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Bioprocessing of Renewable Resources to Commodity Bioproducts
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BIOPROCESSING OF
RENEWABLE RESOURCES
TO COMMODITY
BIOPRODUCTS
BIOPROCESSING OF
RENEWABLE RESOURCES
TO COMMODITY
BIOPRODUCTS
Edited by
Virendra S. Bisaria
Akihiko Kondo
About the Cover: The pyramid represents successive and increasingly selective processing stages in
bioconversion of plant biomass to industrial chemicals. The chemicals in white bubbles are the industrial
commodity bioproducts pertaining to the realm of “white biotechnology”.
Cover illustration/design by Ruchi Uppal.
Rights of Cover Design are owned by Prof. Virendra S. Bisaria.
Copyright © 2014 by John Wiley & Sons, Inc. All rights reserved.
Published by John Wiley & Sons, Inc., Hoboken, New Jersey.
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Library of Congress Cataloging-in-Publication Data:
Bioprocessing of renewable resources to commodity bioproducts / edited by Virendra S. Bisaria,
Akihiko Kondo.
pages cm
Includes bibliographical references and index.
ISBN 978-1-118-17583-5 (hardback)
1. Microbial biotechnology. 2. Biomass energy. I. Bisaria, Virendra S., editor of compilation.
II. Kondo, Akihiko, 1959- editor of compilation.
TP248.27.M53B5626 2014
662′
.88–dc23
2013046035
Printed in the United States of America.
10 9 8 7 6 5 4 3 2 1
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
v
vi CONTENTS
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
CONTENTS vii
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
viii CONTENTS
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
CONTENTS ix
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
x CONTENTS
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
CONTENTS xi
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
xii CONTENTS
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
CONTENTS xiii
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
xiv CONTENTS
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
PREFACE
For the development of a sustainable, industrial society to meet our demands of
energy and materials, it is being increasingly realized that we will have to shift from
our dependence on petroleum to the use of renewable resources, such as starch- and
cellulose-based plant materials. Historically till recently, petroleum-based resources
were mainly targeted for research and development, and subsequent commercialization of the products derived therefrom. However, their rising costs and the anticipated
threat to the earth’s environment are providing the required incentive to find sustainable alternative resources. Biorefineries, based on renewable resources, shall enable
the production of biofuels as well as commodity chemicals (those produced in excess
of about 1 million tons per year). These processes which are based on carbohydrates (such as starch and cellulose) are also favorable from a chemical point of view
because the functional groups that are introduced by costly oxidative process steps
into naphta are already present in them. The commodity bioproducts can be produced
by microbial processes. Most of them are natural products of microorganisms or can
be produced by suitable pathway engineering of industrial organisms. As these bioproducts contain functional groups, they are extremely useful as starting materials for
the chemical industry for synthesis of a wide variety of products such as polymers,
surfactants, lubricants, and resins.
To avoid competition with starchy raw materials, which are largely used as food, as
well as to realize the vision of a successful biorefinery, the renewable resource present
in the form of abundant lignocellulosic biomass needs to be efficiently converted to its
constituent monomers, comprising mainly of hexose (such as glucose, mannose, and
galactose) and pentose sugars (such as xylose and arabinose). Accordingly, the Part I
of the book deals with those enabling technologies that are crucial for the pretreatment
(Chapter 3) and hydrolysis of biomass to give sugars in high yield (Chapter 4) by
cellulolytic enzymes, primarily cellulase and xylanase (Chapter 5). This first part also
covers the general aspect and the issues involved in the sustainability of a biorefinery
(Chapter 1) and biomass feedstock logistics and the design of biomass feedstock
supply systems (Chapter 2). Chapter 6 describes various bioprocessing technologies
that in one form or the other will be required to be implemented for the development
of biorefineries.
The Part II of the book contains state-of-the-art articles on a few chosen commodity bioproducts. These bioproducts represent most of those identified by the US
Department of Energy for intensive investigation for their production from renewable
resources. While covering these bioproducts, major emphasis has been given to the
xv
xvi PREFACE
discipline of metabolic engineering for the development of suitable microbial biocatalysts/cell factories which shall enable their production from renewable resources.
Ethanol which remains the most sought-after chemical and biofuel is covered in two
chapters. While Chapter 7 describes the potential of recombinant bacteria for ethanol
production, Chapter 8 is concerned mainly with strategies being developed to expand
the genetic potential of the yeasts, already employed by the industry. Butanol, an
excellent transportation fuel and a valuable chemical feedstock, is covered in Chapter
9 with respect to the advances that have taken place in recent years in the well-known
ABE fermentation process for its production from renewable feedstock. Chapters 10
and 11 describe the recent advances being made for bio-based production of butanediols and propanediols, used extensively as solvent and for production of different
types of chemicals, polymers, and so on. The feasibility of producing isobutanol,
another higher alcohol besides butanol, possessing chemical features close to that
of gasoline, through implementation of the Ehrlich pathway into several potential
host microorganisms has been dealt with in Chapter 12. Lactic acid (LA), widely
used in the food, pharmaceutical, and polymers industries, is already produced by
microbial fermentations; Chapter 13, therefore, concentrates on production of LA and
LA-based polymers from various genetically modified microorganisms from starchy
and cellulosic materials. Chapter 14 describes the recent progress in biological production of 3-hydroxy propionic acid, used for the production of a wide range of
commercially important chemicals such as acrylic acid, using different microorganisms and renewable substrates. Chapter 15 reviews the recent research and provides
a critical analysis of future perspectives to develop an economically competitive biobased process for producing fumaric acid, which is widely used in the food industry.
Succinic acid with many applications including the production of important bulk
chemicals, namely 1,4-butanediol (BDO), γ-butyrolactone (GBL), and tetrahydrofuran (THF), is covered in Chapter 16 with respect to its production from various
substrates from natural and genetically modified organisms. Glutamic acid is the
major amino acid produced by microbial fermentation on an industrial scale. Chapter
17 reviews the molecular mechanisms and metabolic engineering of glutamic acid
production by Corynebacterium glutamicum and potential use of glutamic acid as a
building block for producing several other chemicals. Xylitol, a natural sugar alcohol
widely used as a sugar substitute in foods, toothpastes, and mouthwashes, is covered
in Chapter 18 with respect to the application of recent approaches of genetic engineering, metabolic engineering, and cofactor engineering for its overproduction. New
approaches for production of adipic acid, mainly used as an intermediate reactant for
the production of nylon-6,6, are highlighted in Chapter 19 from several new feedstocks including lignin-rich streams.The commercial production of some of these
commodity bioproducts in the near future will have a far reaching effect in catalyzing
the realization of our goal of a sustainable biorefinery.
As research and development in this area has not yet achieved its full potential,
the field of bioprocessing of renewable resources into commodity bioproducts will
continue to expand to attain its commercial goal. Additionally, new bioproducts
and fine chemicals will be added to the existing list of commodity bioproducts, as
our capacity to produce sugars from cellulosic residues efficiently and economically