Microbial Sensing in Fermentation

A comprehensive review of the fundamental molecular mechanisms in fermentation and explores the microbiology of fermentation technology and industrial applications

Microbial Sensing in Fermentation presents the fundamental molecular mechanisms involved in the process of fermentation and explores the applied art of microbiology and fermentation technology. The text contains descriptions regarding the extraordinary sensing ability of microorganisms towards small physicochemical changes in their surroundings. The contributors — noted experts in the field — cover a wide range of topics such as microbial metabolism and production (fungi, bacteria, yeast etc); refined and non-refined carbon sources; bioprocessing; microbial synthesis, responses and performance; and biochemical, molecular and extra/intracellular controlling.

This resource contains a compilation of literature on biochemical and cellular level mechanisms for microbial controlled production and includes the most significant recent advances in industrial fermentation.

The text offers a balanced approach between theory and practical application, and helps readers gain a clear understanding of microbial physiological adaptation during fermentation and its cumulative effect on productivity. This important book:

• Presents the fundamental molecular mechanisms involved in microbial sensing in relation to fermentation technology

• Includes information on the significant recent advances in industrial fermentation
• Contains contributions from a panel of highly-respected experts in their respective fields
• Offers a resource that will be essential reading for scientists, professionals and researchers from academia and industry with an interest in the biochemistry and microbiology of fermentation technology

Written for researchers, graduate and undergraduate students from diverse backgrounds, such as biochemistry and applied microbiology, Microbial Sensing in Fermentation offers a review of the fundamental molecular mechanisms involved in the process of fermentation.

About the Editors

Satinder Kaur Brar: Institut national de la recherche scientifique, Centre ??? Eau Terre Environnement, Québec, Canada

Ratul Kumar Das: TERI-Deakin Nanobiotechnology Centre, Biotechnology and Management of Bioresources Division, The Energy and Resources Institute, Haryana, India

Saurabh Jyoti Sarma: Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh, India

List of Contributors xi

1 Biochemical Aspects of Microbial Product Synthesis: a Relook 1
G. Gallastegui, A. Larrañaga, 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-González, 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 Sánchez, José 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

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