Microbial Bioinformatics in the Oil and Gas Industry: Applications to Reservoirs and Processes (Microbes, Materials, and the Engineered Environment)

This book brings together contributions from leading scientists, academics, and experts from the oil and gas industry to discuss microbial-related problems faced by the industry and how bioinformatics and an interdisciplinary scientific approach can address these challenges. **Microbial Bioinformatics in the Oil and Gas Industry: Applications to Reservoirs and Processes** presents the major industrial problems caused by microbes (e.g., souring, biocorrosion) as well as the beneficial activities (e.g., biofuels, bioremediation). FEATURES * Offers a detailed description of how bioinformatics has advanced our understanding of numerous issues in the oil and gas industry * Covers cases from geographically diverse oil fields, laboratories, and research groups * Contains fundamentals and applied information of relevance to the oil and gas sector * Presents contributions from a team of international experts across industry and academia With its cross-disciplinary approach, this comprehensive book provides microbial ecologists, molecular biologists, operators, engineers, chemists, and academics involved in the sector with an improved understanding of the significance of microbial bioinformatics applications in the oil and gas industry. Cover Half Title Series Page Title Page Copyright Page Table of Contents Foreword Preface Editors Contributors Chapter 1: Bioinformatics and Genomics Breakthroughs That Enabled the Microbiome Revolution 1.1 Early DNA Sequencing 1.2 Automated DNA Sequencing 1.3 Next-Generation DNA Sequencing 1.4 Microbiome Sequencing 1.5 Data Analysis References Chapter 2: Unravelling the Oil and Gas Microbiome Using Metagenomics 2.1 Introduction 2.1.1 Sampling and Lab Processing Considerations 2.2 Downstream Processing Considerations 2.3 Single Marker Gene Sequencing 2.4 Single Marker Gene Analysis 2.5 Whole Metagenome Sequencing 2.6 Metagenomic Data Analysis 2.7 Metagenomic Applications to Oil and Gas 2.7.1 Exploration 2.7.2 Production Allocation 2.7.3 Souring and Microbiologically Influenced Corrosion (MIC) Monitoring 2.7.4 Baseline Environmental Assessment and Monitoring 2.7.5 Biofouling and Contamination Control 2.7.6 Novel Biocatalysts for Enzymatic Hydrolysis of Biomass 2.7.7 Biofuel Production 2.8 Concluding Remarks References Chapter 3: A Case for Molecular Biology: How This Information Can Help in Optimizing Petroleum Top Side Facility Operations 3.1 Introduction 3.2 The Oilfield as an Interlinked Set of Artificial Ecosystems 3.2.1 Limits of Life, Seen in the Light of Oilfields 3.2.2 The Oilfield and Its Topside Facilities Described as Industrial Ecosystems 3.2.2.1 Seawater Intake 3.2.2.2 The Oil Reservoir 3.2.2.3 Production Wells 3.2.2.4 Gathering and Trunk Lines 3.2.2.5 Oil Water Separators 3.2.2.6 Water Processing 3.2.2.7 Injectors 3.2.2.8 Open Ponds 3.2.3 Microbial Life Classified according to Redox Reactions, Providing Energy 3.2.4 Different Classification Systems of Microorganisms 3.3 Monitoring Programs 3.3.1 The Molecular Biology Toolbox & Diversity Studies 3.3.2 Quantitative Polymerase Chain Reaction (qPCR) 3.3.3 What Does Such a Monitoring Program Help Answer & What Can be Done with This Information? 3.4 Case Studies 3.4.1 The Effect of Adding Oxygen Scavenger to Produced Water That Contains Low Sulfate 3.4.2 The Effect of Nitrate Addition When Deaerated Seawater Is Mixed with Sulfide Containing Produced Water at Injectors (FPSO-System) 3.4.3 How Molecular Biology Can Determine Where in a System Issues Occur 3.4.4 How Effective Biocide Treatment Can Significantly Reduce Biogenically Formed Suspended FeS 3.5 Conclusions References Chapter 4: Using a Holistic Monitoring Approach to Set Effective Control Strategies: How Data Can Lead to Information and Subsequently to “Wisdom” 4.1 Introduction 4.2 Common Practice – Monitoring and Setting a Strategy 4.3 Case Studies 4.3.1 Case Study 1: Seawater Injection System in the North Sea 4.3.2 Case Study 2: Produced Water Re-Injection System in the North Sea 4.4 Conclusion – A Holistic Monitoring Approach Acknowledgments References Chapter 5: Influence of Chemical Treatments and Topside Processes on the Dominant Microbial Communities at Conventional Oilfields 5.1 Introduction 5.2 Selected Oilfields and Considerations on Main Topside Zones 5.2.1 Production Water (PW) 5.2.2 Inlet of Water Treatment Plant (WTPin) 5.2.3 Outlet of Water Treatment Plant (WTPout) 5.2.4 Injection Wells or Injection Water (IW) 5.3 Dominant Microbial Communities 5.3.1 Bacterial Contamination 5.3.1.1 Variation of Topside Bacterial Profiles 5.3.1.1.1 Antimicrobial Performance and Clostridia 5.3.1.1.2 Gammaproteobacteria Stimulus after Biocide Formulation Changes 5.3.1.1.3 Solids Management, Oxygen Scavengers, and Sulfur-Oxidizing Epsilonproteobacteria 5.3.2 Archaeal Contamination 5.4 Conclusion Acknowledgments References Chapter 6: Microbial Control during Hydraulic Fracking Operations: Challenges, Options, and Outcomes 6.1 Introduction 6.2 Microbial Control in Frac Operations: The Challenges 6.3 Microbial Control in Frac Operations: The Options 6.3.1 Oxidizing Biocides 6.3.2 Non-Oxidizing Biocides 6.4 Microbial Control During Fracking Operations: The Outcomes 6.4.1 Laboratory Evaluation 6.4.2 Field Evaluation References Chapter 7: The Application of Bioinformatics as a Diagnostic Tool for Microbiologically Influenced Corrosion 7.1 Introduction 7.1.1 Microbiologically Influenced Corrosion 7.1.2 MIC Monitoring Techniques 7.2 Case Study 7.2.1 Materials and Methods 7.2.1.1 Site Sampling & DNA Extraction 7.2.1.2 Total Cell Determination and Subgroups via qPCR 7.2.1.3 Microbial Diversity Studies via NGS and Basic Metabolic Mapping 7.2.1.4 Bug Bottles 7.2.2 Applied Sampling Plan 7.2.3 Case Study Results 7.2.3.1 Visual Observation of Water Samples 7.2.3.2 Bug Bottle Analysis 7.2.3.3 qPCR Analysis 7.2.3.4 Next Generation Sequencing Diversity Study 7.2.4 Case Study Discussion and Interpretation 7.2.4.1 Interpretation of qPCR Results 7.2.4.2 Interpretation of NGS Results 7.2.4.3 Comparison of Coupon Corrosion Data with Microbial Data 7.3 Conclusions References Chapter 8: Methanogens and MIC: Leveraging Bioinformatics to Expose an Underappreciated Corrosive Threat to the Oil and Gas Industry 8.1 Introduction 8.1.1 Working with Methanogens 8.2 We’ve Come a Long Way from Bug Bottles 8.3 Archaeal Methanogens 8.3.1 Role in the Biosphere 8.3.1.1 Environments 8.3.1.2 The Human Archaeome 8.3.1.3 Temperature 8.3.1.4 Salinity and pH 8.3.1.5 Osmoprotectants 8.3.1.6 High-Salt-In Strategy 8.3.1.7 pH 8.3.2 Morphology 8.3.3 Archaeal Genetics 8.3.3.1 Lateral Gene Transfer (LGT) 8.3.3.2 Taxonomy 8.3.3.3 Metabolism/Methanogenesis 8.3.3.3.1 Methyl Coenzyme M Reductase ( mcr A) 8.3.3.3.2 Reverse Methanogenesis 8.3.3.3.3 Three Pathways of Methanogenesis 8.3.3.3.3.1 Hydrogenotrophic Methanogens 8.3.3.3.3.2 Methylotrophic Methanogens 8.3.3.3.3.3 Aceticlastic Methanogenesis 8.3.3.3.3.3.1 ACS Pathway 8.3.3.3.3.3.2 AckA/Pta Pathway 8.3.3.4 Syntrophic Relationships 8.3.3.4.1 Kind of a Common Ancestor 8.4 Considerations for Oil and Gas 8.4.1 Crude-oil Biodegradation via Methanogenesis 8.4.2 Methanogen Mediated Iron Corrosion 8.4.2.1 Syntrophic Relationships 8.4.2.2 Direct Iron Oxidation 8.4.2.3 Discovery of MIC Island and a Binary MIC Factor 8.4.2.3.1 MIC Hydrogenase 8.4.2.4 Archaeoglobus 8.4.3 Mitigation of Methanogens 8.5 Methanogen Oilfield Corrosion Examples 8.5.1 Dry Gas Pipeline 8.5.2 West Texas Shale Production 8.5.3 Biofilm reactor coupons – Deepwater Brazil 8.5.4 West Texas Salt Water Disposal Facility 8.5.5 South America Pipeline 8.6 Conclusion References Chapter 9: Molecular Methods for Assessing Microbial Corrosion and Souring Potential in Oilfield Operations 9.1 Introduction 9.1.1 Microbial Reservoir Souring and Its Control 9.1.2 Microbiologically Influenced Corrosion (MIC) 9.2 MMM for Monitoring Oil Field-Associated Microbial Communities 9.2.1 Sampling and Preservation for MMM 9.2.2 Nucleic Acids Extraction 9.2.3 PCR Amplification Using Universal Primers 9.2.4 PCR Amplification of Group-Specific Genes 9.2.5 RNA Analysis 9.2.6 Metagenomics 9.2.7 Multi-Omics Approaches 9.3 Case Studies Highlighting the Use of MMM Related to Souring and MIC 9.3.1 Case Study 1: Using MMM to Pinpoint the Cause of Corrosion in a Water-Transporting Pipeline 9.3.2 Case Study 2: Multi-Omics Analyses for Assessing MIC 9.3.3 Case Study 3: Use of MMM to Determine the Effects of Temperature on Nitrate Treatment of Souring 9.3.4 Case Study 4: Using MMM to Determine the Effects of Seawater Flooding to Produce Crude Oil from an Offshore Reservoir 9.3.5 Case Study 5: Use of MMM to Reveal Dominant Taxa and Metabolisms Associated with Hydraulic Fracturing Fluids 9.4 Summary and Future Directions References Chapter 10: Microbial Reservoir Souring: Communities Relating to the Initiation, Propagation, and Remediation of Souring 10.1 Introduction 10.1.1 Overview of Souring 10.1.2 Sulfide-generating Microorganisms 10.1.3 Mitigation Strategies 10.1.4 Analytical Methods 10.2 Initiation and Propagation 10.2.1 Overview 10.2.2 Laboratory Experiments 10.3 Microbiological Nitrate Reduction 10.3.1 Overview 10.3.2 Field Observations 10.3.3 Laboratory Experiments 10.4 Conclusion Acknowledgments References Chapter 11: Quantitative PCR Approaches for Predicting Anaerobic Hydrocarbon Biodegradation 11.1 Introduction 11.2 Overview of Quantitative PCR and Best Practices 11.3 Quantitative Gene Markers for Monitoring Anaerobic Hydrocarbon Biodegradation 11.3.1 Quantitative PCR Assays for Catabolic Gene Markers 11.3.2 Quantitative PCR Assays for Specific Hydrocarbon-Biodegrading Taxa 11.3.3 Other Useful Gene Markers 11.4 Case Studies 11.4.1 Case Study 1: Determining the Potential for Monitored Natural Attenuation by Biodegradation in Fuel-Contaminated Groundwater 11.4.2 Case Study 2: Demonstrating Anaerobic Benzene Biodegradation at Canadian Forces Base (CFB) Borden 11.5 Conclusion Acknowledgments References Chapter 12: Leveraging Bioinformatics to Elucidate the Genetic and Physiological Adaptation of Pseudomonas aeruginosa to Hydrocarbon-Rich Jet Fuel 12.1 Introduction 12.2 Genomics 12.2.1 Core and Accessory Genome Analysis 12.3 Single Nucleotide Polymorphism (SNPs) and Alk Gene Expression 12.4 Transcriptomics 12.4.1 P. aeruginosa Response to Alkanes and Jet Fuel 12.5 Physiological Adaptations 12.5.1 Biofilm Formation 12.5.2 Solvent Resistance 12.5.3 Trace Elements and Iron Acquisition 12.5.4 Stress Response 12.6 Conclusion Acknowledgment References Index A B C D E F G H I J K L M N O P Q R S T U V W X "This book brings together contributions from leading scientists, academics, and experts from the oil and gas industry to discuss microbial-mediated problems faced by the industry and how bioinformatics and an interdisciplinary scientific approach can address these challenges. This book presents the major industrial problems caused by microbes as well as the beneficial activities. It provides microbial ecologists, molecular biologists, operators, engineers, chemists and academics involved in the sector an improved understanding of the significance of microcosmos in oil and gas detection, production, and degradation, leading to better solutions impacting on operations and profitability"-- Provided by publisher