrA dechlorinating 1,1,1-TCA to 1,1-DCA and CF to DCM, and DcrA dechlorinating 1,1-DCA to CA. The identification of these two RDases indicated the potential co-existence of two Dehalobacter strains in ACT-3. This was later confirmed as two complete Dehalobacter genomes were assembled from metagenomic sequences of ACT-3 and a CF-amended subculture. The coexistence of these two highly similar Dehalobacter genomes in the ACT-3 metagenome resulted in severe fragmentation in the ii preliminary assembly. An in silico gap-resolution method was developed, enabling assembly of Dehalobacter sequences from ACT-3 into a hybrid genome from two strains. By comparing this hybrid genome with the sequencing data from the CF subculture, which has only one of the two Dehalobacter strains, two separate and complete Dehalobacter genomes were obtained. One of the two genomes harbours the gene encoding CfrA and the other harbours the gene encoding DcrA. The analysis of these two genomes has significantly improved our understanding of Dehalobacter. In addition, two distinct Dehalobacter strains were successfully isolated from ACT-3 after a series of dilution-to-extinction transfers using media amended with sterile mixed culture supernatant collected from ACT-3. Finally, the complete genome of a CF- and 1,1,1-TCA-tolerant fermenting Bacteroidales strain was also assembled from metagenomic sequences. iii Acknowledgments Before joining the Edwards lab, my self-confidence was at the lowest point of my life. The research described in this thesis has restored my self-confidence. I have to thank lots of people who have helped me to accomplish this work; in the following, I will highlight some. First of all, I have to thank my supervisor, Elizabeth Edwards. There is no one better than I to appreciate the importance of having a good supervisor for Ph.D. work. “This time, you are in good luck.” This is what I told myself and what I told new students in the lab. I wished I could copy all of her shining traits and paste them into mine. Although it is impossible to learn everything from her, I have definitely learned a lot. I especially appreciate her knowledge, her compassion to anyone, her passion in science, her patience, and her way of empowering people. Everytime I discovered something exciting in my research I couldn’t wait to share it with her because she loves science. Everytime I felt frustrated with difficulties in my research, she always motivated me and gave endless ideas. “Recharged” was what felt after research meetings with her. Before this thesis, my background was bioprocess engineering, which is different from my current work, i.e. anaerobic microbial cultivation, molecular biology and metagenomics. Other than from my supervisor, there are some great teachers in this lab, from whom I learned the new techniques and knowledge. This thesis would be impossible without Ariel Grostern’s work. He is the previous Ph.D. student who established all cultures and passed them to me. He taught me how to grow anaerobic cultures. I learned PCR and Geneious from Laura Hug, a model researcher. I used to bug her frequently with questions in research because she has such a big knowledge base, comprehensive and organized. Cheryl Washer is another great teacher and a good friend. I also need to thank another three colleagues who taught me some important techniques: Melanie Dahumel, teaching me how to fix a glovebox and work with gas cylinders; Winnie Chan, teaching me the blue native polyacrylamide gel electrophoresis technique; and Alison Waller, teaching me the CTAB DNA extraction method. They are all great teachers and nice people to work with. I have to thank supporting staff in BioZone who have made this Ph.D. a lot easier. Endang Susilawati is like our lab mum, who is always ready to help. She saved me lots of time in iv ordering, searching for chemicals and glassware, etc. Before Susie joined the lab, it was Angelika Duffy who helped me with these. She is great too. Weijun Gao is our IT manager and always ready to help. He saved me lots of time installing bioinformatics software packages on our server and taught me great computer skills. Line Lomheim is our research assistant. She has helped with regular lab work and some side projects. She is such a nice coworker. I have to thank Christina heidorn, who taught me nice presentation skills and help correct our English writing. I miss the days playing pingpong with my colleagues, Xiaoming Liang, Fei Luo and Kai Wei. Playing pingpong was the most relaxed thing in my Ph.D. study; thanks for that. Thanks to Ivy Yang, who provided important advice about taking care of my newborn baby. Thanks to Alfredo Perez de Mora, who was friendly and excited about my research progress. Thanks to other colleagues in the Edwards lab, a cozy family; thanks to everyone for being so supportive all the time. Finally, I would thank my wife, Liqin Xu, and my baby, Ella Tang. They are the power that keeps me going forward. Thanks to my mother and father in China for patiently waiting for my graduation. v Table of Contents Abstract ........................................................................................................................................... ii Acknowledgments .......................................................................................................................... iv Table of Contents ........................................................................................................................... vi List of Tables ................................................................................................................................. xi List of Figures ............................................................................................................................... xii List of Appendices ....................................................................................................................... xiv List of Abbreviations ................................................................................................................... xvi Chapter 1 General Introduction ............................................................................................... 1 1.1 CHLOROFORM AND 1,1,1-TRICHLOROETHANE AS GROUNDWATER POLLUTANTS ................................................................................................................... 1 1.2 ORGANOHALIDE RESPIRATION OF CF AND 1,1,1-TCA .......................................... 3 1.3 DEHALOBACTER .............................................................................................................. 5 1.4 REDUCTIVE DEHALOGENASES .................................................................................. 6 1.5 ACT-3 AND ITS SUBCULTURES ................................................................................... 9 1.6 RATIONALE AND RESEARCH OBJECTIVES ............................................................ 11 1.7 THESIS OUTLINE ........................................................................................................... 12 1.8 STATEMENT OF AUTHORSHIP AND PUBLICATION STATUS ............................. 14 Chapter 2 Functional Characterization of Reductive Dehalogenases Using Blue Native Polyacrylamide Gel Electrophoresis ........................................................................................ 17 2.1 ABSTRACT ...................................................................................................................... 17 2.2 INTRODUCTION ............................................................................................................ 17 2.3 MATERIALS AND METHODS ...................................................................................... 19 2.3.1 Cultures and growth conditions ............................................................................ 19 2.3.2 Preparation of crude protein extracts .................................................................... 19 2.3.3
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