Biomedical Engineering/Nanotechnology

Hydrocarbon Biotechnology
Challenges and Future Trends

Editors: Wael Ahmed Ismail, PhD
Jonathan Van Hamme, PhD

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Hydrocarbon Biotechnology

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Hydrocarbon biotechnology offers environmentally friendly technical solutions that can be implemented to solve problems throughout the value chain of the fossil fuel industry. This book, Hydrocarbon Biotechnology: Challenges and Future Trends, presents a compilation of chapters that contribute up-to-date information on the actual and potential applications of microbial biotechnology in the fossil fuel industry. Particular focus is given to the challenges and obstacles that are facing the commercialization of microbial biotechnology in the fossil fuel industry, emerging challenges, and future trends. Furthermore, the book describes the application of systems biology approaches toward better understanding of the ecophysiology of key microbes encountered throughout the value chain. Recent advances in synthetic biology and metabolic engineering are paving the way toward the development of tailor-designed biocatalysts that can be applied in the oil and gas industry.

Written by eminent scientists from both the academia and industry, the book starts with a historical perspective on hydrocarbon chemistry and formation, petroleum microbiology, and biotechnology. This is followed by introducing the fundamentals of petroleum refining and environmental pollution. The most recent developments of microbial hydrocarbon metabolism relevant to the oil and gas industry will be introduced. This includes the biochemistry and molecular biology of key catabolic mechanisms of hydrocarbons from C1 up to complex and heterogeneous structures found in the resin and asphaltene fractions. Chapters elaborating on the applicability of oxygenases and aromatic ring reductases to petroleum hydrocarbon biotransformations will be included. Then, the microbiology of oil fields, reservoirs, and oil-polluted ecosystems will be discussed with emphasis on adaptability and environmental impact of microorganisms inhabiting those niches.

Subsequent chapters will explore how microbial biotechnology exploits microbial metabolic capabilities in upstream processes such as exploration, enhanced recovery, and transportation. Moreover, the book will include chapters on the applicability of hydrocarbon biotechnology in downstream processes such as biodesulfurization and biocatalytic upgrading of heavy oils and refinery residues. Some chapters will be dedicated to the utilization or transformation of petroleum and coal hydrocarbons to utilizable intermediates and products.

The conversion of residual oil and coal to methane by microbial consortia will be addressed as processes such as coal-bed methane production are increasingly being used (biomethanation). A significant part of the book will deal with the application of biocatalysis to valorize low-value refinery streams and wastes for production of fine chemicals. In addition, biochemical engineering aspects and their impact on the efficient implementation of microbial biotechnology in the fossil fuel industry will be presented.

The book presents and discusses the application of systems biology approaches such as metabolomics, proteomics and metagenomics, as enabling tools for comprehensive understanding of the microbial adaptations to hydrocarbons.

Tentative Contents
1. Petroleum Chemistry: A Primer
2. Petroleum Formation and Maturation: Physical, Biological, and Chemical Considerations
3. Petroleum Recovery and Refining: An Overview
4. A History of Petroleum Microbiology: Over a Century in the Making
5. Microbial Interactions with Hydrocarbons: A Physiological Perspective
6. Resin and Asphaltene Chemistry: Challenges for Microorganisms and Chemists
7. C1 to C5 Microbial Hydrocarbon Metabolism under Aerobic and Anaerobic Conditions
8. Microbial Alkane Metabolism
9. Microbial Aromatic Metabolism
10. Microbial Enhanced Oil Recovery
11. Biocatalytic Upgrading of Heavy Crudes and Refining Residues
12. Microbial Diesel Biodesulfurization: The Path to success
13. Biodenitrogenation
14. Biodemetallation
15. Biosurfactants and the Oil Industry: Challenges and Opportunities
16. Microbial Ecology: From Oil Reservoir to Refinery
17. Environmental Applications of Hydrocarbonoclasts
18. Biocatalysis/Bioconversion on Hydrocarbon Feedstocks/Refining Residues
19. Biological Control of Souring and Corrosion
20. Coal-bed Methane: Biology and Environmental Impacts
21. Hydrocarbons from Sugars and Sun: Synthetic Biology Revolution
22. Systems Biology in Oil Fields: Proteomics and Metabolomics Potential

About the Authors / Editors:
Editors: Wael Ahmed Ismail, PhD
Environmental Biotechnology Program, Life Sciences Dept., College of Graduate Studies, Arabian Gulf University, Manama, Bahrain

Wael Ismail, PhD, is a Professor of Microbiology/Environmental Biotechnology for the Arabian Gulf University (and former director of the Biotechnology Program) as well as coordinator of the Environmental Biotechnology Program. He received a BSc in Microbiology and Chemistry from Ain Shams University (Egypt). Then, he joined the Egyptian Petroleum Research Institute (Petroleum Microbiology Group) in 1994 to pursue an MSc in Petroleum Microbiology. During his MSc studies, he conducted research on the microbial degradation of synthetic plastics in collaboration with the Institute of Research and Technology of Plastic Materials (Italy) and the Royal Institute of Technology-Sweden. He joined the Department of Microbiology at Freiburg University, Germany, in 1999 for the PhD studies program (funded by the German Research Foundation). His PhD research was dedicated to studies on the biochemistry and molecular biology of microbial degradation of aromatic compounds, with particular focus on the elucidation of unprecedented catabolic pathways for aromatics degradation. Currently, his research focuses on biodegradation of hydrocarbons (aromatics and steroids), biosurfactants production and applications, biodesulfurization of diesel, and biocatalytic upgrading of heavy oils and refinery residues, and regeneration of spent refining catalysts. A major part of his research deals with the application of proteomics and metabolomics to advance the understanding of biochemical and physiological aspects relevant to diesel biodesulfurization. Dr. Ismail has more than 20 years of research and teaching experience in the field of microbial biodegradation of hydrocarbons. He is working in close association with the oil and gas authorities and research institutes in Bahrain and Kuwait. He previously was affiliated with the University of Massachusetts (Amherst-USA) as a research assistant professor at the Center of Environmental Biotechnology, where he worked within the group of Derek Lovley. During that time, he conducted molecular biology research on Geobacter sulfurreducens and Rhodoferax ferrireducens, which are key players in microbial fuel cells. Dr. Ismail serves on the editorial and reviewers’ board of several international journals, and he is currently affiliated with the journal Frontiers in Microbiology as a guest associate editor for a special issue on Petroleum Biotechnology.

Jonathan Van Hamme, PhD
Department of Biological Sciences, Thompson Rivers University, Kamloops, British Columbia, Canada

Jonathan D. Van Hamme, PhD, is an Associate Professor of Microbiology at Thompson Rivers University in British Columbia, Canada. His work in industrial petroleum microbiology and bioremediation began in his PhD (University of Waterloo, 2000), has been used by Canadian industry and is highly cited internationally (> 280 citations to his primary articles; > 2000 citations to his review articles). More specifically, his PhD work on mixed bacterial cultures for petroleum biodegradation in fermenter-based systems fed directly into patents and operational refinery waste treatment systems (1 million litre scale) developed by Petrozyme Incorporated. He has collaborated on writing 3 major reviews in the field, 2 minor reviews in a technical journal, as well as 1 encyclopedia chapter. He has also authored 5 book chapters more broadly related to the field of biodegradation. The most impactful review was published in 2003 in MMBR and is still highly cited (>1000 citations; Google Scholar; doi: 10.1128/MMBR.67.4.503-549.2003). In 2010 Thompson Reuters listed it as the #1 cited article for the past decade in the special topic of oil spills. During his PDF at the National Centre for Upgrading Technology, funding partners included Imperial Oil, AEC Oil Sands and PanCanadian Petroleum. As a PI, he has applied his skills in microbiology, molecular microbial community analysis, in-house high throughput sequencing, biochemistry, proteomics and analytical chemistry carrying out research projects for a number of industries. He continues to review manuscripts for a number of journals in this field of petroleum microbiology, and has been invited to a number of universities and conferences to speak on the topic. He served as the Meetings Secretary on the Executive Committee of the Canadian Society of Microbiologists (2009-2011). In 2010, he joined the journal Biodegradation as a Managing Editor (>100 articles handled) and was also awarded the Thompson Rivers University Award for Excellence in Scholarship. In 2016 he was awarded the Thompson Rivers University Undergraduate Research Mentor Award. He has reviewed grant proposals and scholarship applications for NSERC, the National Research Foundation in South Africa (SA/Germany Agreement on Cooperation in Science and Technology program), the Qatar National Research Fund, the Academy of Finland, the Indian Department of Biotechnology (DBT), and the Petroleum Research Fund (American Chemical Society). He is also currently affiliated with the journal Frontiers in Microbiology (with Dr. Ismail) as a guest associate editor for a special issue on Petroleum Biotechnology.

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