Bioprocessing of Renewable Resources to Commodity Bioproducts

Virendra S. Bisaria is Professor in the Department of Biochemical Engineering and Biotechnology at the Indian Institute of Technology Delhi, New Delhi, India. He has published more than 100 original papers, 10 reviews and 15 book chapters.  He is Editor of the Journal of Bioscience and Bioengineering (Elsevier) and is on the editorial boards of Journal of Chemical Technology and Biotechnology (Wiley) and Process Biochemistry (Elsevier).  He was one of the International collaborators to recommend assay procedures for cellulase and xylanase activities on behalf of Commission on Biotechnology, International Union of Pure and Applied Chemistry. His awards include the Research Exchange Award from the Korean Society for Biotechnology and Bioengineering and fellowships from UNESCO and UNDP etc. He is Vice President of Asian Federation of Biotechnology from India.Akihiko Kondo is Professor in the Department of Chemical Engineering and Director of Biorefinery Center at Kobe University, Kobe, Japan.  He is Team Leader, Biomass Engineering Program, RIKEN. He has published more than 330 original papers, 75 reviews and 55 book chapters. He is Editor of Journal of Biotechnology (Elsevier), Associate Editor of Biochemical Engineering Journal (Elsevier) and is on the editorial boards of Biotechnology for Biofuels (Springer), Bioresource Technology (Elsevier), Journal of Biological Engineering (Springer) and FEMS Yeast Research (Wiley).  He has won numerous awards which include the Advanced Technology Award by Fuji Sankei Business and Takeda International Contributions Award by Takeda Pharmaceuticals.

• PREFACE xvCONTRIBUTORS xixPART I ENABLING PROCESSING TECHNOLOGIES1 Biorefineries—Concepts for Sustainability 3Michael Sauer, Matthias Steiger, Diethard Mattanovich, and Hans Marx1.1 Introduction 41.2 Three Levels for Biomass Use 51.3 The Sustainable Removal of Biomass from the Field is Crucial for a Successful Biorefinery 71.4 Making Order: Classification of Biorefineries 81.5 Quantities of Sustainably Available Biomass 101.6 Quantification of Sustainability 111.7 Starch- and Sugar-Based Biorefinery 121.7.1 Sugar Crop Raffination 141.7.2 Starch Crop Raffination 141.8 Oilseed Crops 141.9 Lignocellulosic Feedstock 161.9.1 Biochemical Biorefinery (Fractionation Biorefinery) 161.9.2 Syngas Biorefinery (Gasification Biorefinery) 181.10 Green Biorefinery 191.11 Microalgae 201.12 Future Prospects—Aiming for Higher Value from Biomass 21References 242 Biomass Logistics 29Kevin L. Kenney, J. Richard Hess, Nathan A. Stevens, William A. Smith, Ian J. Bonner, and David J. Muth2.1 Introduction 302.2 Method of Assessing Uncertainty, Sensitivity, and Influence of Feedstock Logistic System Parameters 312.2.1 Analysis Step 1—Defining the Model System 312.2.2 Analysis Step 2—Defining Input Parameter Probability Distributions 312.2.3 Analysis Step 3—Perform Deterministic Computations 322.2.4 Analysis Step 4—Deciphering the Results 342.3 Understanding Uncertainty in the Context of Feedstock Logistics 362.3.1 Increasing Biomass Collection Efficiency by Responding to In-Field Variability 362.3.2 Minimizing Storage Losses by Addressing Moisture Variability 382.4 Future Prospects 402.5 Financial Disclosure/Acknowledgments 40References 413 Pretreatment of Lignocellulosic Materials 43Karthik Rajendran and Mohammad J. Taherzadeh3.1 Introduction 443.2 Complexity of Lignocelluloses 453.2.1 Anatomy of Lignocellulosic Biomass 453.2.2 Proteins Present in the Plant Cell Wall 463.2.3 Presence of Lignin in the Cell Wall of Plants 473.2.4 Polymeric Interaction in the Plant Cell Wall 483.2.5 Lignocellulosic Biomass Recalcitrance 493.3 Challenges in Pretreatment of Lignocelluloses 523.4 Pretreatment Methods and Mechanisms 533.4.1 Physical Pretreatment Methods 533.4.2 Chemical and Physicochemical Methods 563.4.3 Biological Methods 613.5 Economic Outlook 643.6 Future Prospects 67References 684 Enzymatic Hydrolysis of Lignocellulosic Biomass 77Jonathan J. Stickel, Roman Brunecky, Richard T. Elander, and James D. McMillan4.1 Introduction 784.2 Cellulase, Hemicellulase, and Accessory Enzyme Systems and Their Synergistic Action on Lignocellulosic Biomass 794.2.1 Biomass Recalcitrance 794.2.2 Cellulases 804.2.3 Hemicellulases 814.2.4 Accessory Enzymes 814.2.5 Synergy with Xylan Removal and Cellulases 824.3 Enzymatic Hydrolysis at High Concentrations of Biomass Solids 834.3.1 Conversion Yield Calculations 844.3.2 Product Inhibition of Enzymes 854.3.3 Slurry Transport and Mixing 864.3.4 Heat and Mass Transport 874.4 Mechanistic Process Modeling and Simulation 884.5 Considerations for Process Integration and Economic Viability 914.5.1 Feedstock 914.5.2 Pretreatment 924.5.3 Downstream Conversion 944.6 Economic Outlook 954.7 Future Prospects 96Acknowledgments 97References 975 Production of Cellulolytic Enzymes 105Ranjita Biswas, Abhishek Persad, and Virendra S. Bisaria5.1 Introduction 1065.2 Hydrolytic Enzymes for Digestion of Lignocelluloses 1075.2.1 Cellulases 1075.2.2 Xylanases 1085.3 Desirable Attributes of Cellulase for Hydrolysis of Cellulose 1095.4 Strategies Used for Enhanced Enzyme Production 1105.4.1 Genetic Methods 1105.4.2 Process Methods 1145.5 Economic Outlook 1235.6 Future Prospects 123References 1246 Bioprocessing Technologies 133Gopal Chotani, Caroline Peres, Alexandra Schuler, and Peyman Moslemy6.1 Introduction 1346.2 Cell Factory Platform 1366.2.1 Properties of a Biocatalyst 1376.2.2 Recent Trends in Cell Factory Construction for Bioprocessing 1406.3 Fermentation Process 1426.4 Recovery Process 1476.4.1 Active Dry Yeast 1486.4.2 Unclarified Enzyme Product 1496.4.3 Clarified Enzyme Product 1506.4.4 BioisopreneTM 1516.5 Formulation Process 1536.5.1 Solid Forms 1546.5.2 Slurry or Paste Forms 1596.5.3 Liquid Forms 1606.6 Final Product Blends 1616.7 Economic Outlook and Future Prospects 162Acknowledgment 163Nomenclature 163References 163PART II SPECIFIC COMMODITY BIOPRODUCTS7 Ethanol from Bacteria 169Hideshi Yanase7.1 Introduction 1707.2 Heteroethanologenic Bacteria 1727.2.1 Escherichia coli 1737.2.2 Klebsiella oxytoca 1777.2.3 Erwinia spp. and Enterobacter asburiae 1787.2.4 Corynebacterium glutamicum 1797.2.5 Thermophilic Bacteria 1807.3 Homoethanologenic Bacteria 1837.3.1 Zymomonas mobilis 1847.3.2 Zymobacter palmae 1897.4 Economic Outlook 1917.5 Future Prospects 192References 1938 Ethanol Production from Yeasts 201Tomohisa Hasunuma, Ryosuke Yamada, and Akihiko Kondo8.1 Introduction 2028.2 Ethanol Production from Starchy Biomass 2058.2.1 Starch Utilization Process 2058.2.2 Yeast Cell–Surface Engineering System for Biomass Utilization 2058.2.3 Ethanol Production from Starchy Biomass Using Amylase-Expressing Yeast 2068.3 Ethanol Production from Lignocellulosic Biomass 2088.3.1 Lignocellulose Utilization Process 2088.3.2 Fermentation of Cellulosic Materials 2098.3.3 Fermentation of Hemicellulosic Materials 2158.3.4 Ethanol Production in the Presence of Fermentation Inhibitors 2178.4 Economic Outlook 2188.5 Future Prospects 220References 2209 Fermentative Biobutanol Production: An Old Topic with Remarkable Recent Advances 227Yi Wang, Holger Janssen and Hans P. Blaschek9.1 Introduction 2289.2 Butanol as a Fuel and Chemical Feedstock 2299.3 History of ABE Fermentation 2309.4 Physiology of Clostridial ABE Fermentation 2329.4.1 The Clostridial Cell Cycle 2329.4.2 Physiology and Enzymes of the Central Metabolic Pathway 2339.5 Abe Fermentation Processes, Butanol Toxicity, and Product Recovery 2369.5.1 ABE Fermentation Processes 2369.5.2 Butanol Toxicity and Butanol-Tolerant Strains 2379.5.3 Fermentation Products Recovery 2389.6 Metabolic Engineering and “Omics”—Analyses of Solventogenic Clostridia 2399.6.1 Development and Application of Metabolic Engineering Techniques 2399.6.2 Butanol Production by Engineered Microbes 2429.6.3 Global Insights into Solventogenic Metabolism Based on “Transcriptomics” and “Proteomics” 2459.7 Economic Outlook 2469.8 Current Status and Future Prospects 247References 25110 Bio-based Butanediols Production: The Contributions of Catalysis, Metabolic Engineering, and Synthetic Biology 261Xiao-Jun Ji and He Huang10.1 Introduction 26210.2 Bio-Based 2,3-Butanediol 26410.2.1 Via Catalytic Hydrogenolysis 26410.2.2 Via Sugar Fermentation 26510.3 Bio-Based 1,4-Butanediol 27610.3.1 Via Catalytic Hydrogenation 27610.3.2 Via Sugar Fermentation 27710.4 Economic Outlook 27910.5 Future Prospects 280Acknowledgments 280References 28011 1,3-Propanediol 289Yaqin Sun, Chengwei Ma, Hongxin Fu, Ying Mu, and Zhilong Xiu11.1 Introduction 29011.2 Bioconversion of Glucose into 1,3-Propanediol 29111.3 Bioconversion of Glycerol into 1,3-Propanediol 29211.3.1 Strains 29211.3.2 Fermentation 29311.3.3 Bioprocess Optimization and Control 30111.4 Metabolic Engineering 30211.4.1 Stoichiometric Analysis/MFA 30211.4.2 Pathway Engineering 30411.5 Down-Processing of 1,3-Propanediol 30811.6 Integrated Processes 31111.6.1 Biodiesel and 1,3-Propanediol 31111.6.2 Glycerol and 1,3-Propanediol 31311.6.3 1,3-Propanediol and Biogas 31411.7 Economic Outlook 31411.8 Future Prospects 315Acknowledgments 316A List of Abbreviations 316References 31712 Isobutanol 327Bernhard J. Eikmanns and Bastian Blombach12.1 Introduction 32812.2 The Access Code for the Microbial Production of Branched-Chain Alcohols: 2-Ketoacid Decarboxylase and an Alcohol Dehydrogenase 32912.3 Metabolic Engineering Strategies for Directed Production of Isobutanol 33112.3.1 Isobutanol Production with Escherichia coli 33112.3.2 Isobutanol Production with Corynebacterium glutamicum 33512.3.3 Isobutanol Production with Bacillus subtilis 33712.3.4 Isobutanol Production with Clostridium cellulolyticum 33912.3.5 Isobutanol Production with Ralstonia eutropha 33912.3.6 Isobutanol Production with Synechococcus elongatus 34012.3.7 Isobutanol Production with Saccharomyces cerevisiae 34112.4 Overcoming Isobutanol Cytotoxicity 34112.5 Process Development for the Production of Isobutanol 34312.6 Economic Outlook 34512.7 Future Prospects 346Abbreviations 347Nomenclature 347References 34913 Lactic Acid 353Kenji Okano, Tsutomu Tanaka, and Akihiko Kondo13.1 History of Lactic Acid 35413.2 Applications of Lactic Acid 35413.3 Poly Lactic Acid 35413.4 Conventional Lactic Acid Production 35613.5 Lactic Acid Production From Renewable Resources 35713.5.1 Lactic Acid Bacteria 35913.5.2 Escherichia coli 36413.5.3 Corynebacterium glutamicum 36813.5.4 Yeasts 37013.6 Economic Outlook 37313.7 Future Prospects 374Nomenclature 374References 37514 Microbial Production of 3-Hydroxypropionic Acid From Renewable Sources: A Green Approach as an Alternative to Conventional Chemistry 381Vinod Kumar, Somasundar Ashok, and Sunghoon Park14.1 Introduction 38214.2 Natural Microbial Production of 3-HP 38314.3 Production of 3-HP from Glucose by Recombinant Microorganisms 38514.4 Production of 3-HP from Glycerol by Recombinant Microorganisms 38814.4.1 Glycerol Metabolism for the Production of 3-HP and Cell Growth 38914.4.2 Synthesis of 3-HP from Glycerol Through the CoA-Dependent Pathway 39014.4.3 Synthesis of 3-HP From Glycerol Through the CoA-Independent Pathway 39214.4.4 Coproduction of 3-HP and PDO From Glycerol 39414.5 Major Challenges for Microbial Production of 3-HP 39614.5.1 Toxicity and Tolerance 39614.5.2 Redox Balance and By-products Formation 39914.5.3 Vitamin B12 Supply 40014.6 Economic Outlook 40014.7 Future Prospects 401Acknowledgment 401List of Abbreviations 402References 40215 Fumaric Acid Biosynthesis and Accumulation 409Israel Goldberg and J. Stefan Rokem15.1 Introduction 41015.1.1 Uses 41015.1.2 Production 41115.2 Microbial Synthesis of Fumaric Acid 41215.2.1 Producer Organisms 41215.2.2 Carbon Sources 41415.2.3 Solid-State Fermentations 41415.2.4 Submerged Fermentation Conditions 41515.2.5 Transport of Fumaric Acid 41615.2.6 Production Processes 41615.3 A Plausible Biochemical Mechanism for Fumaric Acid Biosynthesis and Accumulation in Rhizopus 41715.3.1 How Can the High Molar Yield of Fumaric Acid be Explained? 41715.3.2 Where in the Cell is the Localization of the Reductive Reactions of the TCA Cycle? 41815.3.3 What is the Role of Cytosolic Fumarase in Fumaric Acid Accumulation in Rhizopus Strain? 41915.4 Toward Engineering Rhizopus for Fumaric Acid Production 42215.5 Economic Outlook 42415.6 Future Perspectives 42715.6.1 Biorefinery 42715.6.2 Platform Microorganisms 427Acknowledgment 429References 43016 Succinic Acid 435Boris Litsanov, Melanie Brocker, Marco Oldiges, and Michael Bott16.1 Succinate as an Important Platform Chemical for a Sustainable Bio-Based Chemistry 43616.2 Microorganisms for Bio-Succinate Production—Physiology, Metabolic Routes, and Strain Development 43716.2.1 Anaerobiospirillum succiniciproducens 44316.2.2 Family Pasteurellaceae 44416.2.3 Escherichia coli 44816.2.4 Corynebacterium glutamicum 45116.2.5 Yeast-Based Producers 45416.3 Neutral Versus Acidic Conditions for Product Formation 45516.4 Downstream Processing 45616.5 Companies Involved in Bio-Succinic Acid Manufacturing 45816.5.1 Bioamber Inc. 45916.5.2 Myriant Technologies LLC 45916.5.3 Reverdia 46216.5.4 Succinity GmbH 46216.6 Future Prospects and Economic Outlook 462References 46317 Glutamic Acid 473Takashi Hirasawa and Hiroshi Shimizu17.1 Introduction 47417.2 Glutamic Acid Production by Corynebacterium Glutamicum 47517.2.1 Glutamic Acid Production by Corynebacterium Glutamicum and Its Molecular Mechanism 47517.2.2 Metabolic Engineering of Glutamic Acid Production by Corynebacterium Glutamicum 47817.3 Glutamic Acid as a Building Block 48117.3.1 Production of Chemicals from Glutamic Acid Using Microorganisms 48117.3.2 Production of Other Chemicals from Glutamic Acid 48717.4 Economic Outlook 48717.5 Future Prospects 489List of Abbreviations 489References 48918 Recent Advances for Microbial Production of Xylitol 497Yong-Cheol Park, Sun-Ki Kim, and Jin-Ho Seo18.1 Introduction 49818.2 General Principles for Biological Production of Xylitol 49818.3 Microbial Production of Xylitol 50118.3.1 Carbon Sources 50118.3.2 Aeration 50118.3.3 Optimization of Fermentation Strategies 50318.4 Xylitol Production by Genetically Engineered Microorganisms 50818.4.1 Construction of Xylitol-Producing Recombinant Saccharomyces cerevisiae 50818.4.2 Cofactor Engineering for Xylitol Production in Recombinant Saccharomyces cerevisiae 51018.4.3 Other Recombinant Microorganisms for Xylitol Production 51218.5 Economic Outlook 51418.6 Future Prospects 515Acknowledgments 515Nomenclature 515References 51619 First and Second Generation Production of Bio-Adipic Acid 519Jozef Bernhard Johann Henry van Duuren and Christoph Wittmann19.1 Introduction 52019.2 Production of Bio-Adipic Acid 52319.2.1 Natural Formation by Microorganisms 52319.2.2 First Generation Bio-Adipic Acid 52419.2.3 Second Generation Bio-Adipic Acid 52819.3 Ecological Footprint of Bio-Adipic Acid 53019.4 Economic Outlook 53519.5 Future Prospects 536References 538INDEX 541