Redutive Dehalogenation of Chlorinated Alkanes by Novel Bacteria at the Petroprocessor of Louisiana Inc
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Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2008 Redutive Dehalogenation of Chlorinated Alkanes by Novel Bacteria at the PetroProcessor of Louisiana Inc. Superfund Site Jun Yan Louisiana State University and Agricultural and Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Civil and Environmental Engineering Commons Recommended Citation Yan, Jun, "Redutive Dehalogenation of Chlorinated Alkanes by Novel Bacteria at the PetroProcessor of Louisiana Inc. Superfund Site" (2008). LSU Doctoral Dissertations. 510. https://digitalcommons.lsu.edu/gradschool_dissertations/510 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. REDUCTIVE DEHALOGENATION OF CHLORINATED ALKANES BY NOVEL BACTERIA AT THE PETROPROCESSOR OF LOUISIANA INC. SUPERFUND SITE A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agriculture and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Civil and Environmental Engineering by Jun Yan B.S., Nanjing University, China, 2000 M.S., Nanjing University, China, 2003 May 2009 ACKNOWLEDGMENTS I would like to take this opportunity to express my sincere appreciation to my advisor, Dr. William M. Moe, for offering me such a great opportunity to complete my Ph.D. research under his direction. During my study at LSU, I have enjoyed my research on this project in Dr. Moe’s group. His insightful guidance and generous support always inspire my research and encourage me to pursue the accomplishments of my career. I would like to acknowledge Dr. Fred A. Rainey, for his instruction in the field of microbiology, molecular biology, and phylogenetic analysis in this research, and Dr. John H. Pardue for his instructions on GC-MS analysis of dehalogenation products. My appreciation is also given to Dr. W. David Constant and Dr. Mark Benfield for kindly serving on my dissertation committee. I would like to thank the former and current members in our research group, Dr. Congna Li, Dr. Bing Qi, Dr. Hee-Sung Bae, Dr. Brian Rash, Kimberly Bowman, Dr. Jyoti U Rao, and Marilou Nabatilan for their supports and friendship. I would also like to thank the members from Dr. Pardue’s group, Dr. Xingmao Ma, Dr. Han-Woong Lee, Stephen E. Mbuligwe and Dr. Eun- Ju Lee, and the members of Raineylab, Dr. Manish Shukala and Ryan Callegan. My appreciation also extends to Cindy Henk from the LSU Socolofsky Microscopy Center, and Dr. William G. Henk from the LSU School of Veterinary Medicine for assistance in preparing cell samples and taking microscopy (SEM and TEM) images of bacteria isolated in this research. Special thanks are given to Dr. Milton S. da Costa and his group from Universidade de Coimbra, Portugal, for analysis of DNA G+C content; Dr. Kenneth E. Damann, Jr. from the LSU Department of Plant Pathology and Crop Physiology, and Dr. Gregg S. Pettis and his graduate student, Dongli Guan from the LSU Department of Biological Sciences for assistance with PFGE. ii Finally, I express my deepest appreciation to my wife, Jie Zhu for her encouragement, support, love, and great cooking, and my parents, Aihua Li and Xiliang Yan, for their consistent support and unconditional love. iii TABLE OF CONTENTS ACKNOWLEDGMENTS ............................................................................................................ ii LIST OF TABLES ...................................................................................................................... vii LIST OF FIGURES ................................................................................................................... viii ABSTRACT…...................... ......................................................................................................... x CHAPTER 1. INTRODUCTION AND LITERATURE REVIEW ....................................... 1 1.1 Introduction ...................................................................................................................... 1 1.2 History and Overview ...................................................................................................... 1 1.3 Toxicological Properties .................................................................................................. 3 1.4 Remediation Technologies ............................................................................................... 4 1.5 Biodegradation and Bioavailability .................................................................................. 5 1.5.1 Chlorinated Solvent Biodegradation Under Aerobic Conditions ................................. 5 1.5.2 Chlorinated Solvent Biodegradation Under Anaerobic Conditions ............................. 6 1.6 Research Objectives ....................................................................................................... 13 1.7 Dissertation Organization ............................................................................................... 13 CHAPTER 2. ENRICHMENT AND ISOLATION OF ANAEROBIC REDUCTIVE DECHLORINATION BACTERIA FROM A SUPERFUND SITE ...................................... 14 2.1 Introduction .................................................................................................................... 14 2.2 Materials and Methods ................................................................................................... 14 2.2.1 Chemicals ................................................................................................................... 14 2.2.2 Groundwater Collection ............................................................................................. 15 2.2.3 Enrichment Culture..................................................................................................... 15 2.2.4 Bacterial Isolation ....................................................................................................... 16 2.2.5 DNA Extraction and 16S rRNA Gene Sequencing .................................................... 17 2.2.6 Analytical Methods..................................................................................................... 18 2.3 Results ............................................................................................................................ 18 2.3.1 Construction of Dehalogenation Enrichment Culture ................................................ 18 2.3.2 Isolation of Dehalogenating Bacteria and Phylogenetic Analysis .............................. 19 2.4 Discussion ...................................................................................................................... 21 2.5 Conclusions .................................................................................................................... 22 CHAPTER 3. CHARACTERIZATION OF TWO NOVEL DEHALOGENATING BACTERIA………………… ..................................................................................................... 24 3.1 Introduction .................................................................................................................... 24 3.2 Material and Methods ..................................................................................................... 24 3.2.1 Chemicals ................................................................................................................... 24 3.2.2 Culture and Growth Conditions .................................................................................. 24 3.2.3 Microscopy ................................................................................................................. 25 3.2.4 Denaturing Gradient Gel Electrophoresis (DGGE) .................................................... 25 3.2.5 Southern Blotting ........................................................................................................ 27 iv 3.2.6 16S rRNA Gene Sequencing and Phylogenetic Analysis .......................................... 27 3.2.7 Dechlorination Activities ............................................................................................ 28 3.2.8 Growth, Biochemical Characteristics ......................................................................... 28 3.2.9 Oxygen and Salt Tolerance Test ................................................................................. 29 3.2.10 Pulsed Field Gel Electrophoresis (PFGE) ............................................................... 30 3.2.11 G+C Content of DNA ............................................................................................. 31 3.2.12 qPCR ....................................................................................................................... 31 3.2.13 Analytical Methods ................................................................................................. 32 3.3 Results ............................................................................................................................ 32 3.3.1 Morphology and Culture Purity .................................................................................. 32 3.3.2 Phylogenetic Analysis ................................................................................................ 33 3.3.3 Dehelogenating Activities .........................................................................................