Microbial Sensing in 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 xi1 Biochemical Aspects of Microbial Product Synthesis: a Relook 1G. Gallastegui, A. Larrañaga, Antonio Avalos Ramirez, and Thi Than Ha Pham1.1 Introduction 11.2 History of Industrial Production of Microbial Products 21.2.1 Advances of Biochemical Engineering and Their Effects on Global Market of Microbial Products 31.2.2 Importance of Microbial Sensing in Product Formation 61.3 Conclusion 7Acknowledgments 8References 82 Cellular Events of Microbial Production: Important Findings So Far 11Devangana Bhuyan and Ratul Kumar Das2.1 Introduction 112.2 Microbial Metabolism and Evolution of Metabolic Pathways 122.3 Microbial Fermentation 122.4 The Microbial Cellular Events 152.5 Cell Signalling in Microorganisms 192.6 Microbial Performance Under Stress Conditions 21Acknowledgment 24References 243 Microbial Metabolism in a Refined Carbon Source: Generalities 27Vinayak Laxman Pachapur, Preetika Rajeev Kuknur, Satinder Kaur Brar, and Rosa Galvez-Cloutier3.1 Introduction 273.2 Microbial Metabolism in Presence of Pure and Crude Substrate 293.3 Microbial Metabolism in Presence of Pure and Mixed Cultures 313.4 Microbial Metabolism in the Presence of Co‐Substrate 333.5 Microbial Metabolism in the Presence of Input Parameters 353.6 Microbial Metabolism in the Presence of Varying Fermentation Conditions 373.7 Pros and Cons of Refined Substrate for Metabolic Metabolisms 383.8 Conclusions39 Acknowledgment 40References 404 Non‐refined Carbon Sources and Microbial Performance 43Guneet Kaur4.1 Introduction 434.2 Non‐refined Carbon Sources: a Brief Account 434.3 Microbial Assimilation of Non‐Refined Carbon Sources 454.4 Microbial Sensing to Non‐Refined Carbon Sources 484.4.1 Microbial Metabolism and Regulatory Circuits 484.4.2 CCR Regulation of Carbon Uptake and Metabolism 514.5 Guiding Product Outcomes via Rewiring of Cellular Regulatory Circuit 534.5.1 Cellular Engineering in E. Coli for Bioprocessing of Non‐Refined Carbon Sources 544.5.2 Rewiring S. cerevisiae for Accumulation and Conversion of Non‐refined Carbon Sources 554.6 Conclusions 56References 575 Cellular versus Biochemical Control over Microbial Products 61Carlos S. Osorio-González, Krishnamoorthy Hegde, and Satinder Kaur Brar5.1 Introduction 615.2 3 Hydroxy‐propionic Acid 625.3 Fumaric Acid 645.4 Itaconic Acid 655.5 Glucaric Acid 675.6 Butanol 685.7 Malic Acid 695.8 Gluconic Acid 715.9 Aminovalaric Acid 715.10 Glutamic Acid 735.11 Cadaverine (1,5‐diaminopentane) 745.12 Conclusion 76Acknowledgment 76References 766 Pre‐Treatment of Alternative Carbon Source: How Does it Make Sense to Microorganism at Cellular Level? 89Joseph Sebastian, Pratik Kumar, Krishnamoorthy Hegde, Satinder Kaur Brar, Mausam Verma, and Ratul Kumar Das6.1 Introduction 896.2 Pre‐ Treated Carbon Source and Microbial Assimilation: Cellular and Biochemical Aspects 916.2.1 Alcohols 946.2.1.1 Bioethanol 946.2.1.2 Butanol and Acetone 966.2.2 Hydrogen 986.2.3 Methane/biogas 1016.2.4 Organic Acids 1036.3 Challenges of Inhibitory Hydrolysis Products and Strategic Solution 1066.3.1 Inhibitory Products: Pretreatment Metabolites or By‐products 1066.3.1.1 Aliphatic Compounds 1066.3.1.2 Aromatic Compounds 1076.3.1.3 Furan Aldehydes 1086.3.2 Strategies to Control Inhibitory Effects 1096.3.2.1 Biological Detoxification Strategy for the Inhibitors 1106.3.2.2 Understanding the Mechanism of Microorganism Adaptation for The Detoxification of Inhibitory Compounds 1106.3.2.2.1 Homeostasis 1106.3.2.2.2 Enzymatic Detoxification 1116.3.2.3 Physical and Chemical Detoxification Strategy for Inhibitors 1126.3.3 Correlation (Synergistic Effects) of Inhibitory Compounds and their Detoxification 1186.4 Conclusion 126Acknowledgments 127References 1277 Microbial Metabolic Pathways in the Production of Valued‐added Products 137Gilberto 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 Soccol7.1 Introduction 1377.2 Microbial Molecular Structure 1387.3 Biomass Production 1407.3.1 Single Cell Oil 1407.3.2 Single Cell Protein 1427.4 Enzymes 1487.5 Biofuels 1507.6 Alkaloids, Terpenoids, Polyketides and Flavonoids 1537.7 Organic Acids 1557.8 Rare Sugars 1567.9 Conclusions 157References 1588 Communication for a Collective Response to Environmental Stress: Bacterial and Fungal Perspectives 169Azadeh Kermanshahi Pour8.1 Introduction 1698.2 Quorum Sensing in Bacteria and the Related Phenotypes 1728.3 Fermentation and Quorum Sensing in Bacteria 1778.4 Quorum Sensing in Fungi and the Related Phenotypes 1838.5 Fermentation and Quorum Sensing in Fungi 1868.6 Quorum Sensing in Bacteria and Fungi: Similarities and Differences 188Acknowledgment 189References 1899 Biochemical and Cellular Events in Controlling Microbial Performance: A Comparative Account 201Shadab Ahmed, Shreyas Niphadkar, Somnath Nandi, Satya Eswari, Vishal Pandey, Aishwarya Shankapal, and Aishvarya Agrawal9.1 Biochemical vs. Molecular Cues for Microbial Performances 2019.1.1 Nutritional Parameters Optimization 2019.1.2 Process Condition Optimization 2029.1.3 Process Improvement by Using Batch and Fed‐Batch via Process and Modeling 2039.1.4 Metabolic Engineering for Improving Microbial Performance 2039.1.4.1 Metabolic Flux Balance Analysis 2039.1.4.1.1 Constraint Based Flux Balance Analysis 2039.1.4.1.2 Defining Biological Objective to Optimize a Phenotype 2049.1.4.1.3 Applications of Flux Analysis 2049.1.5 Strain Improvement for Microbial Performance 2059.1.5.1 Mutagenesis for Strain Improvement 2059.1.5.1.1 Physical Mutagenesis 2059.1.5.1.2 Chemical Mutagenesis 2069.1.5.1.3 Biological Mutagenesis 2069.2 Sequential Evidences of Biochemical and Molecular Controlling Over Microbial Performances 2069.3 Biochemically Influenced Molecular Events and Vice Versa 2089.4 Facts at the Interface of Biochemical and Molecular Controlling: Products vs Applied Parameters 2089.4.1 Sulfur‐Delivery into Biosynthetic Pathway 2089.4.2 Synthetic Biochemistry Platform for Production of Glucose 2129.4.3 Biochemical and Molecular Aspects of Metabolic Engineering Approaches 2129.4.3.1 Engineering Regulatory Network 2129.4.3.2 Heterologous Expression of Entire Gene Cluster 2139.4.3.3 Rerouting Metabolic Pathway 2139.4.3.4 Integration of Metabolic Engineering and Process Engineering 2139.5 Conclusions 214References 21410 Qualitative vs. Quantitative Control Over Microbial Products 223Rachna Goswami, Vijay Kumar Mishra, and Radhika Pilli10.1 Introduction 22310.2 Qualitative vs. Quantitative Control Over Microbial Products/Fungal Products 22410.2.1 Qualitative Control and Fungal Product 22510.2.1.1 Diffusion Techniques 22610.2.1.2 Thin Layer Chromatography (TLC) 22910.2.1.3 Chromatography‐bioautography for Screening of Antimicrobial Activity 23110.2.1.4 High‐performance Liquid Chromatography (HPLC) 23210.2.2 Quantitative Control of Fungal Products 23210.2.3 Speeding Up Fungal Product 23410.3 Fungal Morphology and Product Spectrum: a Representative Theme 23710.4 Effectiveness of Qualitative Domain for Different Microorganisms 24110.5 Emphasizing the Need: Qualitative and Quantitative Importance 24510.6 Conclusions 246References 24711 Microbes and Their Products as Sensors in Industrially Important Fermentations 253Ritu Raval and Keyur Raval11.1 Introduction 25311.2 Sensors 25411.3 Transducers in Conjunction With Microbe Sensors 25411.3.1 Dissolved Oxygen (DO) Electrode 25411.3.2 Electron Transfer Measuring Systems 25511.4 Metabolite Measuring Systems 25611.5 Other Measuring Systems 25711.5.1 Bioluminescence Biosensor 25711.6 Applications of Microbe Sensors in Some Commercially Important Products 25811.6.1 Red Wine 26011.6.2 Fermentation of Cereal Products 26011.6.3 Mevalonate Production 26111.6.4 Bioaerosols 26111.6.5 Aptamers 26211.7 Conclusions 263References 26312 Practical Aspects and Case Studies of Industrial Scale Fermentation 267Sara Magdouli, Thana Saffar, Tayssir Guedri, Rouissi Tarek, Satinder Kaur Brar, and Jean François Blais12.1 Introduction 26712.2 Scale Up Challenges 26912.2.1 Agitation 26912.2.2 Mass Transfer of Oxygen (Mass Transfer, Morphology, and Rheology) 27012.2.3 “Shear Damage” 27112.2.4 Measurements for Control 27312.2.5 Other Aspects 27312.3 Microbial Tolerance 27412.4 Phage Invasion 27412.5 Process Failures 27712.6 Potent Inhibitors (e.g. Substrate Inhibition) 27812.7 Case Studies: Biofuels (Biodiesel, Ethanol) Enzymes (Novozymes), Antibiotics, Platform Chemicals 28112.7.1 Biofuels (Biodiesel, Ethanol) 28112.7.2 Enzymes (Novozymes) 28312.7.3 Antibiotics 28612.7.4 Platform Chemicals 28812.8 Conclusions 289Acknowledgments 290References 29013 Future Market and Policy Initiatives of New High Value Products 299Ha Thi Thanh Pham, Maria Puig‐Gamero, Luz Sanchez‐Silva, Paula Sánchez, José Luis Valverde, Michele Heitz, and Antonio Avalos Ramirez13.1 Introduction 29913.2 Market Analysis, Market Trends and Statistics 29913.2.1 Biofuels 29913.2.2 Bio‐surfactants 30213.2.3 Enzymes 30513.3 Public Mobilization Initiatives and Government Policies 30613.3.1 Public Mobilization Initiatives 30613.3.2 Government Policies 30713.3.3 Regional Policy Development for Growing Bio‐based Production 30713.4 Regulations and Conformity – Case of Biofuels 30713.5 Global Marketing and Competitiveness in Biofuel Sector 309References 309Index 311