List of Contributors xi
1 Biochemical Aspects of Microbial Product Synthesis: a Relook 1
G. Gallastegui, A. Larranaga, Antonio Avalos Ramirez, and Thi Than Ha Pham
1.1 Introduction 1
1.2 History of Industrial Production of Microbial Products 2
1.2.1 Advances of Biochemical Engineering and Their Effects on Global Market of Microbial Products 3
1.2.2 Importance of Microbial Sensing in Product Formation 6
1.3 Conclusion 7
Acknowledgments 8
References 8
2 Cellular Events of Microbial Production: Important Findings So Far 11
Devangana Bhuyan and Ratul Kumar Das
2.1 Introduction 11
2.2 Microbial Metabolism and Evolution of Metabolic Pathways 12
2.3 Microbial Fermentation 12
2.4 The Microbial Cellular Events 15
2.5 Cell Signalling in Microorganisms 19
2.6 Microbial Performance Under Stress Conditions 21
Acknowledgment 24
References 24
3 Microbial Metabolism in a Refined Carbon Source: Generalities 27
Vinayak Laxman Pachapur, Preetika Rajeev Kuknur, Satinder Kaur Brar, and Rosa Galvez-Cloutier
3.1 Introduction 27
3.2 Microbial Metabolism in Presence of Pure and Crude Substrate 29
3.3 Microbial Metabolism in Presence of Pure and Mixed Cultures 31
3.4 Microbial Metabolism in the Presence of Co-Substrate 33
3.5 Microbial Metabolism in the Presence of Input Parameters 35
3.6 Microbial Metabolism in the Presence of Varying Fermentation Conditions 37
3.7 Pros and Cons of Refined Substrate for Metabolic Metabolisms 38
3.8 Conclusions
39 Acknowledgment 40
References 40
4 Non-refined Carbon Sources and Microbial Performance 43
Guneet Kaur
4.1 Introduction 43
4.2 Non-refined Carbon Sources: a Brief Account 43
4.3 Microbial Assimilation of Non-Refined Carbon Sources 45
4.4 Microbial Sensing to Non-Refined Carbon Sources 48
4.4.1 Microbial Metabolism and Regulatory Circuits 48
4.4.2 CCR Regulation of Carbon Uptake and Metabolism 51
4.5 Guiding Product Outcomes via Rewiring of Cellular Regulatory Circuit 53
4.5.1 Cellular Engineering in E. Coli for Bioprocessing of Non-Refined Carbon Sources 54
4.5.2 Rewiring S. cerevisiae for Accumulation and Conversion of Non-refined Carbon Sources 55
4.6 Conclusions 56
References 57
5 Cellular versus Biochemical Control over Microbial Products 61
Carlos S. Osorio-Gonzalez, Krishnamoorthy Hegde, and Satinder Kaur Brar
5.1 Introduction 61
5.2 3 Hydroxy-propionic Acid 62
5.3 Fumaric Acid 64
5.4 Itaconic Acid 65
5.5 Glucaric Acid 67
5.6 Butanol 68
5.7 Malic Acid 69
5.8 Gluconic Acid 71
5.9 Aminovalaric Acid 71
5.10 Glutamic Acid 73
5.11 Cadaverine (1,5-diaminopentane) 74
5.12 Conclusion 76
Acknowledgment 76
References 76
6 Pre-Treatment of Alternative Carbon Source: How Does it Make Sense to Microorganism at Cellular Level? 89
Joseph Sebastian, Pratik Kumar, Krishnamoorthy Hegde, Satinder Kaur Brar, Mausam Verma, and Ratul Kumar Das
6.1 Introduction 89
6.2 Pre- Treated Carbon Source and Microbial Assimilation: Cellular and Biochemical Aspects 91
6.2.1 Alcohols 94
6.2.1.1 Bioethanol 94
6.2.1.2 Butanol and Acetone 96
6.2.2 Hydrogen 98
6.2.3 Methane/biogas 101
6.2.4 Organic Acids 103
6.3 Challenges of Inhibitory Hydrolysis Products and Strategic Solution 106
6.3.1 Inhibitory Products: Pretreatment Metabolites or By-products 106
6.3.1.1 Aliphatic Compounds 106
6.3.1.2 Aromatic Compounds 107
6.3.1.3 Furan Aldehydes 108
6.3.2 Strategies to Control Inhibitory Effects 109
6.3.2.1 Biological Detoxification Strategy for the Inhibitors 110
6.3.2.2 Understanding the Mechanism of Microorganism Adaptation for The Detoxification of Inhibitory Compounds 110
6.3.2.2.1 Homeostasis 110
6.3.2.2.2 Enzymatic Detoxification 111
6.3.2.3 Physical and Chemical Detoxification Strategy for Inhibitors 112
6.3.3 Correlation (Synergistic Effects) of Inhibitory Compounds and their Detoxification 118
6.4 Conclusion 126
Acknowledgments 127
References 127
7 Microbial Metabolic Pathways in the Production of Valued-added Products 137
Gilberto V. de Melo Pereira, Ana M. Finco, Luiz A. J. Letti, Susan Grace Karp, Maria G. B. Pagnoncelli, Juliana de Oliveira, Vanete Thomaz Soccol, Satinder Kaur Brar, and Carlos Ricardo Soccol
7.1 Introduction 137
7.2 Microbial Molecular Structure 138
7.3 Biomass Production 140
7.3.1 Single Cell Oil 140
7.3.2 Single Cell Protein 142
7.4 Enzymes 148
7.5 Biofuels 150
7.6 Alkaloids, Terpenoids, Polyketides and Flavonoids 153
7.7 Organic Acids 155
7.8 Rare Sugars 156
7.9 Conclusions 157
References 158
8 Communication for a Collective Response to Environmental Stress: Bacterial and Fungal Perspectives 169
Azadeh Kermanshahi Pour
8.1 Introduction 169
8.2 Quorum Sensing in Bacteria and the Related Phenotypes 172
8.3 Fermentation and Quorum Sensing in Bacteria 177
8.4 Quorum Sensing in Fungi and the Related Phenotypes 183
8.5 Fermentation and Quorum Sensing in Fungi 186
8.6 Quorum Sensing in Bacteria and Fungi: Similarities and Differences 188
Acknowledgment 189
References 189
9 Biochemical and Cellular Events in Controlling Microbial Performance: A Comparative Account 201
Shadab Ahmed, Shreyas Niphadkar, Somnath Nandi, Satya Eswari, Vishal Pandey, Aishwarya Shankapal, and Aishvarya Agrawal
9.1 Biochemical vs. Molecular Cues for Microbial Performances 201
9.1.1 Nutritional Parameters Optimization 201
9.1.2 Process Condition Optimization 202
9.1.3 Process Improvement by Using Batch and Fed-Batch via Process and Modeling 203
9.1.4 Metabolic Engineering for Improving Microbial Performance 203
9.1.4.1 Metabolic Flux Balance Analysis 203
9.1.4.1.1 Constraint Based Flux Balance Analysis 203
9.1.4.1.2 Defining Biological Objective to Optimize a Phenotype 204
9.1.4.1.3 Applications of Flux Analysis 204
9.1.5 Strain Improvement for Microbial Performance 205
9.1.5.1 Mutagenesis for Strain Improvement 205
9.1.5.1.1 Physical Mutagenesis 205
9.1.5.1.2 Chemical Mutagenesis 206
9.1.5.1.3 Biological Mutagenesis 206
9.2 Sequential Evidences of Biochemical and Molecular Controlling Over Microbial Performances 206
9.3 Biochemically Influenced Molecular Events and Vice Versa 208
9.4 Facts at the Interface of Biochemical and Molecular Controlling: Products vs Applied Parameters 208
9.4.1 Sulfur-Delivery into Biosynthetic Pathway 208
9.4.2 Synthetic Biochemistry Platform for Production of Glucose 212
9.4.3 Biochemical and Molecular Aspects of Metabolic Engineering Approaches 212
9.4.3.1 Engineering Regulatory Network 212
9.4.3.2 Heterologous Expression of Entire Gene Cluster 213
9.4.3.3 Rerouting Metabolic Pathway 213
9.4.3.4 Integration of Metabolic Engineering and Process Engineering 213
9.5 Conclusions 214
References 214
10 Qualitative vs. Quantitative Control Over Microbial Products 223
Rachna Goswami, Vijay Kumar Mishra, and Radhika Pilli
10.1 Introduction 223
10.2 Qualitative vs. Quantitative Control Over Microbial Products/Fungal Products 224
10.2.1 Qualitative Control and Fungal Product 225
10.2.1.1 Diffusion Techniques 226
10.2.1.2 Thin Layer Chromatography (TLC) 229
10.2.1.3 Chromatography-bioautography for Screening of Antimicrobial Activity 231
10.2.1.4 High-performance Liquid Chromatography (HPLC) 232
10.2.2 Quantitative Control of Fungal Products 232
10.2.3 Speeding Up Fungal Product 234
10.3 Fungal Morphology and Product Spectrum: a Representative Theme 237
10.4 Effectiveness of Qualitative Domain for Different Microorganisms 241
10.5 Emphasizing the Need: Qualitative and Quantitative Importance 245
10.6 Conclusions 246
References 247
11 Microbes and Their Products as Sensors in Industrially Important Fermentations 253
Ritu Raval and Keyur Raval
11.1 Introduction 253
11.2 Sensors 254
11.3 Transducers in Conjunction With Microbe Sensors 254
11.3.1 Dissolved Oxygen (DO) Electrode 254
11.3.2 Electron Transfer Measuring Systems 255
11.4 Metabolite Measuring Systems 256
11.5 Other Measuring Systems 257
11.5.1 Bioluminescence Biosensor 257
11.6 Applications of Microbe Sensors in Some Commercially Important Products 258
11.6.1 Red Wine 260
11.6.2 Fermentation of Cereal Products 260
11.6.3 Mevalonate Production 261
11.6.4 Bioaerosols 261
11.6.5 Aptamers 262
11.7 Conclusions 263
References 263
12 Practical Aspects and Case Studies of Industrial Scale Fermentation 267
Sara Magdouli, Thana Saffar, Tayssir Guedri, Rouissi Tarek, Satinder Kaur Brar, and Jean François Blais
12.1 Introduction 267
12.2 Scale Up Challenges 269
12.2.1 Agitation 269
12.2.2 Mass Transfer of Oxygen (Mass Transfer, Morphology, and Rheology) 270
12.2.3 "Shear Damage" 271
12.2.4 Measurements for Control 273
12.2.5 Other Aspects 273
12.3 Microbial Tolerance 274
12.4 Phage Invasion 274
12.5 Process Failures 277
12.6 Potent Inhibitors (e.g. Substrate Inhibition) 278
12.7 Case Studies: Biofuels (Biodiesel, Ethanol) Enzymes (Novozymes), Antibiotics, Platform Chemicals 281
12.7.1 Biofuels (Biodiesel, Ethanol) 281
12.7.2 Enzymes (Novozymes) 283
12.7.3 Antibiotics 286
12.7.4 Platform Chemicals 288
12.8 Conclusions 289
Acknowledgments 290
References 290
13 Future Market and Policy Initiatives of New High Value Products 299
Ha Thi Thanh Pham, Maria Puig-Gamero, Luz Sanchez-Silva, Paula Sanchez, Jose Luis Valverde, Michele Heitz, and Antonio Avalos Ramirez
13.1 Introduction 299
13.2 Market Analysis, Market Trends and Statistics 299
13.2.1 Biofuels 299
13.2.2 Bio-surfactants 302
13.2.3 Enzymes 305
13.3 Public Mobilization Initiatives and Government Policies 306
13.3.1 Public Mobilization Initiatives 306
13.3.2 Government Policies 307
13.3.3 Regional Policy Development for Growing Bio-based Production 307
13.4 Regulations and Conformity - Case of Biofuels 307
13.5 Global Marketing and Competitiveness in Biofuel Sector 309
References 309
Index 311
