Bioprocessing of Renewable Resources to Commodity Bioproducts

This book provides the vision of a successful biorefinery—the lignocelluloic biomass needs to be efficiently converted to its constituent monomers, comprising mainly of sugars such as glucose, xylose, mannose and arabinose. Accordingly, the first part of the book deals with aspects crucial for the pretreatment and hydrolysis of biomass to give sugars in high yield, as well as the general aspects of bioprocessing technologies which will enable the development of biorefineries through inputs of metabolic engineering, fermentation, downstream processing and formulation. The second part of the book gives the current status and future directions of the biological processes for production of ethanol (a biofuel as well as an important commodity raw material), solvents (butanol, isobutanol, butanediols, propanediols), organic acids (lactic acid, 3-hydroxy propionic acid, fumaric acid, succinic acid and adipic acid), and amino acid (glutamic acid). The commercial production of some of these commodity bioproducts in the near future will have a far reaching effect in realizing our goal of sustainable conversion of these renewable resources and realizing the concept of biorefinery. Suitable for researchers, practitioners, graduate students and consultants in biochemical/ bioprocess engineering, industrial microbiology, bioprocess technology, metabolic engineering, environmental science and energy, the book offers: Exemplifies the application of metabolic engineering approaches for development of microbial cell factories Provides a unique perspective to the industry about the scientific problems and their possible solutions in making a bioprocess work for commercial production of commodity bioproducts Discusses the processing of renewable resources, such as plant biomass, for  mass production of commodity chemicals and liquid fuels to meet our ever- increasing demands Encourages sustainable green technologies for the utilization of renewable resources Offers timely solutions to help address the energy problem as non-renewable fossil oil will soon be unavailable

Table of Contents:
PREFACE xv CONTRIBUTORS xix PART I ENABLING PROCESSING TECHNOLOGIES 1 Biorefineries—Concepts for Sustainability 3 Michael Sauer, Matthias Steiger, Diethard Mattanovich, and Hans Marx 1.1 Introduction 4 1.2 Three Levels for Biomass Use 5 1.3 The Sustainable Removal of Biomass from the Field is Crucial for a Successful Biorefinery 7 1.4 Making Order: Classification of Biorefineries 8 1.5 Quantities of Sustainably Available Biomass 10 1.6 Quantification of Sustainability 11 1.7 Starch- and Sugar-Based Biorefinery 12 1.7.1 Sugar Crop Raffination 14 1.7.2 Starch Crop Raffination 14 1.8 Oilseed Crops 14 1.9 Lignocellulosic Feedstock 16 1.9.1 Biochemical Biorefinery (Fractionation Biorefinery) 16 1.9.2 Syngas Biorefinery (Gasification Biorefinery) 18 1.10 Green Biorefinery 19 1.11 Microalgae 20 1.12 Future Prospects—Aiming for Higher Value from Biomass 21 References 24 2 Biomass Logistics 29 Kevin L. Kenney, J. Richard Hess, Nathan A. Stevens, William A. Smith, Ian J. Bonner, and David J. Muth 2.1 Introduction 30 2.2 Method of Assessing Uncertainty, Sensitivity, and Influence of Feedstock Logistic System Parameters 31 2.2.1 Analysis Step 1—Defining the Model System 31 2.2.2 Analysis Step 2—Defining Input Parameter Probability Distributions 31 2.2.3 Analysis Step 3—Perform Deterministic Computations 32 2.2.4 Analysis Step 4—Deciphering the Results 34 2.3 Understanding Uncertainty in the Context of Feedstock Logistics 36 2.3.1 Increasing Biomass Collection Efficiency by Responding to In-Field Variability 36 2.3.2 Minimizing Storage Losses by Addressing Moisture Variability 38 2.4 Future Prospects 40 2.5 Financial Disclosure/Acknowledgments 40 References 41 3 Pretreatment of Lignocellulosic Materials 43 Karthik Rajendran and Mohammad J. Taherzadeh 3.1 Introduction 44 3.2 Complexity of Lignocelluloses 45 3.2.1 Anatomy of Lignocellulosic Biomass 45 3.2.2 Proteins Present in the Plant Cell Wall 46 3.2.3 Presence of Lignin in the Cell Wall of Plants 47 3.2.4 Polymeric Interaction in the Plant Cell Wall 48 3.2.5 Lignocellulosic Biomass Recalcitrance 49 3.3 Challenges in Pretreatment of Lignocelluloses 52 3.4 Pretreatment Methods and Mechanisms 53 3.4.1 Physical Pretreatment Methods 53 3.4.2 Chemical and Physicochemical Methods 56 3.4.3 Biological Methods 61 3.5 Economic Outlook 64 3.6 Future Prospects 67 References 68 4 Enzymatic Hydrolysis of Lignocellulosic Biomass 77 Jonathan J. Stickel, Roman Brunecky, Richard T. Elander, and James D. McMillan 4.1 Introduction 78 4.2 Cellulase, Hemicellulase, and Accessory Enzyme Systems and Their Synergistic Action on Lignocellulosic Biomass 79 4.2.1 Biomass Recalcitrance 79 4.2.2 Cellulases 80 4.2.3 Hemicellulases 81 4.2.4 Accessory Enzymes 81 4.2.5 Synergy with Xylan Removal and Cellulases 82 4.3 Enzymatic Hydrolysis at High Concentrations of Biomass Solids 83 4.3.1 Conversion Yield Calculations 84 4.3.2 Product Inhibition of Enzymes 85 4.3.3 Slurry Transport and Mixing 86 4.3.4 Heat and Mass Transport 87 4.4 Mechanistic Process Modeling and Simulation 88 4.5 Considerations for Process Integration and Economic Viability 91 4.5.1 Feedstock 91 4.5.2 Pretreatment 92 4.5.3 Downstream Conversion 94 4.6 Economic Outlook 95 4.7 Future Prospects 96 Acknowledgments 97 References 97 5 Production of Cellulolytic Enzymes 105 Ranjita Biswas, Abhishek Persad, and Virendra S. Bisaria 5.1 Introduction 106 5.2 Hydrolytic Enzymes for Digestion of Lignocelluloses 107 5.2.1 Cellulases 107 5.2.2 Xylanases 108 5.3 Desirable Attributes of Cellulase for Hydrolysis of Cellulose 109 5.4 Strategies Used for Enhanced Enzyme Production 110 5.4.1 Genetic Methods 110 5.4.2 Process Methods 114 5.5 Economic Outlook 123 5.6 Future Prospects 123 References 124 6 Bioprocessing Technologies 133 Gopal Chotani, Caroline Peres, Alexandra Schuler, and Peyman Moslemy 6.1 Introduction 134 6.2 Cell Factory Platform 136 6.2.1 Properties of a Biocatalyst 137 6.2.2 Recent Trends in Cell Factory Construction for Bioprocessing 140 6.3 Fermentation Process 142 6.4 Recovery Process 147 6.4.1 Active Dry Yeast 148 6.4.2 Unclarified Enzyme Product 149 6.4.3 Clarified Enzyme Product 150 6.4.4 BioisopreneTM 151 6.5 Formulation Process 153 6.5.1 Solid Forms 154 6.5.2 Slurry or Paste Forms 159 6.5.3 Liquid Forms 160 6.6 Final Product Blends 161 6.7 Economic Outlook and Future Prospects 162 Acknowledgment 163 Nomenclature 163 References 163 PART II SPECIFIC COMMODITY BIOPRODUCTS 7 Ethanol from Bacteria 169 Hideshi Yanase 7.1 Introduction 170 7.2 Heteroethanologenic Bacteria 172 7.2.1 Escherichia coli 173 7.2.2 Klebsiella oxytoca 177 7.2.3 Erwinia spp. and Enterobacter asburiae 178 7.2.4 Corynebacterium glutamicum 179 7.2.5 Thermophilic Bacteria 180 7.3 Homoethanologenic Bacteria 183 7.3.1 Zymomonas mobilis 184 7.3.2 Zymobacter palmae 189 7.4 Economic Outlook 191 7.5 Future Prospects 192 References 193 8 Ethanol Production from Yeasts 201 Tomohisa Hasunuma, Ryosuke Yamada, and Akihiko Kondo 8.1 Introduction 202 8.2 Ethanol Production from Starchy Biomass 205 8.2.1 Starch Utilization Process 205 8.2.2 Yeast Cell–Surface Engineering System for Biomass Utilization 205 8.2.3 Ethanol Production from Starchy Biomass Using Amylase-Expressing Yeast 206 8.3 Ethanol Production from Lignocellulosic Biomass 208 8.3.1 Lignocellulose Utilization Process 208 8.3.2 Fermentation of Cellulosic Materials 209 8.3.3 Fermentation of Hemicellulosic Materials 215 8.3.4 Ethanol Production in the Presence of Fermentation Inhibitors 217 8.4 Economic Outlook 218 8.5 Future Prospects 220 References 220 9 Fermentative Biobutanol Production: An Old Topic with Remarkable Recent Advances 227 Yi Wang, Holger Janssen and Hans P. Blaschek 9.1 Introduction 228 9.2 Butanol as a Fuel and Chemical Feedstock 229 9.3 History of ABE Fermentation 230 9.4 Physiology of Clostridial ABE Fermentation 232 9.4.1 The Clostridial Cell Cycle 232 9.4.2 Physiology and Enzymes of the Central Metabolic Pathway 233 9.5 Abe Fermentation Processes, Butanol Toxicity, and Product Recovery 236 9.5.1 ABE Fermentation Processes 236 9.5.2 Butanol Toxicity and Butanol-Tolerant Strains 237 9.5.3 Fermentation Products Recovery 238 9.6 Metabolic Engineering and “Omics”—Analyses of Solventogenic Clostridia 239 9.6.1 Development and Application of Metabolic Engineering Techniques 239 9.6.2 Butanol Production by Engineered Microbes 242 9.6.3 Global Insights into Solventogenic Metabolism Based on “Transcriptomics” and “Proteomics” 245 9.7 Economic Outlook 246 9.8 Current Status and Future Prospects 247 References 251 10 Bio-based Butanediols Production: The Contributions of Catalysis, Metabolic Engineering, and Synthetic Biology 261 Xiao-Jun Ji and He Huang 10.1 Introduction 262 10.2 Bio-Based 2,3-Butanediol 264 10.2.1 Via Catalytic Hydrogenolysis 264 10.2.2 Via Sugar Fermentation 265 10.3 Bio-Based 1,4-Butanediol 276 10.3.1 Via Catalytic Hydrogenation 276 10.3.2 Via Sugar Fermentation 277 10.4 Economic Outlook 279 10.5 Future Prospects 280 Acknowledgments 280 References 280 11 1,3-Propanediol 289 Yaqin Sun, Chengwei Ma, Hongxin Fu, Ying Mu, and Zhilong Xiu 11.1 Introduction 290 11.2 Bioconversion of Glucose into 1,3-Propanediol 291 11.3 Bioconversion of Glycerol into 1,3-Propanediol 292 11.3.1 Strains 292 11.3.2 Fermentation 293 11.3.3 Bioprocess Optimization and Control 301 11.4 Metabolic Engineering 302 11.4.1 Stoichiometric Analysis/MFA 302 11.4.2 Pathway Engineering 304 11.5 Down-Processing of 1,3-Propanediol 308 11.6 Integrated Processes 311 11.6.1 Biodiesel and 1,3-Propanediol 311 11.6.2 Glycerol and 1,3-Propanediol 313 11.6.3 1,3-Propanediol and Biogas 314 11.7 Economic Outlook 314 11.8 Future Prospects 315 Acknowledgments 316 A List of Abbreviations 316 References 317 12 Isobutanol 327 Bernhard J. Eikmanns and Bastian Blombach 12.1 Introduction 328 12.2 The Access Code for the Microbial Production of Branched-Chain Alcohols: 2-Ketoacid Decarboxylase and an Alcohol Dehydrogenase 329 12.3 Metabolic Engineering Strategies for Directed Production of Isobutanol 331 12.3.1 Isobutanol Production with Escherichia coli 331 12.3.2 Isobutanol Production with Corynebacterium glutamicum 335 12.3.3 Isobutanol Production with Bacillus subtilis 337 12.3.4 Isobutanol Production with Clostridium cellulolyticum 339 12.3.5 Isobutanol Production with Ralstonia eutropha 339 12.3.6 Isobutanol Production with Synechococcus elongatus 340 12.3.7 Isobutanol Production with Saccharomyces cerevisiae 341 12.4 Overcoming Isobutanol Cytotoxicity 341 12.5 Process Development for the Production of Isobutanol 343 12.6 Economic Outlook 345 12.7 Future Prospects 346 Abbreviations 347 Nomenclature 347 References 349 13 Lactic Acid 353 Kenji Okano, Tsutomu Tanaka, and Akihiko Kondo 13.1 History of Lactic Acid 354 13.2 Applications of Lactic Acid 354 13.3 Poly Lactic Acid 354 13.4 Conventional Lactic Acid Production 356 13.5 Lactic Acid Production From Renewable Resources 357 13.5.1 Lactic Acid Bacteria 359 13.5.2 Escherichia coli 364 13.5.3 Corynebacterium glutamicum 368 13.5.4 Yeasts 370 13.6 Economic Outlook 373 13.7 Future Prospects 374 Nomenclature 374 References 375 14 Microbial Production of 3-Hydroxypropionic Acid From Renewable Sources: A Green Approach as an Alternative to Conventional Chemistry 381 Vinod Kumar, Somasundar Ashok, and Sunghoon Park 14.1 Introduction 382 14.2 Natural Microbial Production of 3-HP 383 14.3 Production of 3-HP from Glucose by Recombinant Microorganisms 385 14.4 Production of 3-HP from Glycerol by Recombinant Microorganisms 388 14.4.1 Glycerol Metabolism for the Production of 3-HP and Cell Growth 389 14.4.2 Synthesis of 3-HP from Glycerol Through the CoA-Dependent Pathway 390 14.4.3 Synthesis of 3-HP From Glycerol Through the CoA-Independent Pathway 392 14.4.4 Coproduction of 3-HP and PDO From Glycerol 394 14.5 Major Challenges for Microbial Production of 3-HP 396 14.5.1 Toxicity and Tolerance 396 14.5.2 Redox Balance and By-products Formation 399 14.5.3 Vitamin B12 Supply 400 14.6 Economic Outlook 400 14.7 Future Prospects 401 Acknowledgment 401 List of Abbreviations 402 References 402 15 Fumaric Acid Biosynthesis and Accumulation 409 Israel Goldberg and J. Stefan Rokem 15.1 Introduction 410 15.1.1 Uses 410 15.1.2 Production 411 15.2 Microbial Synthesis of Fumaric Acid 412 15.2.1 Producer Organisms 412 15.2.2 Carbon Sources 414 15.2.3 Solid-State Fermentations 414 15.2.4 Submerged Fermentation Conditions 415 15.2.5 Transport of Fumaric Acid 416 15.2.6 Production Processes 416 15.3 A Plausible Biochemical Mechanism for Fumaric Acid Biosynthesis and Accumulation in Rhizopus 417 15.3.1 How Can the High Molar Yield of Fumaric Acid be Explained? 417 15.3.2 Where in the Cell is the Localization of the Reductive Reactions of the TCA Cycle? 418 15.3.3 What is the Role of Cytosolic Fumarase in Fumaric Acid Accumulation in Rhizopus Strain? 419 15.4 Toward Engineering Rhizopus for Fumaric Acid Production 422 15.5 Economic Outlook 424 15.6 Future Perspectives 427 15.6.1 Biorefinery 427 15.6.2 Platform Microorganisms 427 Acknowledgment 429 References 430 16 Succinic Acid 435 Boris Litsanov, Melanie Brocker, Marco Oldiges, and Michael Bott 16.1 Succinate as an Important Platform Chemical for a Sustainable Bio-Based Chemistry 436 16.2 Microorganisms for Bio-Succinate Production—Physiology, Metabolic Routes, and Strain Development 437 16.2.1 Anaerobiospirillum succiniciproducens 443 16.2.2 Family Pasteurellaceae 444 16.2.3 Escherichia coli 448 16.2.4 Corynebacterium glutamicum 451 16.2.5 Yeast-Based Producers 454 16.3 Neutral Versus Acidic Conditions for Product Formation 455 16.4 Downstream Processing 456 16.5 Companies Involved in Bio-Succinic Acid Manufacturing 458 16.5.1 Bioamber Inc. 459 16.5.2 Myriant Technologies LLC 459 16.5.3 Reverdia 462 16.5.4 Succinity GmbH 462 16.6 Future Prospects and Economic Outlook 462 References 463 17 Glutamic Acid 473 Takashi Hirasawa and Hiroshi Shimizu 17.1 Introduction 474 17.2 Glutamic Acid Production by Corynebacterium Glutamicum 475 17.2.1 Glutamic Acid Production by Corynebacterium Glutamicum and Its Molecular Mechanism 475 17.2.2 Metabolic Engineering of Glutamic Acid Production by Corynebacterium Glutamicum 478 17.3 Glutamic Acid as a Building Block 481 17.3.1 Production of Chemicals from Glutamic Acid Using Microorganisms 481 17.3.2 Production of Other Chemicals from Glutamic Acid 487 17.4 Economic Outlook 487 17.5 Future Prospects 489 List of Abbreviations 489 References 489 18 Recent Advances for Microbial Production of Xylitol 497 Yong-Cheol Park, Sun-Ki Kim, and Jin-Ho Seo 18.1 Introduction 498 18.2 General Principles for Biological Production of Xylitol 498 18.3 Microbial Production of Xylitol 501 18.3.1 Carbon Sources 501 18.3.2 Aeration 501 18.3.3 Optimization of Fermentation Strategies 503 18.4 Xylitol Production by Genetically Engineered Microorganisms 508 18.4.1 Construction of Xylitol-Producing Recombinant Saccharomyces cerevisiae 508 18.4.2 Cofactor Engineering for Xylitol Production in Recombinant Saccharomyces cerevisiae 510 18.4.3 Other Recombinant Microorganisms for Xylitol Production 512 18.5 Economic Outlook 514 18.6 Future Prospects 515 Acknowledgments 515 Nomenclature 515 References 516 19 First and Second Generation Production of Bio-Adipic Acid 519 Jozef Bernhard Johann Henry van Duuren and Christoph Wittmann 19.1 Introduction 520 19.2 Production of Bio-Adipic Acid 523 19.2.1 Natural Formation by Microorganisms 523 19.2.2 First Generation Bio-Adipic Acid 524 19.2.3 Second Generation Bio-Adipic Acid 528 19.3 Ecological Footprint of Bio-Adipic Acid 530 19.4 Economic Outlook 535 19.5 Future Prospects 536 References 538 INDEX 541

About the Author :
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.