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Pentaerythritol Tetranitrate (PETN) & Pentolite by Environmental Microbes

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Pentaerythritol Tetranitrate (PETN) & Pentolite by Environmental Microbes Biodegradation of 2, 4, 6 Trinitrotoulene (TNT), Pentaerythritol Tetranitrate (PETN) & Pentolite by Environmental Microbes A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy Noble Elizabeth Georgie Department of Biotechnology & Environmental Biology School of Applied Sciences RMIT University August 2011 DECLARATION I certify that except where acknowledgement has been made, the work contained in this thesis is that of the authors alone. The work has not been published either as part or whole to fulfil the requirements of any other academic award. The content of the thesis is the result of work, which has been carried out since the commencement date of the research program; and any editorial work paid or unpaid, carried out by a third party is given due acknowledgement ………………………………….. Noble Elizabeth Georgie 31/08/2011 ii ACKNOWLEDGMENTS I would like to thank my supervisor A/Professor Peter M. Smooker for all his guidance, support, advice and encouragement throughout the course of my study. I would also like to thank Dr Steven Kotsonis (Orica Mining Services), my second supervisor for all his suggestions and support and for the opportunity to work with Orica for both my PhD and as an external contractor. A massive thank you to Dr Clint Brearley (Orica Mining Services), for all the support and encouragement throughout the course of my study. Thank you especially, for taking the time to edit and proof-read my thesis. It would not have been possible without your help. Thank you Dr Kaiyan Liu (Grace from Orica Mining services) for all the help and guidance. A special thank you to Steven Constantinos (Orica Mining Services) for always being my support, a shoulder to cry on when things got tough and a constant source of encouragement. I would like to thank all the lab members in the Biotech lab for their unending support. Thank you to Natalie Kikidopoulos, Aya Taki, Rinu Thomas, Emily Gan iii and Nahla Al-Mansour. Thank you to all the member of other labs especially Saikrithika Gandhi, Shanthana Gouda Admane, Shruthi Saptarshi, Sandip Kamath and Parsa Tehranchian I would like to thank all the academic and technical staff for always offering their help and being supportive. I would like to thank my friends here in Melbourne who has been just as loving as my family: Binu and Joe Elambasseril, Vinu, Kartik, Nikki, and Lavan; who with their presence and words of encouragement helped through some very hard times. I would like to thank my family despite being on the other side of the world have always encouraged and supported me over the years. My mother Valsa Georgie for her unending love and support; my father, Georgie Alexander for letting me come half-way across the world to pursue my studies and his constant support throughout it. My sister, Susan and brother in-law, Robbie for their words of encouragement and wisdom. My husband, Jobin for all the prayers, support and patience. Lastly, I owe everything to the Almighty Lord without whose grace none of this would be possible. Noble Elizabeth Georgie iv DEDICATION This thesis is dedicated to my Ma and Pa who have always supported me throughout my studies both in India and in Australia. I have reached where I am today only because of their guidance, moral support and never ending love. This thesis is also dedicated to my grandmother, who had big plans for me right from the start. I wish you were here to see what I have achieved. v TABLE OF CONTENTS Title page i Declaration ii Acknowledgements iii Dedication v Table of Contents vi List of Figures x List of Tables xii List of Abbreviations xiii Abstract 1 Chapter 1: Literature Review/ Introduction 4 1.1 Explosives 4 1.2 Types of explosives 4 1.3 Development and background of explosives 6 1.3.1 Nitrate ester explosive 6 1.3.2 Nitroaromatic explosive 7 1.3.3 Nitramine Explosives 8 1.4 Toxicity of explosives 8 1.5 Environmental issues surrounding the use of explosives and their role in environmental pollution 12 1.6 Methods of soil remediation and decontamination 13 1.6.1 Incineration 13 1.6.2 Composting 14 1.7 Biodegradation of Explosives 16 1.7.1 Biodegradation of Nitrate ester explosives 17 1.7.2 Biodegradation of Nitroaromatic explosives 18 1.7.3Biodegradatio of Nitroamine Explosives 18 1.8 TNT Degradation 19 1.8.1 Alkaline hydrolysis of TNT 19 1.8.2 Thermal decomposition of TNT 19 1.8.3 Fenton Oxidation of TNT 19 1.8.4 Photocatalysis 20 1.8.5 Biodegradation of TNT 20 1.8.5.1 Microbial metabolism of TNT 30 1.8.5.2 Aerobic Metabolism of TNT by Bacteria 30 1.8.5.3 Anaerobic Metabolism of TNT by Bacteria 31 1.8.5.4 Fungal Metabolism of TNT 32 1.9Degradation of PETN 33 1.9.1 Degradation of PETN on metal surfaces 33 vi 1.9.2 Degradation of PETN by Granular Iron 33 1.9.3 Microbial metabolism of PETN 34 1.9.4 Fungal metabolism of PETN and GTN 37 Aims 39 Chapter 2: Materials and Methods 40 2.1 General Procedures 40 2.2.1 Antibiotics, Media and Chemicals 40 2.2.2 Enzyme stocks 48 2.2.3 Microbiological Methods 49 2.2.3.1Bacterial Growth Conditions 49 2.2.3.2 Storage of bacterial strains 50 2.2.3.3 Estimation of Bacterial Cell Concentration 50 2.2.3.4 Bacterial profiles 51 2.3 DNA Molecular Techniques 51 2.3.1 Genomic DNA extraction 51 2.3.2 Quantification of DNA concentration 52 2.3.3 Polymerase Chain Reaction (PCR) 52 2.3.3.1 Primer Design 52 2.3.3.2 General PCR Amplification 53 2.3.3.3 Gradient PCR 53 2.3.3.4 Touchdown PCR 54 2.3.3.5 DNA Sequencing Reactions 54 2.3.3.5.1 Sodium-Acetate Ethanol Clean –up 55 2.3.4 Agarose Gel Electrophoresis 55 2.3.4.1 Agarose Gel Preparation 55 2.3.4.2 Sample preparation 55 2.3.4.3 Electrophoresis 56 2.3.4.4 Staining of Agarose Gels 56 2.3.4.5 Visualisation of DNA 56 2.3.4.6 Purification of DNA from PCR amplification 56 2.3.4.7 Purification of DNA fragments from Agarose Gel (Gel extraction) 57 2.3.4.8 Purification of PCR products for sequencing 58 2.3.4.9 Electroporation 58 2.3.4.9.1 Preparation of electro competent cells 58 2.4. Protein assays 58 Chapter 3: Isolation, Identification and characterisation of bacteria capable of degrading TNT and PETN 59 3.1 Introduction 59 3.1.1 Co-metabolism 61 3.1.2 Co-substrates 62 3.1.2.1 Surfactants 63 3.1.2.1.1 Trition X-100 63 3.1.2.1.2 Tween-80 63 vii 3.2 Materials and Methods 64 3.2.1 Microcosm 65 3.2.2 Cell Passages 66 3.2.3 Isolation of TNT and PETN degraders 66 3.2.3.1 TNT and PETN overlays 66 3.2.4 Utilization of TNT/ PETN as a nitrogen source 67 3.2.4.1 TNT Preliminary passages 67 3.2.4.2 PETN Preliminary passages 67 3.2.4.2.1 Passages of strains from Site A and B 67 3.2.4.2.2 Passages from strains from Site C and D 68 3.3 Identification of bacterial isolates 69 3.3.1 Phenotypic characteristics 69 3.3.2 Gram reaction determination 69 3.3.3 Biochemical tests 69 3.3.3.1 API® 20 NE Test 70 3.4 Co-Metabolism Degradation studies of TNT 70 3.4.1 Co-metabolism Degradation Experiments 70 3.5 Results 70 3.5.1 Details of soil and water samples from the contaminated. sites A, B, C and D. 70 3.5.2 Microbial load from Sites A, B, C and D 72 3.5.3Microbial content of soil samples from Site C and D 72 3.5.4 TNT Preliminary passages 73 3.5.5 PETN Preliminary passages 74 3.5.6 Phenotypic characteristics 76 3.5.7 Gram reaction 77 3.5.8 Biochemical tests 78 3.5.9 Co-metabolism experimental results 81 3.6 Discussion 83 Chapter 4: Molecular identification and characterisation of Isolates on TNT and PETN 88 4.1 Background 88 4.2 Materials and Methods 89 4.2.1 Genomic DNA extraction 90 4.2.2 Boiling method 90 4.2.3 Colony PCR 90 4.2.4 DNA extraction using commercially available kits 90 4.3 Results 92 4.3.1 Genomic DNA extraction 92 4.3.2 Boiling method 92 4.3.3 Colony PCR 93 4.3.4 DNA extraction using commercially available kits 93 4.3.5 Experiments evaluating the presence of onr and ner genes in Strains 106 4.3.5.1 Enterobacter sp 106 4.3.5.2 Agrobacterium 107 4.3.6 Experiments using Degenerate primers 110 4.4 Discussion 115 viii Chapter 5: Nitrite Activity Assays 120 5.1 Introduction 120 5.1.1 Colorimetric Griess Assay 120 5.2 Materials and Methods 121 5.2.1 Strains 121 5.2.2 Culture conditions 121 5.2.3 Harvesting of culture 121 5.2.4 Nitrite concentration assays 121 5.2.4.1 Resting Cell Activity Assay 123 5.2.4.2 Cell-Free Lysate Activity Assay 124 5.2.4.2.1 Sonication 124 5.2.4.2.2 Nitrate ester reductase activity assay 125 5.2.4.2.3 Nitrite Utilisation Assay 125 5.2.4.2.4 Protein Assay 125 5.3 Results: Characterisation of Isolates 126 5.3.1 Resting cell activity 126 5.3.2 Cell-free lysate activity 131 5.3.3 Comparison of resting cell and cell-free lysate activities 137 5.4 Discussion 140 References 144 Appendices Appendix I: 16S rDNA Sequences 164 Appendix II: CLUSTAL 2.0.12 multiple sequence alignment 168 Appendix III: Resting cell activity of the six GTN and PETN-degrading Isolates 171 Appendix IV: Cofactor preference of the Six GTN/PETN-degrading isolates in cell-free lysate using GTN/ PETN as substrate 172 ix LIST OF FIGURES Figure 1.1 Structures of some important explosive compounds.
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