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
2.1 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 Bioisoprene .................................... 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 В12 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
15.3.7 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
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