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Preface xvii Part 1: Soil Microenvironment and Biotransformation Mechanisms 1 1 Applications of Microorganisms in Agriculture for Nutrients Availability 3 Fehmida Fasim and Bushra Uziar 1.1 Introduction 3 1.1.1 Land and Soil Deterioration 4 1.1.2 Micro-Nutrients Lacks 4 1.2 Biofertilizers 4 1.3 Rhizosphere 5 1.4 Plant Growth Promoting Bacteria 5 1.4.1 Nitrogen Fixation 6 1.4.2 Phosphate Solubilization 8 1.5 Microbial Mechanisms of Phosphate Solubilization 9 1.5.1 Organic Phosphate 9 1.5.2 Organic Phosphate Solubilization 10 1.6 Bacterial and Fungi Coinoculation 11 1.7 Conclusion 11 References 12 2 Native Soil Bacteria: Potential Agent for Bioremediation 17 Ranjan Kumar Mohapatra, Haragobinda Srichandan, Snehasish Mishra and Pankaj Kumar Parhi 2.1 Introduction 17 2.2 Current Soil Pollution Scenario 19 2.2.1 Soil Pollution by Heavy Metals and Xenobiotic Compounds 19 2.2.2 Soil Pollution by Extensive Agricultural and Animal Husbandry Practices 20 2.2.3 Pollution Due to Emerging Pollutants (Wastes from Pharmaceutical and Personal-Care Products) 21 2.2.4 Soil Pollution by Pathogenic Microorganisms 22 2.2.5 Soil Pollution Due to Oil and Petroleum Hydrocarbons 23 2.2.6 Soil Pollution by the Nuclear and Radioactive Wastes 25 2.2.7 Soil Pollution by Military Activities and Warfare 26 2.3 Effects of Soil Pollution 26 2.3.1 Effects of Soil Pollution on Plants 26 2.3.2 Effects of Soil Pollution on Human Health 26 2.4 Diversity of Soil Bacteria from Contaminated Sites 27 2.5 Bioremediation of Toxic Pollutants 27 2.6 Bioremediation Mechanisms 27 2.7 Factors Affecting Bioremediation/Biosorption Process 29 2.8 Microbial Bioremediation Approaches 30 2.8.1 In Situ Bioremediation 30 2.8.2 Ex Situ Bioremediation 30 2.9 Conclusion and Future Prospective 30 Acknowledgements 30 References 31 3 Bacterial Mediated Remediation: A Strategy to Combat Pesticide Residues In Agricultural Soil 35 Atia Iqbal 3.1 Introduction 35 3.2 Effects of Pesticides 36 3.3 Pesticide Degradation 37 3.4 Bacterial Mediated Biodegradation of Various Pesticides 38 3.4.1 Organophosphate Pesticides Degrading Bacteria 38 3.4.2 Methyl Parathion Mineralizing Bacteria (MP) 39 3.4.3 Mesotrione Degrading Bacteria 39 3.4.4 Aromatic Hydrocarbons Biodegradation 39 3.4.5 Bispyribac Sodium (BS) Degrading Bacteria 40 3.4.6 Carbamates (CRBs) Degradation 40 3.4.7 Propanil Degradation 40 3.4.8 Atrazine Degradation 40 3.4.9 Phenanthrene Degradation 40 3.4.10 Imidacloprid Degradation 41 3.4.11 Endusulfan Degradation 41 3.4.12 DDT 42 3.5 Conclusion 42 References 49 4 Study of Plant Microbial Interaction in Formation of Cheese Production: A Vegan’s Delight 55 Sundaresan Bhavaniramya, Ramar Vanajothi, Selvaraju Vishnupriya and Dharmar Baskaran 4.1 Introduction 55 4.2 Cheese Concern - Vegan’s Delight 57 4.3 Microorganism Interaction Pattern 57 4.4 Types of Microorganism Involved in Cheese Production 57 4.5 Lactic Acid Role in Fermentation 59 4.6 Microorganism Involved in Lactic Acid Fermentation 59 4.7 Streptococcus 60 4.8 Propionibacterium 60 4.9 Leuconostoc 60 4.10 Microorganisms in Flavor Development 61 4.11 Flavor Production 63 4.12 Enzymes Interaction during Ripening of Cheese 63 4.13 Pathways Involved in Cheese Ripening 64 4.14 Microbes of Interest in Flavor Formation 66 4.15 Structure of Flavored Compound in Cheese 67 4.16 Plant-Based Cheese Analogues 67 4.17 Plant-Based Proteins 68 4.18 Aspartic Protease 69 4.19 Cysteine Protease 69 4.20 Plant-Based Milk Alternatives 69 4.21 Types of Vegan Cheese 70 4.22 Future Scope and Conclusion 71 Acknowledgment 71 References 71 5 Microbial Remediation of Pesticide Polluted Soils 75 Cesar Quintela and Cristiano Varrone 5.1 Introduction 75 5.2 Types of Pesticides 77 5.3 Fate of Pesticides in the Environment 81 5.3.1 Factors Affecting Pesticide Fate 81 5.3.2 Pesticides Degradation 84 5.3.3 Pesticide Remediation 85 5.4 Screening for Pesticide Degrading Microorganisms 85 5.4.1 Case Study 86 5.5 Designing Pesticide Degrading Consortia 87 5.5.1 Case Study 88 5.6 Challenges to be Addressed and Future Perspectives 88 References 90 6 Eco-Friendly and Economical Method for Detoxification of Pesticides by Microbes 95 Anjani Kumar Upadhyay, Abhik Mojumdar, Vishakha Raina and Lopamudra Ray 6.1 Introduction 95 6.2 Classification of Pesticides 96 6.3 Fate of Pesticide in Soil 96 6.3.1 Transport of Pesticides in the Environment 96 6.3.2 Interaction of Pesticides with Soil 98 6.4 Microbial and Phytoremediation of Pesticides 99 6.4.1 Biodegradation and Bioremediation 99 6.4.2 Microbial Remediation of Pesticides 102 6.4.3 Phytoremediation of Pesticides 103 6.4.4 Strategies to Enhance the Efficiency of Bioremediation 103 6.4.5 Metabolic Aspects of Pesticides Bioremediation 105 6.5 Effects on Human and Environment 106 6.6 Advancement in Pesticide Bioremediation 107 6.7 Limitations of Bioremediation 107 6.8 Future Perspectives 108 Acknowledgement 108 References 108 Part 2: Synergistic Effects Between Substrates and Microbes 115 7 Bioleaching: A Bioremediation Process to Treat Hazardous Wastes 117 Haragobinda Srichandan, Ranjan K. Mohapatra, Pankaj K. Parhi and Snehasish Mishra 7.1 Introduction 117 7.2 Microbes in Bioleaching 118 7.2.1 Bacteria 118 7.2.2 Fungi 119 7.3 Acidophilic Bioleaching 119 7.3.1 Contact (Direct) Mechanism 119 7.3.2 Non-Contact (Indirect) Mechanism 120 7.4 Metal Removal Pathways 120 7.4.1 Thiosulphate Pathway 120 7.4.2 Polysulphide Pathway 121 7.5 Fungal Bioleaching 122 7.6 Various Hazardous Wastes 122 7.6.1 Electronic Wastes (E-Wastes) 123 7.6.2 Spent Petroleum Catalyst 123 7.6.3 Sludge 123 7.6.4 Slag 123 7.7 Applications of Bioleaching Approach to Various Hazardous Wastes 123 7.7.1 Bioleaching of Electronic Wastes 124 7.7.2 Bioleaching of Spent Catalyst 124 7.7.3 Bioleaching of Sludge (Containing Heavy or Toxic metals) 125 7.7.4 Bioleaching of Slag 125 7.8 Conclusion 126 Acknowledgements 126 References 126 8 Microbial Bioremediation of Azo Dyes in Textile Industry Effluent: A Review on Bioreactor-Based Studies 131 Shweta Agrawal, Devayani Tipre and Shailesh Dave 8.1 Introduction 131 8.2 Microorganism Involved in Dye Bioremediation 132 8.2.1 Bacterial Remediation of Dyes 132 8.2.2 Mycoremediation 135 8.2.3 Phycoremediation 135 8.2.4 Consortial (Co-Culture) Dye Bioremediation 135 8.3 Mechanism of Dye Biodegradation 139 8.3.1 Anaerobic Azo Dye Reduction 139 8.3.2 Aerobic Oxidation of Aromatic Amines 140 8.3.3 Combined Anaerobic-Aerobic Treatment of Azo Dyes 141 8.4 Reactor Design for Dye Bioremediation 141 8.4.1 Anaerobic Reactors 142 8.4.2 Aerobic Reactors 154 8.4.3 Combined (Integrated/Sequential) Bioreactor 157 8.4.4 Combinatorial Approaches 162 8.5 Limitations and Future Prospects 163 8.6 Conclusions 163 References 164 9 Antibiofilm Property of Biosurfactant Produced by Nesterenkonia sp. MCCB 225 Against Shrimp Pathogen, Vibrio harveyi 173 Gopalakrishnan Menon, Issac Sarojini Bright Singh, Prasannan Geetha Preena and Sumitra Datta 9.1 Introduction 173 9.2 Materials and Methods 174 9.2.1 Isolation, Screening and Identification of Bacteria 174 9.2.2 Biofilm Disruption Studies 175 9.3 Results and Discussion 175 9.3.1 Bacterial Identification 175 9.3.2 Biofilm Disruption Studies 175 9.4 Conclusion 178 Acknowledgements 178 References 178 10 Role of Cr (VI) Resistant Bacillus megaterium in Phytoremediation 181 Rabia Faryad Khan and Rida Batool 10.1 Introduction 181 10.2 Materials and Methods 183 10.2.1 Isolation and Characterization of Chromate Resistant Bacteria 183 10.2.2 Determination of MIC (Minimum Inhibitory Concentration) of Chromate 183 10.2.3 Ribo-Typing of Bacterial Isolate rCrI 183 10.2.4 Estimation of Chromate Reduction Potential 183 10.2.5 Antibiotic and Heavy Metal Resistance Profiling 183 10.2.6 Growth Curve Studies 184 10.2.7 Chromium Uptake Estimation 185 10.2.8 Statistical Analysis 185 10.3 Results 185 10.3.1 Isolation and Characterization of Cr(VI) Resistant Bacterial Isolates 185 10.3.2 Antibiotic and Heavy Metal Resistance Profiling 186 10.3.3 Estimation of Cr(VI) Reduction Potential 186 10.3.4 Ribo-Typing of Bacterial Isolate 186 10.3.5 Growth Curve Studies 186 10.3.6 Plant Microbe Interaction Studies Under Laboratory Conditions 187 10.3.7 Biochemical Parameters 188 10.3.8 Plant Microbe Interaction Studies Under Field Conditions 190 10.3.8.4 Number of Roots 190 10.3.9 Biochemical Parameters 190 10.4 Discussion 191 10.5 Conclusion 193 Acknowledgment 193 References 193 11 Conjugate Magnetic Nanoparticles and Microbial Remediation, a Genuine Technology to Remediate Radioactive Waste 197 Bushra Uzair, Anum Shaukat, Fehmida Fasim, Sadaf Maqbool 11.1 Introduction 197 11.2 Use of Magnetic Nanoparticles Conjugates 199 11.2.1 Potential Benefits 199 11.2.2 Synthesis and Application 200 11.2.3 Factors Affecting Sorption 200 11.2.4 Limitations 203 11.3 Microbial Communities 203 11.3.1 Fungi as Radio-Nuclides Remade 203 11.3.2 Immobilization of Radionuclide Through Enzymatic Reduction 204 11.3.3 Immobilization Through Non-Enzymatic Reduction 204 11.3.4 Bio-Sorption of Radio-Nuclides 205 11.3.5 Biostimulation 206 11.3.6 Genetically Modified Microbes 206 11.3.7 Constraints 207 11.4 Conclusion 207 References 208 Part 3: Polyhydroxyalakanoates: Resources, Demands and Sustainability 213 12 Microbial Degradation of Plastics: New Plastic Degraders, Mixed Cultures and Engineering Strategies 215 Samantha Jenkins, Alba Martinez i Quer, Cesar Fonseca and Cristiano Varrone 12.1 Introduction 215 12.2 Plastics 216 12.2.1 Polyethylene Terephthalate (PET) 217 12.2.2 Low-Density Polyethylene (LDPE) 217 12.3 Plastic Disposal, Reuse and Recycling 218 12.4 Plastic Biodegradation 219 12.4.1 Plastic-Degrading Microorganisms and Enzymes 221 12.4.2 Biofilms and Plastic Biodegradation 224 12.4.3 Boosting Plastic Biodegradation by Physical and Chemical Processes 225 12.4.4 Pathway and Protein Engineering for Enhanced Plastic Biodegradation 226 12.4.5 Designing Plastic Degrading Consortia 229 12.5 Analytical Techniques to Study Plastic Degradation 230 12.6 Future Perspectives 232 References 233 13 Fatty acids as Novel Building-Blocks for Biomaterial Synthesis 239 Prasun Kumar 13.1 Introduction 239 13.2 Polyurethane (PUs) 241 13.3 Polyhydroxyalkanoates (PHAs) 243 13.4 Other Functional Attributes 246 13.4.1 Biosurfactants 246 13.4.2 Antibacterials and Biocontrol Agents 246 13.5 Future Perspectives 249 References 249 14 Polyhydroxyalkanoates: Resources, Demands and Sustainability 253 Binita Bhattacharyya, Himadri Tanaya Behera, Abhik Mojumdar, Vishakha Raina and Lopamudra Ray 14.1 Introduction 253 14.2 Polyhydroxyalkanoates 255 14.2.1 Properties of PHAs 258 14.2.2 Production of PHA 261 14.2.3 PHA Biosynthesis in Natural Isolates 261 14.2.4 Production of PHA by Digestion of Biological Wastes 262 14.2.5 PHA Production by Recombinant Bacteria 262 14..2.6 Production of PHA by Genetically Engineered Plants 264 14.2.7 PHA Production by Methylotrophs 264 14.2.8 PHA Production Using Waste Vegetable Oil by Pseudomonas sp. Strain DR2 264 14.2.9 Mass Production of PHA 265 14.3 Applications of PHA 266 14.4 Future Prospects 267 References 267 15 Polyhydroxyalkanoates Synthesis by Bacillus aryabhattai C48 Isolated from Cassava Dumpsites in South-Western, Nigeria 271 Fadipe Temitope O., Nazia Jamil and Lawal Adekunle K. 15.1 Introduction 271 15.2 Materials and Methods 272 15.2.1 Morphological, Biochemical and Molecular Characterisation 272 15.2.2 Detection of PHA Production 273 15.2.3 Evaluation of PHA Production 273 15.2.4 Extraction of PHA 273 15.2.5 Fourier Transform Infrared Spectroscopy of Extracted PHA 274 15.2.6 Amplification of PhaC and PhaR Genes of Bacillus aryabhattai C48 274 15.3 Results and Discussion 274 15.4 Conclusion 280 Acknowledgements 280 References 280 Part 4: Cellulose-Based Biomaterials: Benefits and Challenges 283 16 Cellulose Nanocrystals-Based Composites 285 Teboho Clement Mokhena, Maya Jacob John, Mokgaotsa Jonas Mochane, Asanda Mtibe, Teboho Simon Motsoeneng, Thabang Hendrica Mokhothu and Cyrus Alushavhiwi Tshifularo 16.1 Introduction 285 16.2 Classification of Polymers 286 16.3 Preparation of Cellulose Nanocrystals Composites 286 16.3.1 Solution Casting 287 16.3.2 Three Dimensional Printing (3D-Printing) 292 16.3.3 Electrospinning 294 16.3.4 Other Processing Techniques 294 16.4 Cellulose Nanocrystals Reinforced Biopolymers 294 16.4.1 Starch 294 16.4.2 Alginate 295 16.4.3 Chitosan 296 16.4.4 Cellulose 297 16.4.5 Other Biopolymers 298 16.5 Hybrids 298 16.6 Conclusion and Future Trends 300 Acknowledgements 300 References 300 17 Progress on Production of Cellulose from Bacteria 307 Tladi Gideon Mofokeng, Mokgaotsa Jonas Mochane, Vincent Ojijo, Suprakas Sinha Ray and Teboho Clement Mokhena 17.1 Introduction 307 17.2 Production of Microbial Cellulose (MC) 308 17.3 Applications of Microbial Cellulose (MC) 312 17.3.1 Skin Therapy and Wound Healing System 313 17.3.2 Scaffolds for Artificial Cornea 314 17.3.3 Cardiovascular Implants 315 Future Perspective 315 References 316 18 Recent Developments of Cellulose-Based Biomaterials 319 Asanda Mtibe, Teboho Clement Mokhena, Thabang Hendrica Mokhothu and Mokgaotsa Jonas Mochane 18.1 Introduction 319 18.2 Extraction of Cellulose Fibers 320 18.3 Nanocellulose 324 18.4 Surface Modification 327 18.4.1 Alkali Treatment (Mercerization) 327 18.4.2 Silane Treatment 328 18.4.3 Acetylation 328 18.5 Cellulose-Based Biomaterials 329 18.5.1 Cellulose-Based Biomaterials for Tissue Engineering 329 18.5.2 Cellulose-Based Biomaterials for Drug Delivery 331 18.5.3 Cellulose-Based Biomaterials for Wound Dressing 332 18.6 Summary and Future Prospect of Cellulose-Based Biomaterials 333 Reference 334 19 Insights of Bacterial Cellulose: Bio and Nano-Polymer Composites Towards Industrial Application 339 Vishnupriya Selvaraju, Bhavaniramya Sundaresan, Baskaran Dharmar 19.1 Introduction 339 19.1.1 Nanocellulose 340 19.2 Bacterial Cellulose 343 19.2.1 Bacterial Strains Producing Cellulose 343 19.2.2 Different Methods of Bacterial Cellulose Production 344 19.3 Nanocomposites 346 19.3.1 Bio-Nanocomposite-Based on CNF 346 19.3.2 Bio-Nanocomposite-Based on CNC 346 19.3.3 Bacterial Cellulose Nanocomposites 346 19.4 Methods of Synthesis of Bacterial Cellulose Composites 347 19.5 Combination of Bacterial Cellulose with Other Materials 349 19.5.1 Polymer 349 19.5.2 Metals and Solid Materials 350 19.6 Industrial Applications of Bacterial Cellulose Composites 350 19.6.1 Biomedical Applications 350 19.6.2 Food Application 351 19.6.3 Electrical Industry 351 19.7 Future Scope and Conclusion 352 Acknowledgement 352 References 352 20 Biodegradable Polymers Reinforced with Lignin and Lignocellulosic Materials 357 M.A. Sibeko, V.C. Agbakoba, T.C. Mokhena, P.S. Hlangothi 20.1 Introduction 357 20.2 Biodegradable Polymers 358 20.2.1 Natural Polymers 359 20.2.2 Biodegradable Polyesters 360 20.2.3 Biodegradation 362 20.3 Biodegradable Fillers 362 20.3.1 Plant Fibers as Biodegradable Fillers 363 20.3.2 Cellulose as Biodegradable Fillers 364 20.3.3 Lignin as Biodegradable Fillers 364 20.4 Properties of Different Biopolymers Reinforced with Lignin 365 20.4.1 Surface Morphology 365 20.4.2 Mechanical Properties 366 20.4.3 Thermal Properties 368 20.5 Applications of Bio-Nanocomposites 369 Concluding Remarks 369 Acknowledgements 370 References 370 21 Structure and Properties of Lignin-Based Biopolymers in Polymer Production 375 Teboho Simon Motsoeneng, Mokgaotsa Jonas Mochane, Teboho Clement Mokhena and Maya Jacob John 21.1 Introduction 375 21.2 An Insight on the Biopolymers 376 21.2.1 Natural Lignin Biopolymer 377 21.2.2 Drawbacks of Lignin Biopolymer 378 21.3 Extraction and Post-Treatment of Lignin Biomaterial 378 21.3.1 Extraction Methods and their Effect on the Recovery and Functionality 379 21.3.2 Modification of Lignin Functional Groups 381 21.3.3 Preparation of Lignin-Based Biopolymers Blends (LBBs) 383 21.4 Characterization Methods and Validation of Lignin-Biopolymers 386 21.4.1 Chemical Interaction Between Lignin and Synthetic Polymers 386 21.4.2 Morphology-Property Relationship of the LBB 387 21.5 Indispensability of LBB on the Chemical Release Control in the Environment 388 21.6 Conclusion and Future Remarks 388 References 389 Index 393

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