Applied Microbiology and Molecular Biology in Oilfield Systems (eBook)

Dr Corinne Whitby is a lecturer in Environmental Microbiology at the University of Essex, UK. She has over 10 years primary research experience in molecular microbial ecology. Her research is focused upon the application of Molecular Microbiological Methods (MMM) to analyze the biodegradation of hydrocarbons (e.g. naphthenic acids and polyaromatic hydrocarbons) and how nanoparticles affect hydrocarbon biodegradation. Her research is also involved in analyzing the biogeochemical cycling of nutrients in marine, freshwater and terrestrial systems. She was the original founders of ISMOS1 (with Dr Skovhus) and co-organised ISMOS2, Denmark, 2009 and the forthcoming ISMOS3, Calgary, 2011.   Dr. Torben Lund Skovhus graduated from the University of Aarhus, Denmark, in 2002 with a Master's degree in Biology. In 2005 he finished his PhD from Department of Microbiology, University of Aarhus. In 2005 Torben was employed at Danish Technological Institute (DTI) in the Centre for Chemistry and Water Technology, where he got responsibility for the consultancy activities for the oil and gas industry, molecular detection of troublesome microbes in process and domestic waters and development and introduction of new molecular monitoring tools for the industries. Torben was Head of the DTI Microbiology Laboratories from 2006 to 2008 while he was building up several consultancy activities with the oil and gas industry. He is now in a position as Team Leader in DTI Oil & Gas Center. The team counts dedicated chemists, microbiologists, engineers, consultants. All with a long history in general troubleshooting of technical industrial systems for microbiologically caused problems and with a particular focus on oil, gas and petroleum systems.

Preface 5
Acknowledgements 7
Contents 8
Contributors 12
Part I Introduction, Sampling and Procedures 16
1 Introduction 17
References 19
2 Sampling and Nucleic Extraction Procedures from Oil Reservoir Samples 20
Introduction 20
Points of Concern When Sampling Oilfield Brine Waters 21
Case Study 1: Brine Water Samples from a Dutch Oilfield and Its Surface Facility Units 21
Pretreatment of Filters After Filtration with Brine Water Samples 23
Alternative Sampling Using Specific Commercial Concentrator Kits 24
Taking Oilfield Core Fragments Without Contamination 24
Case Study 2: Sampling and Treatment of Different Core Samples 25
Core 1: Unconsolidated Sandstone from an Oilfield in Gabon (Africa) 25
Core 2: Sandstone from an Oilfield in Rotterdam (The Netherlands) 26
Standard DNA Extraction Method (Brine Water Samples and Core 1) 26
Alternative and Improved DNA Extraction Methods 27
Conclusions 27
References 28
Part II Application of Molecular Microbiological Methods to the Oil Industry 30
3 Application of Molecular Microbiological Methods to the Oil Industry to Analyse DNA, RNA and Proteins 31
Overview of Molecular Microbiological Methods (MMM) 31
References 37
4 Which Microbial Communities Are Present Importance of Selecting Appropriate Primers and Probes for Use in Molecular Microbiological Methods (MMM) in Oilfields 39
Introduction 39
Primers and Probes that Target the 16S rRNA Gene 39
Primers that Target Specific Functional Genes 40
Conclusions 42
References 42
5 Which Microbial Communities are Present Application of PCR-DGGE: Case Study on an Oilfield Core Sample 44
Introduction 44
PCR-DGGE Fingerprinting 44
The PCR Cycle 45
The DGGE Analysis 46
Possible Improvements on the PCR Programme 48
RNA Analysis Using PCR-DGGE 49
Benefits of the PCR-DGGE Technique 49
Limitations of the PCR-DGGE Technique 50
Case Study 1: PCR-DGGE on an Oilfield Core Sample 50
Results 51
Conclusions 53
References 54
6 Which Microbial Communities Are Present Application of Clone Libraries: Syntrophic Acetate Degradation to Methane in a High-Temperature Petroleum Reservoir Culture-Based and 16S rRNA Genes Characterisation 55
Introduction 55
Case Study: Physicochemical and Microbiological Characteristics of the Dagang Oilfield 56
16S rRNA Gene Clone Libraries 56
Isolation of Pure Cultures and Reconstruction of Syntrophic Acetate Degradation to Methane 59
Discussion 60
References 62
7 Which Microbial Communities Are Present Using Fluorescence In Situ Hybridisation (FISH): Microscopic Techniques for Enumeration of Troublesome Microorganisms in Oil and Fuel Samples 64
Introduction 64
Drawbacks with Culturing Bacteria 64
Counting All Prokaryotes in Oilfield or Fuel Samples with DAPI 65
Counting All Active Prokaryotes with Quantitative FISH 66
Case Study: Application of the FISH/DAPI Method to Control Microbial Growth in Diesel Tanks Using Biocides 67
References 69
8 Which Microbial Communities Are Present? Sequence-Based Metagenomics 71
Introduction 71
Amplicon (PyroTag) Sequencing 74
Methodologies 74
Applications 75
Conclusions 76
Total DNA Random Shotgun Sequencing 77
Methodologies 78
Applications 79
Conclusion 80
Metatranscriptomics 80
Methodologies 81
Applications 81
Conclusion 82
References 82
9 How Many Microorganisms Are Present Quantitative Reverse Transcription PCR (qRT-PCR) 85
Introduction 85
Principles 85
Case Study: Detection of SRP Activity in Produced Water Samples by Quantification of mRNA for the Dissimilatory (Bi)Sulphite Reductase Gene (dsrA Sub-unit) by Reverse Transcriptase qPCR 89
References 92
10 How Many Microorganisms Are Present? Techniques for Enumerating Microorganisms in Oilfields 93
Introduction 93
Case Study: The Halfdan Field 95
Development of qPCR Assay 95
Distribution of SRB and SRA in the Oilfields 96
Conclusions 98
References 99
11 Which Members of the Microbial Communities Are Active? Microarrays 100
Introduction 100
Microarray Technology 101
Case Study 102
Concluding Remarks 103
References 104
Part III Problems Caused by Microbes to the Oil Industry and Treatment Strategies 107
12 Problems Caused by Microbes and Treatment Strategies: Monitoring and Preventing Reservoir Souring Using Molecular Microbiological Methods (MMM) 108
Introduction 108
Case Study 109
Conclusions 111
References 112
13 Problems Caused by Microbes and Treatment Strategies: The Effect of Nitrate Injection in Oil Reservoirs Experience with Nitrate Injection in the Halfdan Oilfield 113
Introduction 113
Case Study: The Halfdan Oilfield 114
Monitoring of Halfdan Producing Wells with Seawater Breakthrough 114
Total Bacterial Abundance and Enumeration of Specific Bacterial Groups 116
Determination of the Activity of SRB from the Halfdan Oilfield 117
Conclusion 118
References 119
14 Problems Caused by Microbes and Treatment Strategies: Monitoring Microbial Responses to Biocides Bioassays A Concept to Test the Effect of Biocides on both Archaea and Bacteria in Oilfield Systems
Introduction 120
Case Study 1: The Effect of Biocide Treatment on Pure Cultures of Sulphate-Reducing Microorganisms and Methanogens 121
Case Study 2: Biocide Testing on Produced Water Samples from a North Sea Oil Platform Using Bioassays 123
Conclusions 125
Perspectives 126
References 126
15 Problems Caused by Microbes and Treatment Strategies: Identification of H2S-Producing Bacteria in Corrosion Product of a Gas Pipeline 128
Introduction 128
Conclusion 132
References 132
16 Problems Caused by Microbes and Treatment Strategies: Rapid Diagnostics of Microbiologically Influenced Corrosion (MIC) in Oilfield Systems with a DNA-Based Test Kit 135
Introduction 135
Key Organisms Causing MIC in Oilfields 136
Case: Diagnostics of MIC in High Pressure Separator at Halfdan Oilfield 137
Microbiological Investigation 138
Chemical and Surface Characterisation 139
Discussion 139
Novel DNA-Based Approach to MIC Diagnostics and Mitigation 140
References 141
17 Problems Caused by Microbes and Treatment Strategies: Anaerobic Hydrocarbon Biodegradation and Biocorrosion: A Case Study 143
Introduction 143
Importance of Biofilms 144
Metabolite Profiling 144
Microbial Profiling 146
Importance and Implications 148
References 150
18 Problems Caused by Microbes and Treatment Strategies: Health and Safety Issues from the Production of Hydrogen Sulphide 152
Introduction 152
Sources of Hydrogen Sulphide 153
Physiological Effects of Hydrogen Sulphide 154
Reaction with Materials 155
Microbiologically Influenced Corrosion (MIC) 156
Workplace Regulations 156
References 157
19 Problems Caused by Microbes and Treatment Strategies: Downstream Petroleum Microbiology An Industry Perspective 159
Introduction 159
The Nature of Hydrocarbon-Utilising Microbes 161
Operational Issues 162
Prevention and Control 163
Historical Perspective 163
Case Study 1 163
Biofuels 164
Impact of Biodiesel on Microbial Activity 165
Case Study 2 165
Case Study 3 166
Conclusion 166
Notes 167
References 167
Part IV How Specific Microbial Communities Benefit the Oil Industry 168
20 How Specific Microbial Communities Benefit the Oil Industry: Biorefining and Bioprocessing for Upgrading Petroleum Oil 169
Introduction 169
Biodesulphurisation 169
Biodenitrogenation 171
Biodemetallation 172
Biocatalysis for Novel Compounds 172
Biotransformation of Heavy Crudes into Lighter Crudes 172
Biodemulsification 173
Conclusions 174
Glossary 174
References 175
21 How Specific Microbial Communities Benefit the Oil Industry: Microbial-Enhanced Oil Recovery (MEOR) 177
Introduction 177
Selection of Microbes for MEOR Purposes 178
Sub-surface Environment 178
Case Study: Applying Clostridium tyrobutiricum in MEOR 179
Adaptation to Higher Salinities 180
Acid Production and Change of Permeability 183
Conclusions 184
References 185
22 How Specific Microbial Communities Benefit the Oil Industry: Anaerobic Microbial Processes and the Prospect for Methane Production from Oil 186
Introduction 186
Methanogenic Hydrocarbon Metabolism 187
References 188
23 How Specific Microbial Communities Benefit the Oil Industry: Case Study Proof of Concept that Oil Entrained in Marginal Reservoirs Can Be Bioconverted to Methane Gas as a Green Energy Recovery Strategy 190
Introduction 190
Experiments and Key Findings 191
Conclusions 194
References 194
24 How Specific Microbial Communities Benefit the Oil Industry: Dynamics of Alcanivorax spp. in Oil-Contaminated Intertidal Beach Sediments Undergoing Bioremediation 196
Introduction 196
Case Study Results 198
Effects of Inorganic Nutrient Treatment on Oil Degradation 199
Bacterial Community Dynamics and Quantitative Analysis of Alcanivorax spp. 200
Qualitative Analysis of Alcanivorax and alkB Genes 202
Discussion and Conclusions 203
References 204
25 How Specific Microbial Communities Benefit the Oil Industry: Significant Contribution of Methyl/Methanol-Utilising Methanogenic Pathway in a Subsurface Biogas Environment 207
Introduction 207
Case Study: Results 207
Conclusions 211
References 212
Part V Fuel for the Future 213
26 Fuel for the Future: Development of New Fuels, e.g. Biofuels 214
Introduction 214
Case Study: Production of Biodiesel at Daka Biodiesel 216
Challenges Associated with the Use of Biodiesel 217
Low-Temperature Properties 217
Stability of Biodiesel Blends 218
Growth Studies 219
Conclusions 223
References 223
27 Fuel for the Future: Biodiesel - A Case study 224
Introduction 224
Conclusions 229
References 230
28 Fuel for the Future: Unlocking New Fuel Resources 231
Introduction 231
Chemical Composition and Methods of Characterising NAs 232
Case Study: Biodegradation of Aliphatic and Aromatic NAs 232
Conclusions 237
Future Perspectives 237
References 237
Appendix: Description of the Methods Used by Some of the Contributing Authors in This Book 239
Index 271