Applied Microbiology (eBook)

Sanjai Saxena currently is an Associate Professor in Department of Biotechnology, Thapar University, Patiala, India. Concurrently Dr. Saxena is also Coordinator of Centre of Relevance and Excellence (CORE) in Agro & Industrial Biotechnology, established by TIFAC, Department of Science and Technology, Government of India jointly with the University. Dr. Saxena possess over 15 years of research and teaching experience in microbial secondary metabolites, microbial biochemistry, microbial diversity, biological control, mycology and drug discovery. His research work has resulted in significant extramural funding, over 35 refereed journal articles, 25 abstracts, 5 book chapters, 1 US and 2 Indian patents. Recognizing his work, Association of Advancement of Biodiversity Science, Karnataka has conferred upon him Eminent Microbiologist Award in the year 2014 and inducted him as a fellow in the society.

Preface 6
Acknowledgments 8
Contents 10
About the Author 16
1: Diversity of Industrially Relevant Microbes 17
1.1 Introduction 17
1.2 Realm of Microbial Existence 17
1.2.1 Diversity of Soil Microbes 18
1.2.1.1 Neutral Associations 18
1.2.1.2 Positive Associations 18
1.2.1.3 Negative Associations 19
1.2.2 Marine Microbial Diversity 19
Box 1.1: Marine Microorganism 20
Box 1.2: Facts About Marine Microbes 20
Box 1.3: Significant Achievements in Marine Microbiology 20
1.2.2.1 Symbiotic Interactions with Marine Invertebrates 21
1.2.3 Halophilic Environment 22
1.2.4 Plant: Microbe Interaction 22
1.2.5 Microbe–Microbe Interactions 24
1.2.6 Animal–Microbe Interactions 24
1.3 Summary 25
Selected Reading 25
2: Microbial Technology and Biotechnology 28
2.1 Introduction 28
2.2 Healthcare Industry and GMMOs 29
2.3 GMMOs in Agriculture 30
2.4 Role of GMMOs in Chemical Industry 30
2.5 GMMOs in Textile Industry 31
2.6 Environmental Applications of GMMOs 31
2.7 Food Industry and the Role of GMMOs 32
2.8 GMMOs for Bioethanol Production 32
2.9 Summary 33
Selected Reading 33
3: Fermentation Technology 34
3.1 Introduction 34
3.2 Batch Fermentation 34
3.3 Continuous Fermentation 37
3.4 Fed-Batch Fermentation 37
3.4.1 Fixed-Volume Fed-Batch 37
3.4.2 Variable-Volume Fed-Batch 38
3.5 Components in a Typical Bioreactor 38
3.6 Types of Submerged Bioreactors 40
3.6.1 Stirred Tank Fermenter (STF) 40
3.6.2 Airlift Fermenter (ALF) 41
3.6.3 Bubble Column Fermenter (BCF) 41
3.6.3.1 Fluidised Bed Fermenter (FBF) 41
3.6.3.2 Trickle Bed Fermenter (TBF) 41
3.7 Solid Substrate Fermentation 41
3.8 Role of Bioreactor in Solid Substrate Fermentation 43
3.9 Types of Solid Substrate Bioreactors 43
3.10 Media for Industrial Fermentations 45
3.11 Downstream Processing 47
3.12 Summary 49
Selected Reading 49
4: Agricultural Applications of Microbes 51
4.1 Introduction 51
4.2 Biofertilisers 51
4.2.1 Nitrogen-Fixing Microorganisms as Biofertilisers 51
4.2.1.1 Symbiotic Nitrogen-Fixing Microorganisms 52
4.2.1.2 Non-symbiotic/Associative Nitrogen-Fixing Microorganisms 53
4.2.2 Phosphate Solubilising Microorganisms as Biofertilisers 53
4.2.3 PGPB (Plant Growth Promoting Bacteria): Plant Growth Promoters 54
4.3 Biopesticides 55
4.3.1 Bio-weedicides 56
4.3.1.1 Classical Biological Control 56
4.3.1.2 Innundative or Bioherbicidal Approach 56
4.3.2 Bioinsecticides 57
4.3.3 Biofungicides 60
4.4 Precincts of Biological Control 60
4.5 Biorational Pesticides of Microbial Origin 62
4.5.1 Bacterial Secondary Metabolites as Agrochemicals 62
4.5.2 Agroactive Compounds from Actinomycetes 62
4.5.3 Fungal Secondary Metabolites as Agrochemical 63
4.5.3.1 Phytotoxins as Mycoherbicide 63
4.5.3.2 Toxins of Entomopathogenic Fungi 65
4.5.3.3 Fungal Secondary Metabolites as Biofungicides 66
4.6 Summary 66
Selected Reading 67
5: Environment and Microbes 69
5.1 Introduction 69
5.2 Microbial Bioremediation 69
5.2.1 In Situ Bioremediation by Microbes 69
5.2.2 Ex Situ Bioremediation by Microbes 70
5.3 Biodegradation of Xenobiotic Compounds 71
5.4 Bioremediation of Heavy Metals 72
5.5 Biomining 74
5.5.1 Extraction of Copper 75
5.5.2 Extraction of Uranium 75
5.5.3 Extraction of Gold 76
5.6 Microbially Enhanced Oil Recovery (MEOR) 76
5.7 Summary 77
Selected Reading 77
6: Microbes in the Food Industry 79
6.1 Introduction 79
6.2 Fermented Foods 79
6.2.1 Milk Products 79
6.2.2 Fermented Vegetables 81
6.2.3 Fermented Meat Preparations 81
6.2.4 Traditional Fermented Food 81
6.2.5 Bakery Products 81
6.3 Fermented Beverages 82
6.3.1 Wine 82
6.3.2 Beer 82
6.3.3 Whiskey 83
6.3.4 Kombucha 83
6.4 Summary 83
Selected Reading 83
7: Microbes in Production of Commodity Chemicals 84
7.1 Introduction 84
7.2 Commercial Production of Ethanol 84
7.3 Industrial Production of Acrylamide 86
7.4 Industrial Production of Citric Acid 88
7.4.1 Citric Acid Production by Surface Fermentation 89
7.4.2 Submerged Fermentation for Citric Acid Production 89
7.4.3 Solid–Substrate Fermentation for Citric Acid Production 90
7.4.4 Recovery of Citric Acid 91
7.5 Microbial Production of Adipic Acid 91
7.6 Microbial Production of 1, 2-Propanediol 92
7.7 Penicillin as a Commodity Chemical 92
7.7.1 Production of Penicillin 93
7.7.2 Recovery and Purification of Penicillin 93
7.8 Summary 93
Selected Reading 93
8: Microbes in Production of Fine Chemicals (Antibiotics, Drugs, Vitamins, and Amino Acids) 95
8.1 Introduction 95
8.2 Pharmaceutical Fine Chemicals 95
8.2.1 Antibiosis and Antibiotics 95
8.2.2 Discovery of Penicillin: Beginning of the Antibiotic Era 97
8.2.3 Antibiotics Discovered from Fungi 97
8.2.4 Actinomycetes in Antibiotic Discovery 101
8.2.5 Antibiotics Discovered from Bacteria 103
8.2.6 Microorganisms Producing Other Pharmaceutically Active Metabolites 105
8.2.6.1 Anti-hypercholesterolemic Agents from Microbes 106
8.2.6.2 Microbially Produced Anti-­diabetic Agents 107
8.2.6.3 Immunosuppressants Produced by Microorganisms 107
8.2.6.4 Anti-cancer/Anti-tumor Agents of Microbial Origin 108
8.2.6.5 Drugs for Alzheimer’s Dementia 108
8.2.7 Endophytic Microbes as Sources of Putative Phytochemicals 109
8.3 Engineering Microbes in the Production of Plant Products 112
8.3.1 Isoprenoid Biosynthesis Engineering 112
8.4 Microbial Synthesis of Vitamins 114
8.4.1 Vitamin E 114
8.4.2 Vitamin K 116
8.4.3 ?-Carotene (Provitamin A) 116
8.4.4 Vitamin B2 117
8.4.5 Vitamin B12 118
8.5 Production of Amino Acids 120
8.5.1 Ajinomoto Process of Fermentative Production of l-Glutamate 121
8.5.2 Fermentative Production of l?Lysine 122
8.6 Microbes in the Production of Dyes and Pigments 123
8.6.1 Microbial Pigments in the Textile Industry 123
8.6.2 Microbial Pigments in the Food Industry 124
8.7 Microbial Production of Flavors and Fragrances 125
8.8 Summary 127
Selected Reading 128
9: Microbial Enzymes and Their Industrial Applications 133
9.1 Introduction 133
9.1.1 Advantages of Microbial Enzymes 133
9.1.2 Modest Beginnings of Enzyme Technology 134
9.2 Microbial Enzymes: Diversity and Exploitation 135
9.3 Application of Microbial Enzymes: Broad Avenues 136
9.3.1 Therapeutic Agents 137
9.3.1.1 Food Disorder Therapy by Enzymes 137
9.3.1.2 Enzymes in Wound Healing 138
9.3.1.3 Antimicrobial Activity of Enzymes 139
9.3.1.4 Anti-cancer Potential 139
9.3.1.5 Thrombolytic Agents 141
9.3.1.6 Generalized Therapy 142
9.3.2 Diagnostics 142
9.4 Chemical Industry 142
9.4.1 Cell-Free Biocatalysis 143
9.4.2 Whole Cell Biocatalysis 144
9.4.3 Phytochemical Extraction with Microbial Enzymes 145
9.5 Food and Feed Industry 146
9.5.1 Acetolactate Decarboxylase 147
9.5.2 Amylases 147
9.5.3 ?-Galactosidase 147
9.5.4 Cellulases 147
9.5.5 Dextranases and Invertases 148
9.5.6 Keratinases 148
9.5.7 Lipases 149
9.5.8 Naringinases 150
9.5.9 Pectinases 150
9.5.10 Phytases 151
9.5.11 Tannases 151
9.5.12 Transglutaminase 151
9.6 Detergent 152
9.6.1 Proteases 152
9.6.2 Use of Microbial Lipase as Detergent Additive 153
9.6.3 Amylases as Detergent Additive 154
9.6.4 Other Enzymes Used in Detergent Formulations 155
9.7 Textile Industry 155
9.8 Leather Industry 157
9.9 Pulp and Paper Processing 159
9.10 Biofuels 161
9.11 Personal Care Products 162
9.12 Summary 163
Selected Reading 163
10: Strategies of Strain Improvement of Industrial Microbes 167
10.1 Introduction 167
10.2 Spontaneous Mutations 167
10.3 Classical Mutagenesis 168
10.4 Mutant Selection in Classical Mutagenesis 170
10.4.1 Morphological Mutants 172
10.4.2 Auxotrophic Mutants 172
10.4.3 Mutants Exhibiting Resistance to Antimetabolites 172
10.4.4 Enhanced Production of the End Product: Agar Zone Mutants 173
10.5 Recombination 174
10.6 Recombinant DNA Technology 175
10.7 Integrated Strain Improvement: Precision Engineering Technology 178
10.7.1 Production of High Lovastatin-Producing Strains Through Precision Engineering 179
10.8 Summary 180
Selected Reading 181
11: Vaccines and Their Production 184
11.1 Introduction 184
11.2 Traditional Vaccines 184
11.2.1 Live Attenuated Vaccines 184
11.2.2 Dead, Inactivated Vaccines 185
11.2.3 Toxoids 185
11.2.4 Pathogen-Derived Antigens 185
11.3 Modern Vaccines 186
11.3.1 Subunit Vaccines 187
11.3.1.1 Virus-Like Particles (VLPs) 187
11.3.2 Conjugate Vaccines 187
11.3.3 Recombinant Vaccines 188
11.3.3.1 Live Genetically Modified Organisms 188
11.3.3.2 Genetic or DNA Vaccines 189
11.3.4 Peptide Vaccines 189
11.4 Summary 189
Selected Reading 189
12: Immobilisation and Biosensors 190
12.1 Introduction 190
12.2 Strategies of Whole Cell Immobilisation 190
12.2.1 Adsorption 190
12.2.2 Covalent Binding 191
12.2.3 Cell to Cell Cross-Linking 192
12.2.4 Encapsulation 192
12.2.5 Entrapment 193
12.2.5.1 Precipitation of Polymers 193
12.2.5.2 Ionotropic Gelation of Polymers 193
12.3 Alginate Method of Whole Cell Immobilisation 194
12.4 Microbes as Biosensors 195
12.4.1 Microbial Electrochemical Biosensors 196
12.4.1.1 Microbial Potentiometric Biosensors 196
12.4.1.2 Microbial Conductometric Biosensors 197
12.4.2 Optical Microbial Biosensors 197
12.4.2.1 Fluorescence Biosensor 197
12.4.2.2 Bioluminescent Microbial Biosensor 198
12.5 Summary 199
Selected Reading 199