Recent advances in Applied Microbiology (eBook)

Prof. Pratyoosh Shukla, PhD, is a Professor and Head of the Department of Microbiology at the Maharshi Dayanand University, Rohtak, India. His primary research interests are in Enzyme Technology, Microbial Biotechnology and Protein Bioinformatics. He completed his PhD in the field of Microbiology and Fungal Biotechnology at the APS, University Rewa, India. Following his PhD, he pursued his postdoctoral studies at the Department of Biotechnology & Food Technology, Durban University of Technology, South Africa. He has 15 years of research and 17 years of teaching experience. He has produced 73 scientific publications, and has authored or edited 6 books. He also has filed a patent on Novel β-1, 4-endoxylanase from Thermomyces lanuginosus SS-8 and the mode of action thereof. He is a life member of a number of academic bodies, including the Indian Science Congress Association (ISCA), India Society for Technical Education (ISTE), Mycological Society of India (MSI), Asian Federation of Biotechnology (AFoB), American Society for Microbiology (ASM), European Federation of Biotechnology (EFB) etc. He also holds the roles of Associate Editor, BMC Microbiology; Editor, Indian Journal of Microbiology (Springer); Editor-in-Chief, Journal of Microbiology, Internet Scientific Publishers, USA (2007-2009); Reviewer and Member of the Editorial Board for the Journal of Applied Sciences in Environmental Sanitation, ITS, Indonesia, etc. He is currently the General Secretary of the Association of Microbiologists of India (AMI) (since 2014). He has also been presented with a number of academic awards, such as the ASM-IUSSTF Indo-US Professorship Award in Microbiology by the American Society of Microbiology (2014); AMI Alembic Award in industrial microbiology, and the Fast Track Young Scientist by DST, Govt. of India (2012). He was also selected as a Scientist / Project Investigator and participated in the Southern Ocean Antarctica Expedition (Ministry of Earth Sciences, Govt. of India) (January-March, 2011).

Foreword 5
Contents 6
Contributors 8
About the Editor 11
Part I: Microbial Biotechnology 12
1: Immobilization of A. oryzae ?-galactosidase on Silica Nanoparticles: Development of an Effective Biosensor for Determination of Lactose in Milk Whey 13
1.1 Introduction 14
1.2 Results 15
1.2.1 ?-galactosidase Assay and Protein Estimation 15
1.2.2 Activation of Silica Nanoparticles 15
1.2.3 Immobilization of ?-galactosidase on Activated Silica Nanoparticles 16
1.2.4 Physical Characterization of Immobilized Silica Nanoparticles 16
1.2.5 Optimization of Immobilization Conditions 16
1.2.6 Enzymatic Characterization 18
1.2.7 Determination of Kinetic Parameters 20
1.2.8 Reusability of the Immobilized ?-galactosidase 20
1.2.9 Application of Immobilized ?-galactosidase in Lactose and Whey Hydrolysis 21
1.3 Conclusion 22
References 25
2: Bacterial Polyhydroxyalkanoates: Recent Trends in Production and Applications 29
2.1 Introduction 29
2.2 Classification 30
2.2.1 Short-Chain-Length (SCL) PHAs 30
2.2.2 Medium-Chain-Length (MCL) PHAs 31
2.2.3 Short-Chain-Length Medium-Chain-Length (SCL-MCL) PHAs 31
2.3 General Properties 32
2.4 PHA-Producing Bacteria 33
2.5 Mechanism of PHA Biosynthesis 33
2.5.1 Pathway I (The Acetyl-CoA to 3-hydroxybutyryl-CoA Pathway) 33
2.5.2 Pathway II (The ?-Oxidation Pathway) 34
2.5.3 Pathway III (The In Situ Fatty Acid Synthesis Pathway) 34
2.6 Major Enzymes Involved in PHA Biosynthesis 35
2.6.1 ?-Ketoacyl-CoA Thiolase (PhaA) 35
2.6.2 Acetoacetyl-CoA Reductase 36
2.6.3 PHA Synthase 36
2.7 Large-Scale PHA Production Strategies 38
2.7.1 Batch Fermentation 38
2.7.2 Fed-Batch Fermentation 42
2.7.3 Continuous Fermentation 43
2.8 Recombinant PHA Production 43
2.9 Applications of PHAs 47
2.10 Conclusion and Future Perspectives 50
References 51
3: Biosurfactant-Aided Bioprocessing: Industrial Applications and Environmental Impact 64
3.1 Introduction 65
3.2 Surfactants and Their Classification 69
3.3 Ionic (Anionic and Cationic) Surfactants 69
3.4 Nonionic Surfactants 70
3.5 Zwitterionic (Amphoteric) Surfactants 74
3.6 Biosurfactants 74
3.7 Classification and Properties of Biosurfactants 75
3.8 Microbes Used for Production of Biosurfactants 77
3.9 Application of Surfactants in Bioprocessing 77
3.10 Hydrocarbon Bioremediation 79
3.11 Heavy Metal Bioremediation 81
3.12 Bioconversion of Lignocellulosic Biomass 82
3.13 Future Perspectives 86
3.14 Conclusions 88
References 89
Part II: Microbes in Health 98
4: Autophagy and Bacterial Pathogenesis: An Interactive Overview 99
4.1 Introduction 99
4.2 Interaction of Bacteria with the Autophagy System of Host Cells 101
4.2.1 Listeria monocytogenes 101
4.2.2 Salmonella typhimurium 102
4.2.3 Mycobacterium tuberculosis 104
4.2.4 Shigella flexneri 105
4.2.5 Legionella pneumophila 106
4.2.6 Streptococcus pyogenes 107
4.2.7 Streptococcus pneumoniae 108
4.3 Conclusions 108
References 109
5: Emergence of Multidrug-Resistant Bacteria in Freshwater Ecosystems (River) and Screening of Natural Therapeutics Against the Probable Drug Targets of Drug-Resistant Pathogens by Computational Biology Approaches 116
5.1 Environmental Pollution in Freshwater Ecosystems (Rivers) 117
5.2 Water Pollution in Indian Rivers 119
5.2.1 Water Pollution in River Cauvery: A Case Study from South India 120
5.2.2 Global Status of River Pollution 121
5.3 Emergence of Multidrug-Resistant Bacteria in Freshwater Ecosystem: A Major Global Health Concern 122
5.4 Importance of Water Quality Monitoring and Conservation of Freshwater Ecosystem 125
5.4.1 Conventional Treatment Methods 125
5.4.2 Need for Physiochemical Characterization and Microbial Count Estimation 126
5.4.3 Need for Antibiotic Susceptibility Profiling 127
5.5 Need for an Alternative Therapy 128
5.5.1 Need for Computational Modeling and Virtual Screening 129
5.6 Conclusion 132
References 133
6: Probiotics for Human Health: Current Progress and Applications 140
6.1 Introduction 141
6.2 Probiotic Foods 142
6.3 Probiotic Microorganisms 143
6.4 Probiotics: Mechanism of Action 143
6.5 Applications of Probiotics in Human Health 145
6.5.1 Treatment of Diarrhea 145
6.5.2 Eradication of Helicobacter pylori Infections 147
6.5.3 Cardiovascular Diseases 147
6.5.4 Cancer Prevention 147
6.5.5 Prevention of Allergy 148
6.5.6 Irritable Bowel Syndrome 148
6.5.7 Inflammatory Bowel Disease 148
6.5.8 Lactose Malabsorption 149
6.5.9 Immune System Modulation 149
6.6 Application in Animal and Plant Health 150
6.7 Conclusion and Future Perspectives 150
References 151
Part III: Microbial Interactions 155
7: Functionalities of Phosphate-­Solubilizing Bacteria of Rice Rhizosphere: Techniques and Perspectives 156
7.1 Introduction 157
7.2 Types of Phosphorous in Soil 158
7.3 Plant Growth-Promoting Bacteria 158
7.4 Bacteria Involved in Phosphate Mineralization 158
7.5 Mechanisms of Phosphate Solubilization 159
7.6 Techniques Used to Evaluate Phosphate-Solubilizing Bacteria 162
7.7 Phosphate Solubilization in Rhizospheric Soil and Effect on Crop Productivity Including Rice 163
7.8 Biofertilizers 164
7.9 Conclusion 165
References 165
8: Tolerance of Microorganisms in Soil Contaminated with Trace Metals: An Overview 169
8.1 Introduction 170
8.1.1 Microbial Diversity in Extreme Habitats 170
8.1.2 Heavy Metal Resistance in Fungi 170
8.1.3 Heavy Metal Resistance of Bacteria 171
8.1.4 Characterization of Fungal and Metal-Resistant Bacteria Isolates 172
8.1.5 Metal-Resistant Fungal Isolates 172
8.1.6 Identification and Characterization of Metal-Resistant Bacteria Isolates 176
8.2 Conclusion 188
8.2.1 Future Prospective 189
References 189
9: Transformation, Purification, and Quantification of Soy Isoflavone from Lactobacillus sp. and Bifidobacterium sp. 198
9.1 Introduction 198
9.2 Isoflavones 199
9.3 ?-Galactosidase 200
9.4 Genistein 201
9.5 Daidzein 201
9.6 Strains and Culture Conditions 202
9.7 Fermentation 203
9.8 Preparation and Fermentation of Soy Milk 203
9.9 Extraction of Soy Isoflavones 203
9.10 Purification of Fermented Soy Isoflavones 204
9.10.1 Various Methodologies of TLC Technique 204
9.10.2 Analytical Methods for Soy Isoflavones 205
9.11 HPLC Analysis 206
9.12 Liquid Chromatography Mass Spectrophotometry 207
9.13 Conclusion 210
References 210
10: Burkholderia to Paraburkholderia: The Journey of a Plant-Beneficial-Environmental Bacterium 215
10.1 Introduction 216
10.2 Classification of Burkholderia 217
10.2.1 Earlier Scheme of Classification of Burkholderia 217
10.2.2 Proposals for Bifurcation of Genus Burkholderia 218
10.2.3 Revival of the Genus Caballeronia 220
10.3 Agro-biotechnological Potential of Burkholderia 221
10.4 Future of Paraburkholderia in Agro-biotechnology 225
10.5 Conclusion 225
References 226
11: WRKY Transcription Factors: Involvement in Plant–Pathogen Interactions 231
11.1 Introduction 232
11.2 WRKY Transcription Factors 232
11.3 Plant–Pathogen Interactions: Network of WRKY, MAPK, and Phytohormones 236
11.4 Defensive Roles of WRKY TFs in Arabidopsis 238
11.5 Defensive Roles of WRKY TFs in Rice 239
11.6 Defensive Roles of WRKY TFs in Wheat 240
11.7 Defensive Roles of WRKY TFs in Tomato 241
11.8 Role of WRKY TFs in Abiotic Stress and Nutrient Deficiency 241
11.9 WRKY and Reactive Oxygen Species (ROS) 242
11.10 Conclusion 242
References 243
Part IV: Computational Approaches in Microbiology 249
12: Humoral Responses of In Silico Designed Immunodominant Antigenic Peptide Cocktails from Anthrax Lethal Toxin Components 250
12.1 Introduction 251
12.2 Determination of Serum IgG 252
12.3 Determination of Antibody Avidity 252
12.4 Discussion 254
12.5 Conclusion 256
References 257
13: Microbial Enzyme Engineering: Applications and Perspectives 260
13.1 Introduction 261
13.2 Improvement of Enzymes by Tailoring Their Protein Sequences 261
13.2.1 Improvement of Enzyme Properties by Site-Directed Mutagenesis 262
13.2.2 Improvement of Enzyme Properties by Random Mutagenesis 263
13.3 Changing Pathways: Synthetic Metabolic Engineering 264
13.4 Immobilization of Microbial Enzyme 265
13.4.1 Microbial Enzyme Immobilization Using Nanotechnology 267
13.4.2 Immobilization by Forming CLEAs 269
13.5 Homologue Augmentation and Substitution 269
13.6 Conclusion and Future Perspectives 269
References 270
14: Fungal Chondroitinase: Production and Prospects for Therapeutic Application 275
14.1 Introduction 276
14.1.1 Screening and Isolation of Fungi Capable of Utilizing Chondroitin Sulphate 278
14.1.1.1 Submerged Fermentation 279
14.1.1.2 Estimation of Chondroitinase Activity 279
14.1.2 Optimization of Cultural Conditions for Chondroitinase Production 280
14.1.2.1 Factorial Design Studies 284
14.1.2.2 Plackett-Burman Design 285
14.1.2.3 Box-Behnken Design 286
14.1.3 Studies on Enzyme Separation and Cytotoxicity Profile 287
14.2 Conclusion 287
14.3 Conflicts of Interest 288
References 288
Erratum to: Recent Advances in Applied Microbiology 291