Contents

Cover

Title page

Copyright page

Preface

Chapter 1: Background

List of Abbreviations and Nomenclature
1.1 Petroleum
1.2 Petroleum Composition
1.3 Sulfur Compounds
1.4 Sulfur in Petroleum Major Refinery Products
1.5 Sulfur Problem
1.6 Legislative Regulations of Sulfur Levels in Fuels
References

Chapter 2: Desulfurization Technologies

List of Abbreviations and Nomenclature
2.1 Introduction
2.2 Hydrodesulfurization
2.3 Oxidative Desulfurization
2.4 Selective Adsorption
2.5 Biocatalytic Desulfurization
References

Chapter 3: Biodesulfurization of Natural Gas

List of Abbreviations and Nomenclature
3.1 Introduction
3.2 Natural Gas Processing
3.3 Desulfurization Processes
References

Chapter 4: Microbial Denitrogenation of Petroleum and its Fractions

List of Abbreviations and Nomenclature
4.1 Introduction
4.2 Denitrogenation of Petroleum and its Fractions
4.3 Microbial Attack of Nitrogen Polyaromatic Heterocyclic Compounds (NPAHs)
4.4 Enhancing Biodegradation of NPAHs by Magnetic Nanoparticles
4.5 Challenges and Opportunities for BDN in Petroleum Industries
References

Chapter 5: Bioadsorptive Desulfurization of Liquid Fuels

List of Abbreviations and Nomenclature
5.1 Introduction
5.2 ADS by Agroindustrial-Wastes Activated Carbon
5.3 ADS on Modified Activated Carbon
5.4 ADS on Carbon Aerogels
5.5 ADS on Activated Carbon Fibers
5.6 ADS on Natural Clay and Zeolites
5.7 ADS on New Adsorbents Prepared from Different Biowastes
References

Chapter 6: Microbial Attack of Organosulfur Compounds

List of Abbreviations and Nomenclature
6.1 Introduction
6.2 Biodegradation of Sulfur Compounds in the Environment
6.3 Microbial Attack on Non–Heterocyclic Sulfur–Containing Hydrocarbons
6.4 Microbial Attack of Heterocyclic Sulfur – Hydrocarbons
6.5 Recent Elucidated DBT-BDS Pathways
References

Chapter 7: Enzymology and Genetics of Biodesulfurization Process

List of Abbreviations and Nomenclature
7.1 Introduction
7.2 Genetics of PASHs BDS Pathway
7.3 The Desulfurization dsz Genes
7.4 Enzymes Involved in Specific Desulfurization of Thiophenic Compounds
7.5 Repression of dsz Genes
7.6 Recombinant Biocatalysts for BDS
References

Chapter 8: Factors Affecting the Biodesulfurization Process

List of Abbreviations and Nomenclature
8.1 Introduction
8.2 Effect of Incubation Period
8.3 Effect of Temperature and pH
8.4 Effect of Dissolved Oxygen Concentration
8.5 Effect of Agitation Speed
8.6 Effect of Initial Biomass Concentration
8.7 Effect of Biocatalyst Age
8.8 Effect of Mass Transfer
8.9 Effect of Surfactant
8.10 Effect of Initial Sulfur Concentration
8.11 Effect of Type of S-Compounds
8.12 Effect of Organic Solvent and Oil to Water Phase Ratio
8.13 Effect of Medium Composition
8.14 Effect of Growing and Resting Cells
8.15 Inhibitory Effect of Byproducts
8.16 Statistical Optimization
References

Chapter 9: Kinetics of Batch Biodesulfurization Process

List of Abbreviations and Nomenclature
9.1 Introduction
9.2 General Background
9.3 Microbial Growth Kinetics
9.4 Some of the Classical Kinetic Models Applied in BDS-Studies
9.5 Factors Affecting the Rate of Microbial Growth
9.6 Enzyme Kinetics
9.7 Michaelis-Menten Equation
9.8 Kinetics of a Multi-Substrates System
9.9 Traditional 4S-Pathway
9.10 Different Kinetic Studies on the Parameters Affecting the BDS Process
9.11 Evaluation of the Tested Biocatalysts
References

Chapter 10: Enhancement of BDS Efficiency

List of Abbreviations and Nomenclature
10.1 Introduction
10.2 Isolation of Selective Biodesulfurizing Microorganisms with Broad Versatility on Different S-Compounds
10.3 Genetics and its Role in Improvement of BDS Process
10.4 Overcoming the Repression Effects of Byproducts
10.5 Enzymatic Oxidation of Organosulfur Compounds
10.6 Enhancement of Biodesulfurization via Immobilization
10.7 Application of Nano-Technology in BDS Process
10.8 Role of Analytical Techniques in BDS
References

Chapter 11: Biodesulfurization of Real Oil Feed

List of Abbreviations and Nomenclature
11.1 Introduction
11.2 Biodesulfurization of Crude Oil
11.3 Biodesulfurization of Different Oil Distillates
11.4 BDS of Crude Oil and its Distillates by Thermophilic Microorganisms
11.5 Application of Yeast and Fungi in BDS of Real Oil Feed
11.6 Biocatalytic Oxidation
11.7 Anaerobic BDS of Real Oil Feed
11.8 Deep Desulfurization of Fuel Streams by Integrating Microbial with Non-Microbial Methods
11.9 BDS of other Petroleum Products
References

Chapter 12: Challenges and Opportunities

List of Abbreviations and Nomenclature
12.1 Introduction
12.2 New Strains with Broad Versatility
12.3 New Strains with Higher Hydrocarbon Tolerance
12.4 Overcoming the Feedback Inhibition of the End-Products
12.5 Biodesulfurization under Thermophilic Conditions
12.6 Anaerobic Biodesulfurization
12.7 Biocatalytic Oxidation
12.8 Perspectives for Enhancing the Rate of BDS
12.9 Production of Valuable Products
12.10 Storage of Fuel and Sulfur
12.11 Process Engineering Research
12.12 BDS Process of Real Oil Feed
12.13 BDS as a Complementary Technology
12.14 Future Perspectives
12.15 Techno-Economic Studies
12.16 Economic Feasibility
12.17 Fields of Developments
12.18 BDS Now and Then
12.19 Conclusion
References

Glossary

Index

End User License Agreement

List of Illustrations

Chapter 1

Figure 1.1 Molecular Structure of the 16-PAHs Selected by the US-EPA as Priority Pollutants.
Figure 1.2 Examples of Proposed Molecular Structures of Asphaltenes. (A: Speight and Moschopedis, (1981) and B: Ancheyta et al., 2009).
Figure 1.3 Representative Structures of the Various Types of Organosulfur Compounds Found in Petroleum. 1, alkane thiols; 2, cycloalkanes thiols; 3, dialkylsulfides; 4, polysulfides; 5, cyclic sulfides 6, alkylcycloalkylsulfides; 7, arene thiols; 8, alkyl aryl sulfides; 9, thiaindanes; 10, thiophenes 11, benzothiophenes; 12, thienothiophenes; 13, thienopyridines; 14, dibenzothiophenes 15, naphtha-thiophenes; 16, benzonaphthothiophenes; 17, phenanthrothiophenes.
Figure 1.4 Distribution of Sulfur Content in Different Petroleum Distillates.
Figure 1.5 A Simplified Schematic Diagram for the Refining Process of Crude Oil (El-Gendy and Speight, 2016).

Chapter 2

Figure 2.1 SARA Fractions in Crude Oil.
Figure 2.2 Examples of Organosulfur Compounds in Gasoline and Diesel Oil.
Figure 2.3 Desulfurization Technologies Classified According to the Nature of Sulfur Removal Key Processes.
Figure 2.4 A Simple HDS-Process.
Figure 2.5 Schematic Diagram for a Simple Multi-Step HDS-Process.
Figure 2.6 Schematic Diagram for the Cocurrent/Countercurrent HDS-Process.
Figure 2.7 Schematic Diagram for ExxonMobil’s SCANfining Process for Selective Naphtha HDS.
Figure 2.8 Schematic Diagram for IFP’s Prime G+ Process.
Figure 2.9 Schematic Diagram for ExxonMobil’s OCTGain Process for Selective Naphtha HDS.
Figure 2.10 Schematic Diagram for Deep-Desulfurization of Full-Range FCC Naphtha.
Figure 2.11 Simplified Flow Diagram for Conversion and Extractive Desulfurization (CEDS).
Figure 2.12 Simplified Flow-Chart of the Eni-UOP ODS Process.
Figure 2.13 Simplified Flow Chart for Hydrodynamic Cavitative ODS.
Figure 2.14 Simplified Flow Diagram for Integrated Hydrodesulfurization/Oxidative Desulfurization Process.
Figure 2.15 Simplified Flow Chart for Integrated SARS and HDSCS for Deep Desulfurization Process.
Figure 2.16 Desulfurization by Adsorption.

Chapter 3

Figure 3.1 Distribution of Proved Reserves of Natural Gas in 2011, as Reported by (Duissenov, 2013).
Figure 3.2 General Scheme of the Natural Gas Industry.
Figure 3.3 H₂S Removal Technologies.
Figure 3.4 Types of H₂S Scavengers.
Figure 3.5 The Bio-SR Process Flow Scheme.
Figure 3.6 A Simple Diagram for H₂S Adsorption Plant.
Figure 3.7 A Simple Diagram for LO-CAT Process.
Figure 3.8 A Simple Diagram for the Dry Oxidation Processes.
Figure 3.9 Classic Claus Plant.
Figure 3.10 Simplified Block Flow Diagram of the SCOT Process.
Figure 3.11 A High Pressure Absorber with a Split.
Figure 3.12 Simplified Block Flow Diagram of the THIOPAQ™ Process.
Figure 3.13 Phototrophic Microbial Acid Gas Bioconversion Plant.
Figure 3.14 Fed-Batch or Continuous Flow Reactor.
Figure 3.15 A Two-Step Process for Microbial Conversion of Sulfate to Sulfur.
Figure 3.16 Phototube reactors (a) Horizontal (b) Vertical.
Figure 3.17 Process of Exhaust Gas Purification in Cellulose Filament Manufacturing Plant.
Figure 3.18 Different Systems Used for H2S Removal.
Figure 3.19 Immobilized-Cells Bioreactor System.
Figure 3.20 Pilot-Scale Peat Bio-Filter.
Figure 3.21 Continuous Micro-Aerobic Bioreactor.
Figure 3.22 Bench-Scale Bio-Filter System.
Figure 3.23 Pilot-Scale for Chemical–Biological Process.
Figure 3.24 A Simple Diagram of Chemo-Biochemical Process for Desulfurization of Gas.
Figure 3.25 H₂S Treatment by Combined Chemical-Biological Reactor.
Figure 3.26 Integrated Process for Biogas BDS and Wastewater Biodenitrogenation.
Figure 3.27 Micro-Aerobic Desulfurization Unit.
Figure 3.28 A Schematic Diagram for Acidic Bio-Trickling Filter Systems.
Figure 3.29 A Schematic for a New Design Bio-Trickling Filter Reactor (Pirolli et al., 2016).
Figure 3.30 Bio-Trickling Filter Packed with Open Pore Polyurethane Foam.
Figure 3.31 The Possible In-Situ Desulfurization Mechanisms by Iron Ores During Anaerobic Digestion System The release of H₂S in digesters without iron ores (b) the control of H₂S by iron ores.

Chapter 4

Figure 4.1 Different NPAHs Found in Crude Oil and its Fractions.
Figure 4.2 HDN-Pathway.
Figure 4.3 The Proposed Genetic Arrangement and Enzymatic Mechanism of CARDO (Riddle et al., 2003a).
Figure 4.4 Pathways for Microbial Utilization of Carbazole.
Figure 4.5 Oxidation Reaction Catalyzed by CARDO of Pseudomonas sp. Strain CA10 (Nojiri et al., 1999).
Figure 4.6 DBT-Biodegradation Pathway by Arthrobacter sp. P1–1 (Jong et al., 2006).
Figure 4.7 CAR-Biodegradation Pathway by Arthrobacter sp. P1–1 (Jong et al., 2006).
Figure 4.8 Different Biotransformation Pathways of Indole.
Figure 4.9 More Elucidated Biotransformation Pathways of Indole.
Figure 4.10 Metabolic Pathway for Quinoline by Pseudomonas stutzeri (Shukla, 1989).
Figure 4.11 Quinoline BDN by Ps. ayucida IGTN9m (Kilbane et al., 2001).
Figure 4.12 A BDN Process of Quinoline in Crude Oil Under Storage (as proposed by Sugaya et al., 2010).
Figure 4.13 The Proposed Pathway for 2-MQn Metabolism Under Denitrifying Conditions (Wang et al., 2013).
Figure 4.14 Metabolic Pathways for Pyridine Biodegradation.
Figure 4.15 Magnetic Separation of Magnetized Particles.
Figure 4.16 Immobilized-Cell Bioreactor (Heitkamp et al., 1990).
Figure 4.17 A Schematic Diagram for the Packed Reactor of a Semi-Continuous Fuel-BDN.

Chapter 5

Figure 5.1 Two-step Adsorption Process Using Activated Carbon Fiber for Deep Desulfurization of Diesel Oil.

Chapter 6

Figure 6.1 Desulfurization of Dimethylsulfide and Methionine by P. putida (Kertesz, 2004).
Figure 6.2 Metabolic Pathway of Yperite by C. versicolor and T. palustris (Wariishi et al., 2002).
Figure 6.3 BDS of DBS by Gordonia sp. IITR100 (Ahmad et al., 2015).
Figure 6.4 Examples of Thiolanes and Thianes Found in Non-Biodegraded Petroleum (the total number of carbon atoms in these compounds ranged from at least C₈ to C₃₀).
Figure 6.5 Release of Sulfite from DBT-Sulfone and Hypothesized Release of Sulfite from Sulfolane by Strain WP1 (Greene et al., 2000) (the compounds in square brackets have not been detected in cultures of strain WP1).
Figure 6.6 Metabolic Pathway of 2HMT by C. versicolor (Ichinose et al., 2002b).
Figure 6.7 Non-Aqueous Biocatalytic Conversion of Sulfur-Containing Heterocycles by FE-9 (Finnerty, 1993a).
Figure 6.8 Pathways for the Biotransformation of Benzothiophene by Pseudomonas putida RE204.
Figure 6.9 Examples for Bacterial Oxidation of Methyl-benzothiophenes.
Figure 6.10 Comparison of Proposed BT Desulfurization Pathway with DBT Desulfurization Pathway (Gilbert et al., 1998).
Figure 6.11 Postulated Pathway for BT Desulfurization by G. rubropertinctus T08 (Matsui et al, 2001a). (1) BT; (2) BT-sulfoxide; (3) BT-sulfone; (4) BT-sultine; (5) BT-sultone; (6) o-Hydroxystyrene; (7) Coumarane; (8) 2-Coumaranone
Figure 6.12 Divergent Pathways of Benzothiophene Metabolism by (A) G. desulfuricans strain 213E (Gilbert et al., 1998), (B) Paenibacillus sp. strain A11-2 (Konishi et al., 2000), (A and B) Rhodococcus sp. strain WU-K2R (Kirimura et al., 2002) (1) Benzothiophene; (2) Benzothiophene-S-oxide (sulfoxide); (3) Benzothiophene-S,S-dioxide (sulfone); (4) 2-(2′-hydroxyphenyl)ethen-1-sulfinate; (5) Benzo[e][1,2]oxathiin-S-oxide (sultine); (6) o-Hydroxystyrene; (7) 2-(2′-hydroxyphenyl)ethan-1-al; (8) benzofuran. Sulfite has not been definitively shown as the final sulfur species. Products (5) and (8) formed by abiotic reactions under acidic extraction conditions.
Figure 6.13 BT Desulfurization Pathway by Rhodococcus sp. Strain T09 (Onaka et al., 2002).
Figure 6.14 Proposed Pathway for NTH Desulfurization by Rhodococcus sp. Strain WU-K2R (Kirimura et al., 2002).
Figure 6.15 Proposed Pathway for 2-ethylNTH Desulfurization by Mycobacterium pheli WU-F1 (Furuya et al., 2002).
Figure 6.16 Proposed Pathway for BNT Desulfurization by Gordonia sp. IITR 100 (Chauhan et al., 2015).
Figure 6.17 Kodama Pathway for the Biotransformation of DBT by Attacking the Benzene Ring.
Figure 6.18 Putative Pathway for DBT Degradation by P. fluorescens 17 (FinkelStein et al., 1997). (1) DBT-sulfoxide; (2) DBT-sulfone; (3) 3-Hydroxy-2-formylbenzothiophene; (4) 2,3-Dihydroxybenzothiophene; (5) Thiosalicyclic acid; (6) 2,2′-Dithiosalicyclic acid; (7) 2,2′-bibenzo[b]thiophene]-3,3′-diol.
Figure 6.19 The Two Predicted Pathways for DBT Degradation by Pseudomonas putida (Stoner et al., 1990).
Figure 6.20 Proposed Metabolic Pathway for the Degradation of DBT by a Brevibacterium sp. (Van-Afferden et al., 1993).
Figure 6.21 DBT-BDS via the 4S-Pathway.
Figure 6.22 The Suggested Hydroxynitrobiphenyls Produced by Corynebacterium sp. strain SY1 Omori et al. (1992).
Figure 6.23 4S-Pathway Accompanied by Methoxylation (Okada et al., 2002b).
Figure 6.24 BDS of 4,6-Diethyl-DBT by Rhodococcus sp. Strain ECRD-1 (Grossman et al., 1999).
Figure 6.25 BDS of DBT and 4,6-Dimethyl-DBT by Gordonia sp. JDZX13. (Feng et al., 2016).
Figure 6.26 Anaerobic Biodesulfurization of DBT by D. desulfuricans M6.
Figure 6.27 DBT-BDS Pathway by Arthrobacter sp. NSh39 (El-Gendy, 2004).
Figure 6.28 DBT-BDS Pathway by Agrobacterium sp. NSh10 (El-Gendy et al., 2005).
Figure 6.29 DBT-Biodegradation Pathway by (A) Aureobacterium sp. NShB1 and (B) Enterobacter sp. NShB2 (El-Gendy, 2006).
Figure 6.30 DBT-Biodegradation Pathway by Staphylococcus gallinarum NK1 (El-Gendy and Abo State, 2008).
Figure 6.31 DBT-Biodegradation Pathway by Bacillus sphaericus HN1 Nassar et al. (2010).
Figure 6.32 DBT-Biodegradation Pathway by C. variabilis sp. Sh42 (El-Gendy et al., 2010). 1, dibenzothiophene (DBT); 2, DBT-sulfoxide; 3, DBT-sulfone; 4,2-hydroxybiphenyl sulfinic acid; 5, 2-hydroxybiphenyl sulforic acid; 6,2-hydroxybiphenyl; 7, 2,2′-bihydroxybiphenyl; 7’, 2,3-bihydroxybiphenyl; 8, 2-hydroxy-6-oxo-phenylhexa-2,4-dienoic acid;9, benzoic acid; 10, 2,2′,3-trihydroxybiphenyl; 11, 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienoic acid; 12, salicylic acid; 13, catechol; 14, 2-hydroxy-2,4-pentadienoic acid; 15, pyruvic acid; 16, 2,2′,3,3′-tetrahydroxybipheny; 17, 2-hydroxy-6-(2,3-dihydroxyphenyl)-6-oxo-2,4-hexadienoic acid; 18, 2,3-dihydroxybenzoic acid; 19, pyrogallol; 20, 2-hydroxymuconic semialdehyde; 21, 2-hydroxymuconic acid.
Figure 6.33 DBT-BDS Pathway via the Production of Biphenyl as a Dead End Product.
Figure 6.34 DBT-BDS Pathway by Rhodococcus erythropolis HN2 (El-Gendy et al., 2014).
Figure 6.35 Different Metabolites of DBT-BDS by P. aeruginosa-S25 (Al-Jailawi et al., 2015).
Figure 6.36 Proposed Pathways for the Conversion of DBT by A. aegerita (a) and C. radians (b). Dotted and hollow arrows indicate reactions solely observed in the in-vitro and in-vivo experiments, respectively (Aranda et al., 2009).
Figure 6.37 Proposed Modified 4S-Pathway by Exophiala spinifera Strain FM (Elmi et al., 2015).
Figure 6.38 Proposed Metabolic Pathways for Aromatic Thiophene Derivatives by Coriolus versicolor (Ichinose et al. 2002b).

Chapter 7

Figure 7.1 Proposed Metabolic Pathway for the Anaerobic BDS of DBT by Desulfovibrio desulfuricans M6 (Kim et al., 1995).
Figure 7.2 The Main Aerobic BDS Pathways of DBT and BT.
Figure 7.3 Proposed Pathway of 2-HBP Biodegradation. Legend: Initial metabolism of 2-HBP and 2,2’-BHBP in P.azelaica HBP1 (Kohler et al., 1993). The enzymes responsible for catalyzing the different reactions are HbpA catalyzing the NADH-dependent ortho hydroxylation of 2-HBP (I) to 2,3-dihydroxybiphenyl (II), HbpC catalyzing the cleaving of 2,3-dihydroxybiphenyl at a meta position, which results in 2-hydroxy-6-oxo-6-phenyl-2,4-hexadienoic acid (III). This compound is then hydrolyzed by HbpD to benzoic acid and 2-hydroxy-2,4-pentadienoic acid (IV and V, respectively).
Figure 7.4 Proposed Pathway of 2,2’-BHBP Biodegradation. Legend: Pathway proposed for the metabolism of 2,2’-bihydroxybiphenyl by Pseudomonas sp. strain HBP1 (Sondossi et al., 2004). (1) 2,2’-BHBP; (2) 2,2’,3-trihydroxybiphenyl; (3) 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienoic acid; (4) 3-(chroman-4-on-2-yl) pyruvate; (5) salicylic acid; (6) 2-hydroxy-2,4-hexadienoic acid; (7) catechol; (8) 2-hydroxymuconic semialdehyde; (9) 2,2’,3,3’-tetrahydroxybiphenyl; (10) 2-hydroxy-6-(2,3-dihydroxyphenyl)-6-oxo-2,4-hexadienoic acid; (11) 3-(8-hydroxychroman-4-on-2-yl) pyruvate; (12) 2,3-dihydroxybenzoic acid; (13) pyrogallol; (14) 2-hydroxymuconic acid.
Figure 7.5 dszABC Genes Encode the Enzymes for the Four-Step Conversion of DBT to 2-HBP.
Figure 7.6 The dszABC Operon of R. erythropolis IGTS8.
Figure 7.7 Protein Binding Site and Promoter Region of dsz Operon in R. erythropolis IGTS8.
Figure 7.8 Biodesulfurizing Enzymes Involved in 4S Pathway.
Figure 7.9 Formation and Consumption of Sulfite and Sulfate for Biomass Formation During BDS of DBT.
Figure 7.10 A Genetic Rearrangement Strategy for Improving the Metabolic Pathway of DBT (gray bars represent genes and dark gray bars represent overlap regions).

Chapter 8

Figure 8.1 Proposed Pathway for Biodegradation of DBT by Bacillus sphaericus HN1 (Nassar, 2009).
Figure 8.2 Certain Molecular Pathways Operating in a Hypothetical Aerobic Bacterium Involved in the DBT-BDS Process This bioenergetics scheme focuses on the cell’s need for hydrogen and electron donor molecules, such as NAD⁺/NADH and NADP⁺/NADPH. The pentose phosphate pathway starts from glucose 6-phosphate and this pathway is actively involved in the formation of NAD⁺ and FAD. Ribose-5-phosphate from this pathway is also involved in the synthesis of NADP⁺. The determination of the roles of NAD⁺ and FAD in ATP synthesis through the electron transport chain and electron phosphorylation is also shown. Involvement of the intermediates of the TCA cycle during amino-acid synthesis through glutamate–glutamine formation is also presented (Zubay, 1998; Kilbane and Robbins, 2007; Berg et al., 2010).
Figure 8.3 4S-Pathway by Rhodococcus erythropolis HN2 (El-Gendy et al., 2014)
Figure 8.4 Response Surface 3D-Plot (a) and 2D Contour Plot (b) for the Effect of YE (g/L) and DMSO (mM) on Cell Growth (Deriase et al., 2012).
Figure 8.5 Response Surface 3D-Plot (a) and 2D Contour Plot (b) for the Effect of YE (g/L) and DMSO (mM) on the Remaining DBT (i.e. the removal efficiency) (Deriase et al., 2012).
Figure 8.6 Response Surface 3D-Plot (a) and 2D Contour Plot (b) for the Effect of YE (g/L) and MgSO₄ (g/L) on Cell Growth (Deriase et al., 2012).
Figure 8.7 Response Surface 3D-Plot (a) and 2D Contour Plot (b) for the Effect of YE (g/L) and MgSO₄ (g/L) on the Remaining DBT (i.e. the removal efficiency) (Deriase et al., 2012).
Figure 8.8 The Response Surface Plots of Studied Variables on Different Responses: Cell Growth, BDS Percentage, 2-HBP Production and 2,2′-DMBP in Batch DBT-BDS by R. erythropolis HN2 (El-Gendy et al., 2014).

Chapter 9

Figure 9.1 Four Main Phases of Microbial Growth.
Figure 9.2 Graphical Representation of Microbial Growth (a) Exponential and (b) Logistic Model Equations.
Figure 9.3 Graphical Representation of Monod Kinetic Equation.
Figure 9.4 The Cardinal Temperatures: Minimum, Optimum, and Maximum.
Figure 9.5 Temperature and Growth Rate Response in Different Temperature Classes of Micro organisms.
Figure 9.6 Effect of Temperature on Specific Growth Rate of Microorganisms.
Figure 9.7 Effect of Acidity and Alkalinity on Growth of Microorganism.
Figure 9.8 Effect of Dissolved Oxygen Concentration on Growth of Microorganisms.
Figure 9.9 Change in Concentrations of substrate (S), product (P), enzyme (E), and enzyme complex (ES).
Figure 9.10 Zero Order Reaction Rate is Independent on the Substrate Concentration.
Figure 9.11 Effect of Substrate Concentration on Reaction Velocity.
Figure 9.12 Lock – Key Theory.
Figure 9.13 Non-Competitive Inhibition.
Figure 9.14 Substrate Becomes Rate Inhibition.
Figure 9.15 Substrate Inhibition.
Figure 9.16 Effect of Temperature on Reaction Rate.
Figure 9.17 Effect of pH on Reaction Rate.
Figure 9.18 Lineweaver-Burk (a) and Eadie-Hofstee (b) Plots Methods.
Figure 9.19 Selective Desulfurization of Benzothiophene (BT) and Dibenzothiophene (DBT).

Chapter 10

Figure 10.1 The Pathway of Biological Desulfurization of DBT as a Model Compound (Denome et al, 1993 and 1994). NADH is a reduced nicotinamide adenosine dinucleotide, FMN is a flavin mononucleotide, and D_SZA, D_SZB, D_SZC, and D_SZD are the catalytic gene products of dszA, dszB, dszC, and dszD, respectively.
Figure 10.2 Schematic Diagram of Electro-Kinetic Setup for BDS.
Figure 10.3 Advantages of Immobilized Cell Systems.
Figure 10.4 Ideal Criteria of Immobilizing Material.
Figure 10.5 Types of Immobilized Material.
Figure 10.6 Immobilization Techniques.
Figure 10.7 In-Situ Adsorption-Bioregeneration System.
Figure 10.8 Chemical Structures of Calcium Alginate Hydrogel.
Figure 10.9 Preparation of Calcium Alginate Immobilized Cells’ Beads.
Figure 10.10 The Conversion of PVAc to PVA. In dark gray are the acetate groups, whereas in gray are the hydroxyl groups.
Figure 10.11 Magnetic Separation of Decorated BDSM.
Figure 10.12 Enhancement of BDS Process by Using γ-AL₂O₃ NPs Coated Cells.
Figure 10.13 Adsorption Mechanism Between Fe₃O₄ NPs and BDSM.
Figure 10.14 Size and Shape of Cells Immobilized Calcium Alginate Beads.
Figure 10.15 TEM Images Showing the Well Adsorption of Fe₃O₄ MNPs on the Surfaces of BDSM.
Figure 10.16 Recovery of Magnetically Coated BDSM.

Chapter 11

Figure 11.1 A Conceptual Diagram of Some of the Steps in the Biodesulfurization of Oil.
Figure 11.2 Biodesulfurization of Diesel Oil by Airlift Reactor.
Figure 11.3 GC/FPD Chromatograms of Diesel Oil Before and After BDS Using Different Strains (Nassar, 2015).
Figure 11.4 Suggested Strategies for Integrating BDS with HDS.
Figure 11.5 The In-Situ Adsorption-Bioregeneration System (Li et al., 2009).

Chapter 12

Figure 12.1 Enrichment and Isolation of Tolerable and Efficient BDSM.
Figure 12.2 Mechanistic Steps in a BDS System at High Cell Density. Biocatalyst may be present in one of three populations: free cells in an aqueous phase, oil-adhered cells, and cells in aggregates. Oxygen transport and uptake is necessary because the 4S pathway is an oxidative pathway that requires 3 moles of O₂ per mole of DBT desulfurized (R may be an alkyl or H).
Figure 12.3 Schematic Map of Tri-Parental Mate.
Figure 12.4 Conversion of the BDS Intermediate Cx-HPBSi to Value-Added Surfactants.
Figure 12.5 Process Flow-Sheet for a BDS Process.
Figure 12.6 An Integrated Biodesulfurization Process. (including inoculum preparation, desulfurization, and sulfate removal in a single step for removing sulfur from oils).
Figure 12.7 Schematic Diagram for a Two-Layer and Continuous Bioreactor.
Figure 12.8 Schematic Diagram of Experimental Setup of ALR.
Figure 12.9 Example of a Draft-Tube Airlift Bioreactor Containing Water-In-Oil Micro-Emulsion.
Figure 12.10 Double-Y Channel Design of the MicroChannel Reactor.
Figure 12.11 Schematic Representation of the Trickle Bed Bioreactor and the Packing Materials (a), Characteristic Sphere (b), and Contacting Pattern of Spheres (c).
Figure 12.12 Asphaltene Structure and Regions Susceptible of Fragmentation its Molecule. 1: Photooxidation; 2: beta-oxidation; 3: Dibenzothiophene metabolic path; 4: Path similar to dibenzothiophene; 5: Pyrene path; 6: Path similar to benzo(a)pyrene; 7: Similar to carbazoles.
Figure 12.13 Proposed Integration of BDS with HDS.
Figure 12.14 Integration of Biorefining Process in Petroleum Industry.
Figure 12.15 Biodesulfurization Pilot Plant (adapted from Monticello, 2000).
Figure 12.16 TEM Micro-Graphs of Magnetic Fe₃O₄ (a) and Coated Bacterial Isolates, Brevibacillus invocatus C19 (b), Micrococcus lutes RM1 (c), and Bacillus clausii BS1 (d).
Figure 12.17 Preliminary Bench-Scale Process Design to Test High-Sulfur Content Diesel Oil Biodesulfurization by Magnetic NPs-Coated Bacterial Cells.
Figure 12.18 The 2 Different Paths Under Study for DBT-BDS by G. alkanivorans strain 1B.
Figure 12.19 Schematic Diagram for an Example of Petroleum Bioprocessing Process - BDS.

List of Illustrations

Chapter 1

Table 1.1 The Estimated Proven Reserve Holders as of January 2013 (Duissenov, 2013).
Table 1.2 Crude oil classifications according to S-content and API-gravity (Duissenov, 2013).
Table 1.3 Petroleum-Sulfur Content in Different Countries All Over the World (El-Gendy and Speight, 2016).
Table 1.4 Average Regional and Global Crude Oil Quality for 2008 (Actual) and 2030 (Projected) (The International Council of Clean Transportation ICCT, 2011)
Table 1.5 Crude Oil Distillate Products (Riazi, 2005).
Table 1.6 Toxicity of H₂S.
Table 1.7 Expected Regional Gasoline Sulfur Content (OPEC, 2013).
Table 1.8 Expected Regional On-Road Diesel Sulfur Content (OPEC, 2013).

Chapter 2

Table 2.1 Sulfur Content, Types, and Recalcitrance within Petroleum Distillates.
Table 2.2 Electron densities on S-atoms and rate of ODS in some S-compounds using H₂O₂/organic acid oxidative system (Otsuki et al., 2000).
Table 2.3 A Comparison of FCC Gasoline Desulfurization Processes.

Chapter 3

Table 3.1 Natural Gas Composition (Heinz, 2008).
Table 3.2 Classification of Natural Gas According to its Composition (vol.%) (Rojey, 1997).
Table 3.3 Biogas Composition Produced by the Anaerobic Digestion of Different Substrates. http://www.biogas-renewable-energy.info/biogas_composition.html.
Table 3.4 Sulfur Content in % of Fresh Matter and in g/kg for Typical Biogas Substrates. Naegele et al. (2013)

Chapter 4

Table 4.1 CAR-Degradation Ability of Microorganisms in One- or Two- Phase Systems.
Table 4.2 CAR Biodegrading Microorganisms.

Chapter 5

Table 5.1 Composition of Activated Carbon (as Element Content %).

Chapter 6

Table 6.1 Bond Strength of Various C-S, C-C, and C–H Bonds (Bressler et al., 1998).
Table 6.2 Summary of Sulfur-Containing Metabolites Produced from Benzothiophene (BT) and All of the Methyl-Benzothiophenes (MBT) by Four Bacterial Isolates (Kropp et al., 1994a).
Table 6.3 Summary of Sulfur-Containing Products Found in Extracts of Three Bacterial Cultures After Incubation with Various Dimethylbenzothiophenes for Seven Days (the products were found in cultures grown on 1-methylnaphtahlene or glucose) (Kropp et al., 1996).

Chapter 7

Table 7.1 Genetic Engineering Approaches to Overcome the Major Problems of the BDS Process (Martínez et al., 2016)

Chapter 8

Table 8.1 The DBT-BDS Efficiency of Reported Resting Cell Strains.
Table 8.2 Degree of the Predicted Polynomial for Batch DBT-BDS using Bacillus sphaericus HN1, Nassar (2009).
Table 8.3 Predicted Model Equations Together with Corresponding Goodness of Fit Parameters for Batch DBT-BDS Using Growing Cells of R. erythropolis HN2 (Nassar et al., 2017b).

Chapter 9

Table 9.1 Mathematical Description of Microbial Growth Phases.
Table 9.2 Different Microbial Growth Model Equations.
Table 9.3 Classical Empirical Growth Kinetic Models.
Table 9.4 Reaction Order with Respect to Substrate Concentration.

Chapter 10

Table 10.1 Potential Dibenzothiophene (DBT) Degrading Microorganisms Discovered on the Basis of dsz Genes and Their Unique Properties.
Table 10.2 TLC and Gibbs Assay Results with Kodama, 4S pathways Metabolites (Monticello et al., 1985; Tanaka et al., 2002)
Table 10.3 Analytical Techniques in BDS

Chapter 11

Table 11.1 Major Distillates of Crude Oil and Their Main S-Compounds.
Table 11.2 Three-Step Integrated Desulfurization Process of Crude Oil.

Chapter 12

Table 12.1 Selective Biodesulfurization of DBT.
Table 12.2 Biodesulfurizing Microorganisms (BDSM) with Broad Versatility.
Table 12.3 BDS of DBT in Biphasic System.
Table 12.4 BDS of DBT Using Thermotolerant BDSM.
Table 12.5 DBT-BDS Using Recombinant Strains.
Table 12.6 DBT-BDS Using Resting Cells.
Table 12.7 BDS of Real Oil Feed Using Different Bioreactors.
Table 12.8 Comparative Data for BDS of Model Oil by R. erythropolis.
Table 12.9 BDS of Real Oil Feed.
Table 12.10 Summary of Energy Requirements and CO₂ Generation from BDS vs. HDS of Diesel Oil (Linguist and Pacheco, 1999).
Table 12.11 Estimated Annual Operating Cost of PetroStar Inc. Desulfurization Process (Nunn et al., 2006)
Table 12.12 Estimated Operating Cost for BDS of High-Sulfur Content Diesel Oil Using Free and Magnetic NPs-Coated Bacterial Cells
Table 12.13 Energy Consumption and Cost Analysis of Different Scenarios for Application of BDS Path (2) to Reach ULSD

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Library of Congress Cataloging-in-Publication Data

ISBN 978-1-119-22358-0

Preface

Biotechnology is now accepted as an attractive means of improving the efficiency of many industrial processes and resolving serious environmental problems. One of the reasons for this is the extraordinary metabolic capability that exists within the bacterial world. Microbial enzymes are capable of biotransforming a wide range of compounds and the increasing worldwide attention paid to this concept can be attributed to several factors, including the presence of a wide variety of catabolic enzymes and the ability of many microbial enzymes to transform a broad range of unnatural compounds (xenobiotics), as well as natural compounds. Biotransformation processes have several advantages compared to chemical processes, such as: (i) Microbial enzyme reactions often being more selective; (ii) Biotransformation processes often being more energy-efficient; (iii) Microbial enzymes being active under mild conditions; and (iv) Microbial enzymes being environmentally friendly biocatalysts. Although many biotransformation processes have been described, only a few of these have been used as part of the industrial process. Many opportunities remain in this area.

Biotechnology has been successfully applied at the industrial level in the medical, fine chemical, agricultural, and food sectors. Petroleum biotechnology is based on biotransformation processes. Petroleum microbiology research is advancing on many fronts, spurred on most recently by new knowledge of cellular structure and function gained through molecular and protein engineering techniques, combined with more conventional microbial methods. Several applications of biotechnology in the oil and energy industry are becoming foreseen. Current applied research on petroleum microbiology encompasses oil spill remediation, fermenter- and wetland-based hydrocarbon treatment, bio-filtration of volatile hydrocarbons, enhanced oil recovery, oil and fuel biorefining, fine-chemical production, and microbial community based site assessment. The production of biofuels in large volumes is now a reality, although there are some concerns about the use of land, water, and crops to produce fuels. These come from the biofuels produced by agroindustrial wastes, lignocellulosic wastes, waste oils, and micro- and macro-algae. In the oil industry, biotechnology has found its place in bioremediation and microbial enhanced oil recovery (MEOR). There are other opportunities in the processing (biorefining) and upgrading (bio-upgrading) of problematic oil fractions and heavy crude oils. In the context of increasing energy demand, conventional oil depletion, climate change, and increased environmental regulations on atmospheric emissions, biorefining is a possible alternative to some of the current oil-refining processes. The major potential applications of biorefining are biodesulfurization, biodenitrogenation, biodemetallization, and biotransformation of heavy crude oils into lighter crude oils, i.e., upgrading heavy oils (degradation of asphaltenes and removal of metals). The most advanced area is biodesulfurization, for which pilot plants exist and the results obtained for biodesulfurization may be generally applicable to other areas of biorefining.

This book reviews the worldwide status of current regulations regarding fuel properties that have environmental impacts, such as sulfur and nitrogen content, cetane number, and aromatic content, summarizes the cumulative, and highlights the recent scientific and technological advances in different desulfurization techniques, including: physical (for example, adsorptive desulfurization ADS), chemical (for example, hydrodesulfurization HDS, oxidative desulfurization ODS), and biological (for example, bio-adsorptive desulfurization BADS, aerobic and anaerobic biodesulfurization BDS, and biocatalytic oxidation as alternative to BODS) techniques. It will also cover denitrogenation processes (physical, chemical and biological ones). Since basic nitrogen compounds inactivate HDS catalysts and non-basic compounds can be converted to basic ones during the refining/catalytic cracking process, they are also potential inhibitors of the HDS process. So, denitrogenation is advantageous both from an environmental point of view (reduction of NOx emissions) and from an operational point of view (to avoid catalyst deactivation, corrosion of refinery equipment, and chemical instability of refined petroleum).

The advantages and limitations of each technique are discussed. The application of molecular biology and the possibility of integration of bio-nano-technology in oil production plants, future oil refineries and bioprocessing of oil, for the production of ultra-low sulfur fuels are also summarized in this book. Challenges and future perspectives of BDS in the petroleum industry and their applications for detoxification of chemical warfare agents, or the production of other valuable products, such as: surfactants, antibiotics, polythioesters, and various specialty chemicals are also covered in this book.

Dr. Nour Sh. El-Gendy
Professor of Petroleum and Environmental Biotechnology

Dr. Hussein N. Nassar
Researcher of Petroleum and Environmental Biotechnology

October 2017