Applied Microbiology and Molecular Biology in Oilfield Systems

PART I: INTRODUCTION, SAMPLING AND PROCEDURES <strong> </strong> <strong>1. Introduction</strong> Corinne Whitby and Torben Lund Skovhus <strong> </strong> <strong>2: Sampling and nucleic extraction procedures from oil reservoir samples</strong> Geert M. van der Kraan, Maarten de Ridder, Bart Lomans and Gerard Muyzer   PART II: APPLICATION OF MOLECULAR MICROBIAL METHODS TO THE OIL INDUSTRY <strong> </strong> <strong>3. Application of molecular microbial methods to the oil industry to analyze DNA, RNA and proteins</strong> Sean Caffrey <strong> </strong> <strong>4. Which microbial communities are present? </strong><strong>Importance of selecting appropriate primers and probes for use in molecular microbiology methods (MMM) in oil fields </strong> Ketil Sørensen <strong> </strong> <strong>5. Which microbial communities are present? Application of PCR-DGGE: case study on an oil field core sample</strong> Geert M. van der Kraan, Floris Buijzen, Cor Kuijvenhoven and Gerard Muyzer <strong> </strong> <strong>6. Which microbial communities are present? Application of clone libraries: syntrophic acetate degradation to methane in a high-temperature petroleum reservoir</strong> Natalya Shestakova, Valeriy Ivoilov, Tatiana Tourova, Sergey Belyaev, Andrei Poltaraus, and Tamara Nazina <strong> </strong> <strong>7. Which microbial communities are present? Using Fluorescent in situ hybridisation (FISH): Microscopic Techniques for Enumeration</strong><strong> of Troublesome Microorganisms in Oil and Fuel Samples</strong> Lars Holmkvist, Jette Johanne Østergaardand Torben Lund Skovhus <strong> </strong> <strong>8. Which microbial communities are present? Sequence based Metagenomics</strong> Sean Caffrey <strong> </strong> <strong>9. How many microorganisms are present? </strong><strong>Quantitative Reverse Transcription PCR (qRT- PCR)</strong> Andy Price, Laura Acuña Álvarez, Corinne Whitby and Jan Larsen <strong> </strong> <strong>10. How many microorganisms are present? Techniques for enumerating microorganisms in oil fields</strong> Ketil Sørensen, Torben Lund Skovhus and Jan Larsen <strong> </strong> <strong>11. Which members of the microbial communities are active? </strong><strong>Microarrays</strong> Brandon Morris   PART III: PROBLEMS CAUSED BY MICROBES TO THE OIL INDUSTRY AND TREATMENT STRATEGIES <strong> </strong> <strong>12. Problems caused by microbes and treatment strategies. Monitoring and preventing reservoir souring using molecular microbial methods</strong> Antje Gittel <strong> </strong> <strong>13. Problems caused by microbes and treatment strategies. The effect of nitrate injection in oil reservoirs: Experience with Nitrate Injection in the</strong><strong> Halfdan Oil Field</strong> Jan Larsen and Torben Lund Skovhus   <strong>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 oil field systems</strong> Lars Holmkvist, Uffe Sognstrup Thomsen, Jan Larsen, Michael Jensen and Torben Lund Skovhus <strong> </strong> <strong>15. Problems caused by microbes and treatment strategies. </strong><strong>Identification of H₂S-producing bacteria in corrosion product of a gas pipeline</strong> Márcia Lutterbach and Luciana Contador <strong> </strong> <strong>16. Problems caused by microbes and treatment strategies. Rapid diagnostics of Microbiologically Influenced Corrosion (MIC) in oil field systems with a DNA-based test kit</strong> Torben Lund Skovhus, Ketil Sørensen and Jan Larsen <strong> </strong> <strong>17. Problems caused by microbes and treatment strategies. Anaerobic Hydrocarbon Biodegradation and Biocorrosion.</strong> Joseph Suflita and Kathleen Duncan <strong> </strong> <strong>18. Problems caused by microbes and treatment strategies. Health and safety issues from the production of hydrogen sulphide</strong> Nicole Williamson <strong> </strong> <strong>19. Problems caused by microbes and treatment strategies. Downstream Petroleum Microbiology: An Industry Perspective</strong> Elaine McFarlane   PART IV: HOW SPECIFIC MICRIOBIAL COMMUNITIES BENEFIT THE OIL INDUSTRY <strong> </strong> <strong>20. How specific microbial communities benefit the oil industry. Biorefining and Bioprocessing for Upgrading Petroleum Oil</strong> Ajay Singh <strong> </strong> <strong>21. How specific microbial communities benefit the oil industry. Microbial Enhanced Oil Recovery (MEOR)</strong> Svetlana Rudyk and Erik Sogaard <strong> </strong> <strong>22. How specific microbial communities benefit the oil industry. Anaerobic microbial processes and the prospect for methane production from oil </strong> Lisa Gieg <strong> </strong> <strong>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</strong> Lisa Gieg <strong> </strong> <strong>24. How specific microbial communities benefit the oil industry. Dynamics of Alcanivorax spp. in oil contaminated intertidal beach sediments undergoing bioremediation</strong> Arvind Singh, Angela Sherry, Neil Gray, Martin Jones, Wilfred Röling and Ian Head <strong> </strong> <strong>25. How specific microbial communities benefit the oil industry. Significant contribution of methyl/methanol-utilizing methanogenic pathway in a subsurface biogas environment</strong> Dariusz Strąpoć, Matt Ashby,Ladonna Wood, Rick Levinson andBradley Huizinga   PART V FUEL FOR THE FUTURE <strong> </strong> <strong>26. Fuel for the future. Development of new fuels, e.g. biofuels</strong> Gitte Sørensen, Ketil Sørensen, Hans Ove Hansen and Sune Nygaard <strong> </strong> <strong>27. Fuel for the future. Biodiesel: A Case study</strong> Márcia Lutterbach and Mariana Galvão <strong> </strong> <strong>28. Fuel for the future. Unlocking New Fuel Resources</strong> Richard Johnson and Corinne Whitby   APPENDIX I <strong>Description of Methods used by some of the contributing authors in this book</strong>