Preface	6
	Contents	9
	Editors and Contributors	11
	1 Introduction to Environmental Protection and Management	17
	Abstract	17
	2 Mathematical Modeling in Bioremediation	23
	2.1 Basics of Flow of Groundwater and Transport of Contaminants	24
	2.1.1 Introduction	24
	2.1.2 Concepts of Groundwater	26
	2.1.3 Concepts of Contaminant Transport Processes	31
	2.1.4 Other Terminologies	35
	2.2 Model Equations for Bioremediation	35
	2.2.1 Theory	35
	2.2.2 Analytical Models	38
	2.3 Recent Advances in Mathematical Modeling in Bioremediation	39
	References	42
	3 Evaluation of Next-Generation Sequencing Technologies for Environmental Monitoring in Wastewater Abatement	44
	Abstract	44
	3.1 Introduction	45
	3.2 Wastewater Treatment Mechanism	47
	3.2.1 Biological Wastewater Treatment	48
	3.2.2 Types of Microbes in Wastewater Treatment Plant	48
	3.2.3 Water Quality Analysis	50
	3.3 Infrastructure of Wastewater Treatment Plant	51
	3.3.1 Drinking Water Distribution System	51
	3.3.2 Types of Water Sampling	52
	3.3.2.1 Bulk Water Sampling	52
	3.3.2.2 Biofilm Water Sampling	53
	3.4 Microbiological Techniques	53
	3.4.1 Microbial Detection and Enumeration	54
	3.4.1.1 Culture-Dependent Techniques	54
	3.4.1.2 Culture-Independent Techniques	55
	3.4.1.3 Fluorescent in situ Hybridization (FISH)	55
	3.4.1.4 Flow Cytometry (FC)	56
	3.4.1.5 PCR-Based Methods	57
	3.4.2 Microbial Community Composition	58
	3.4.2.1 Phospholipid Fatty Acids	58
	3.4.2.2 Bioinformatic Tools	58
	3.4.2.3 Fingerprinting Techniques	59
	3.4.2.4 Terminal Restriction Fragment Length Polymorphism (TeRFLP)	60
	3.4.2.5 Amplified Ribosomal DNA Restriction Analysis (ARDRA)	60
	3.4.2.6 Automated Ribosomal Intergenic Spacer Analysis (ARISA)	60
	3.4.3 Sequencing-Based Approaches	60
	3.5 Next-Generation Sequencing	61
	3.5.1 Stable Isotope Probing (SIP) Technique	62
	3.5.2 Challenges in NGS	63
	3.5.3 NGS Technologies and Analysis Methods	63
	3.5.4 Limitations in NGS	64
	3.5.5 Application of NGS in Water Quality Analysis	64
	3.5.6 Microbial Safety of Drinking Water	65
	References	66
	4 Genetically Modified Organisms and Its Impact on the Enhancement of Bioremediation	68
	Abstract	68
	4.1 Introduction	69
	4.1.1 Bioremediation	69
	4.1.2 Types of Bioremediation	70
	4.1.2.1 In Situ Bioremediation	70
	4.1.2.2 Intrinsic In Situ Bioremediation	70
	4.1.2.3 Ex Situ Bioremediation	71
	4.2 Genetically Modified Microorganisms and Its Application in Bioremediation	72
	4.2.1 Factors Influencing Genetically Engineered Microorganisms	75
	4.2.2 Strategies to Control GEMs Transfer	77
	4.2.2.1 Mini-transposon-mediated GEM Transfer Control	77
	4.2.2.2 Suicide Genes-mediated GEM Transfer Control	77
	4.2.2.3 gef Gene Expression and GEM Transfer Control	77
	4.2.2.4 Composting and GEM Transfer Control	78
	4.2.3 Techniques to Identify Genetically Modified Microbes	78
	4.2.3.1 PCR-based Techniques	78
	4.2.3.2 Fluorescent-based DNA Hybridization Technique	78
	4.2.3.3 Bioluminescence-mediated Technique	79
	4.2.3.4 DNA Microarray Technique	79
	4.3 Molecular Tools for Construction of Genetic Engineering of Microbes for Bioremediation	79
	4.3.1 Molecular Cloning	79
	4.3.2 Electroporation	80
	4.3.3 Protoplast Transformation	80
	4.3.4 Biolistic Transformation	82
	4.4 Genetically Modified Microorganisms for Bioremediation Purposes	82
	4.4.1 GMOs in Removal of Toxic Heavy Metals	82
	4.4.2 GMOs in Phytoremediation	83
	4.5 Pros and Cons of Genetically Engineering Organisms	84
	4.5.1 The Pros	84
	4.5.2 The Cons	85
	4.6 Ethical Issues and Risk Assessments in Usage of GMOs in Bioremediation	85
	4.7 Conclusion	88
	References	88
	5 Integration of Lignin Removal from Black Liquor and Biotransformation Process	92
	Abstract	92
	5.1 Introduction	93
	5.2 Structure of Lignin	93
	5.3 Lignin Isolation Processes	96
	5.3.1 Kraft Lignin	96
	5.3.2 Lignosulfonate Lignin	97
	5.3.3 Soda Lignin	97
	5.3.4 Organosolv Lignin	98
	5.3.5 Steam Explosion Lignin	98
	5.3.6 Ionic Liquid Lignin	99
	5.4 Physicochemical Properties of Lignin	99
	5.5 Lignin: Recent Advances Applications	100
	5.5.1 Lignin for Power-Fuel Gas Production	100
	5.5.2 Lignin for Macromolecule Synthesis	100
	5.5.3 Fine Chemical Synthesis	101
	5.6 Lignin Removal in Paper and Pulp Industry	102
	5.6.1 Lignin Removal by Coagulation Process	102
	5.6.2 Lignin Precipitation by Acidification Process	103
	5.6.3 Electrocoagulation Process	103
	5.7 Biodegradation and Bioremediation of Lignin	105
	5.7.1 Bacteria	106
	5.7.2 Algae	107
	5.7.3 Soft-Rot Fungi	108
	5.7.4 Microfungi or Molds	108
	5.7.4.1 Brown-Rot and White-Rot Basidiomycetes	108
	References	109
	6 Role of Nanofibers in Bioremediation	113
	Abstract	113
	6.1 Introduction	113
	6.2 Nanofibers	115
	6.3 Electrospinning	115
	6.4 Biohybrid Nanofibers	116
	6.5 Immobilization	117
	6.6 Types of Microorganism Immobilizations	118
	6.6.1 Adsorption	118
	6.6.2 Covalent Binding/Cross-Linking	119
	6.6.3 Entrapment	119
	6.6.4 Encapsulation	119
	6.7 Fabrication of Biohybrid Nanofibers	120
	6.7.1 Monolithic Nanofibers	120
	6.7.2 Core–Shell Nanofibers	121
	6.8 Biohybrid Nanofibers for Bioremedial Applications	122
	6.8.1 Nanofibers on Dye Removal	122
	6.8.2 Nanofibers on Atrazine Removal	123
	6.8.3 Nanofibers on Chromium Removal	124
	6.8.4 Nanofibers on Nitrate and Ammonium Removal	124
	6.8.5 Nanofibers on Heavy Metal Removal	125
	6.9 Analysis of Advantages–Disadvantages	125
	6.10 Conclusion	126
	References	126
	7 Bioremediation of Industrial Wastewater Using Bioelectrochemical Treatment	129
	Abstract	129
	7.1 Introduction	129
	7.2 Organic Matter Removal Using Different System	130
	7.3 Metal Removal Using Bioelectrochemical System	131
	7.3.1 Metal Ions Using Abiotic Cathode System in MFC	133
	7.3.2 Metal Removal Using Abiotic Cathode in MEC	134
	7.3.3 Metal Ion Removal and Recovery Using Biocathode MFC System	135
	7.3.4 Metal Ion Removal and Recovery Using Biocathode MEC System	136
	7.4 Conclusion	137
	References	137
	8 Biosorption Strategies in the Remediation of Toxic Pollutants from Contaminated Water Bodies	141
	Abstract	141
	8.1 Introduction	142
	8.2 Potential of Biosorption	145
	8.3 Biosorption and the Pollutants	147
	8.3.1 Biosorption and Heavy Metal	147
	8.3.2 Biosorption and Dyes	152
	8.3.3 Biosorption and Phenol	153
	8.3.4 Biosorption and Radioactive Waste	154
	8.4 Factors Consideration in Biosorption Process	154
	8.4.1 Cost of Biosorbents	154
	8.4.2 Biosorbent Regeneration	155
	8.4.3 Biosorbent Immobilization	155
	8.4.4 Charge of Biomass	156
	8.4.5 Biosorption Process Design	157
	8.5 Biomass Types	157
	8.5.1 Biosorption Using Algae	161
	8.5.2 Biosorption Using Bacteria	163
	8.5.3 Biosorption Using Fungi	163
	8.5.4 Biosorbents from Agricultural Waste	165
	8.5.5 Biosorption from Industrial Waste	166
	8.6 Application of Biosorbents	166
	8.7 Conclusion	167
	References	167
	9 Bioremediation of Heavy Metals	178
	Abstract	178
	9.1 Introduction	179
	9.2 Heavy Metal-Polluted Environments	179
	9.2.1 Types of Heavy Metals and Their Toxicity	181
	9.2.1.1 Arsenic	181
	9.2.1.2 Lead	181
	9.2.1.3 Zinc	182
	9.2.1.4 Cadmium	182
	9.2.1.5 Copper	182
	9.2.1.6 Chromium	183
	9.2.1.7 Mercury	184
	9.2.1.8 Silver	184
	9.2.1.9 Gold	185
	9.2.1.10 Nickel	185
	9.2.1.11 Selenium	186
	9.2.1.12 Uranium	186
	9.3 Bioremediation	187
	9.3.1 Principle of Bioremediation	187
	9.3.2 Types of Bioremediation	188
	9.3.2.1 In Situ Bioremediation	188
	Types of In Situ Bioremediation	188
	Advantages and Disadvantages of In Situ Bioremediation	190
	9.3.2.2 Ex Situ Bioremediation	190
	Type of Ex Situ Bioremediation	190
	Advantages and Disadvantages of Ex Situ Bioremediation	192
	9.3.3 Factor Affecting Bioremediation	192
	9.3.3.1 Microbial Populations for Bioremediation	192
	9.3.3.2 Chemical Factors	193
	Bioavailability of Pollutants	193
	Biodegradability of Pollutants	193
	9.3.3.3 Environmental Factors	193
	Temperature	193
	pH	194
	Nutrients	194
	Moisture Content and Water Availability	194
	9.3.4 Bioremediation of Heavy Metals by Microorganism	194
	9.3.4.1 Mechanisms	196
	9.3.5 Bioremediation of Heavy Metals by Plants	197
	9.3.5.1 Mechanisms of Bioremediation by Plants	197
	Phytoextraction	197
	Phytostabilization	199
	Rhizofiltration	199
	Phytovolatilization	200
	9.3.6 Bioremediation of Heavy Metals by Algae	200
	9.3.6.1 Mechanisms	201
	9.3.7 Bioreactors	201
	9.3.7.1 Stirred Tank Bioreactor (STRs)	202
	9.3.7.2 Fluidized Bed Bioreactor (FBRs)	202
	9.3.7.3 Airlift Reactors (ALRs)	202
	9.3.7.4 Fixed-Bed Bioreactors (FXRs)	202
	9.3.7.5 Rotating Biological Bioreactor (RBC)	203
	9.4 Recent Trends	203
	9.4.1 Application of Genetic Engineering	203
	9.4.1.1 Genetically Modified Microorganisms	203
	9.4.1.2 Genetically Modified Plants	204
	9.4.2 Rhizosphere Engineering	204
	9.4.3 Application of Nanotechnology	205
	9.4.4 Effect of Plant–Microbe Symbiosis	206
	9.5 Conclusion	206
	References	206
	10 Pesticides Bioremediation	209
	Abstract	209
	10.1 Introduction and General Overview	210
	10.2 Pesticides	211
	10.3 Different Categories of Pesticides	212
	10.3.1 Organochlorine Pesticides	212
	10.3.1.1 DDT	214
	10.3.1.2 Lindane	214
	10.3.1.3 Chlordane	215
	10.3.1.4 Endosulfan	215
	10.3.2 Organophosphate Pesticides	216
	10.3.2.1 Chlorpyrifos	216
	10.3.2.2 Methyl Parathion	217
	10.3.3 Carbamates	217
	10.3.3.1 Carbaryl	218
	10.4 Risk Correlated with Pesticides	218
	10.4.1 Threats to Human Health	219
	10.4.2 Threats to Plants	220
	10.4.3 Threats to Aquatic System	220
	10.4.4 Threats to Soil	221
	10.5 Bioremediation History	221
	10.6 Classes of Bioremediation	222
	10.6.1 In Situ Process	222
	10.6.2 Ex Situ Process	222
	10.7 Bioremediation of Pesticides	223
	10.8 Upside of Bioremediation	223
	10.9 Downside of Bioremediation	224
	10.10 Strategies of Pesticides Bioremediation	224
	10.10.1 Involvement of Microbes in Bioremediation of Pesticides	224
	10.10.1.1 Bacterial Bioremediation	225
	10.10.1.2 Mycoremediation	227
	10.10.1.3 Phycoremediation	228
	10.10.2 Phytoremediation of Pesticides	229
	10.11 Future Recommendations	230
	10.12 Conclusion	231
	References	231
	11 Application of Microbes in Remediation of Hazardous Wastes: A Review	235
	Abstract	235
	11.1 Introduction	236
	11.2 Remediation Methods	238
	11.2.1 Physicochemical Methods	238
	11.2.2 Biological Methods	239
	11.3 Bioremediation Processes: Two Main Categories	239
	11.3.1 In situ Bioremediation	239
	11.3.2 Ex situ Bioremediation	239
	11.4 Microbial Application for the Bioremediation of Hazardous Wastes	240
	11.4.1 Bacterial Treatment of Wastes	240
	11.4.2 Algal Treatment of Hazardous Wastes	240
	11.4.3 Fungal Treatment of Hazardous Wastes	241
	11.5 Degradation of Hazardous Waste Using Microbial Consortia	243
	11.6 Mechanism of Bioremediation	243
	11.7 Factors Affecting Bioremediation	244
	11.8 Waste Valorization	246
	11.9 Advantages and Disadvantages of Bioremediation	247
	11.10 Hazardous Waste Management	248
	11.11 Conclusion	249
	Acknowledgements	249
	References	249
	12 Phytoremediation Techniques for the Removal of Dye in Wastewater	254
	Abstract	254
	12.1 Introduction	255
	12.1.1 Phytoremediation	256
	12.2 Mechanisms of Phytoremediation	257
	12.3 Phytoremediation Process	257
	12.3.1 Selection of Plants for Remediation of Textile Dyes	258
	12.3.2 Phytoremediation of Textile Dyes	259
	12.4 Removal of Azo Dyes	261
	12.5 Advantages of Phytoremediation	261
	References	261
	13 Phenol Degradation from Industrial Wastewater by Engineered Microbes	264
	Abstract	264
	13.1 Introduction	264
	13.2 Manifestation of Phenol Pollution	269
	13.2.1 Aromatic Alcohol	270
	13.3 Phenolic Compounds Toxicity Data	271
	13.3.1 Deleterious Effects on Ecosystem	272
	13.3.2 Impact and Fate of Phenolic Compounds on Humans	274
	13.4 Biodegradation of Phenols	275
	13.4.1 Genetic Engineering in Biodegradation	277
	13.5 Engineered Plasmids for Phenol Treatment	280
	13.6 Risk Assessment in Genetic Engineering	282
	13.7 Regulatory Affairs	283
	13.8 Conclusions	283
	References	284
	14 Insect Gut Bacteria and Their Potential Application in Degradation of Lignocellulosic Biomass: A Review	288
	Abstract	288
	14.1 Introduction	288
	14.2 Insect Gut Environment	290
	14.3 Microbial Colonization Within Insect Gut	291
	14.4 Insect Gut Microbial Composition	291
	14.4.1 According to Diet	293
	14.4.2 Role in Partner Selection	294
	14.4.3 Genome Evolution	295
	14.5 Lignocellulose as a Component: Physiological Property	296
	14.6 Enzymatic Breakdown of Lignocellulose	297
	14.7 Cellulosomes Complex	298
	14.8 Biotechnological Application of Cellulase Enzyme	299
	14.8.1 In Waste Management	300
	14.8.2 Food and Brewage Industry	300
	14.8.3 Ethanol Production from Lignocellulosic Biomasses	300
	14.8.4 Pulp and Paper Industry	302
	14.8.5 Textile Industry	302
	14.9 Conclusion	303
	Acknowledgements	303
	References	303
	15 Bioremediation of Volatile Organic Compounds in Biofilters	311
	Abstract	311
	15.1 Introduction	312
	15.1.1 Air Pollution	312
	15.1.2 Effect of Volatile Organic Compounds	314
	15.1.3 Environmental and Health Hazards	314
	15.1.4 VOCs Removal Techniques by Non-biological and Biological Methods	318
	15.2 Degradation of VOCs Using Microorganisms	322
	15.2.1 Biodegradation of VOCs Using Pure Culture	323
	15.2.1.1 Biodegradation of VOCs Using Bacteria	323
	15.2.1.2 Biodegradation of VOCs Using Fungi	324
	15.2.2 Biodegradation of VOCs Using Mixed Culture	327
	15.3 Biofilters	327
	15.3.1 Type of Bioreactors Employed for Toluene Removal	331
	15.3.1.1 Biotrickling Bioreactor (BTBR)	332
	15.3.1.2 Bioscrubber Bioreactor (BSBR)	333
	15.3.1.3 Two-Phase Partitioning Bioreactor (TPPB)	334
	15.3.1.4 Fluidized Bed Bioreactor (FBR)	334
	15.3.1.5 Fixed Film Bioreactor (FFBR)	335
	15.3.1.6 Upflow Packed Bed Reactor (UFPBR)	335
	15.3.1.7 Foam Emulsion Bioreactor (FEBR)	335
	15.3.1.8 Membrane Bioreactor (MBR)	336
	15.3.2 Packing Materials	336
	15.3.3 Suggestions and Future Scope of Work	337
	15.4 Summary	337
	References	338
	16 Bioremediation of Industrial and Municipal Wastewater Using Microalgae	341
	Abstract	341
	16.1 Introduction	342
	16.2 Bioremediation	343
	16.3 Phycoremediation	344
	16.4 Microalgae in Wastewater Treatment	346
	16.5 Methodology	347
	16.5.1 Microalgae Wastewater Treatment in Waste Stabilization Ponds (WSP)	347
	16.5.2 Facultative Ponds	348
	16.5.3 High-Rate Algal Ponds (HRAPs)	349
	16.5.4 Cell Immobilization	350
	16.5.5 Use of Strains with Special Attributes	351
	16.6 Bioreactor Design	352
	16.6.1 Open Raceway Ponds	352
	16.6.2 Photobioreactor	353
	16.6.3 Activated Sludge Process	354
	16.7 Harvesting Strategy	355
	16.8 Advantage—Dual Role of Microalgae	356
	16.9 Nonfuel Applications	356
	16.10 Fuel-Based Applications	356
	16.11 Applications	357
	16.11.1 Treating Municipal Wastewater	357
	16.11.2 Treating Food Processing Industrial Wastewater	358
	16.11.3 Treating Paper Industrial Wastewater	359
	16.11.4 Treating Agro-Industrial Wastes	359
	16.12 Cost Analysis	360
	16.13 Additional Features	361
	16.14 Challenges	361
	16.15 Summary	363
	References	364
	17 Phytoremediation of Textile Dye Effluents	368
	Abstract	368
	17.1 Introduction	369
	17.2 Characterization of Textile Effluents (Source and its Characterization)	369
	17.2.1 Textile Effluents	369
	17.2.2 Characteristics of Textile Effluents	370
	17.2.3 Adsorption	370
	17.2.4 Flocculation	371
	17.2.5 Microbial Treatment	371
	17.2.5.1 Factors Affecting Color Removal Using Microbes	372
	17.3 Phytoremediation	373
	17.4 Mechanisms of Phytoremediation	373
	17.4.1 Phytoextraction	373
	17.4.2 Phytostabilisation	375
	17.4.3 Rhizofiltration	375
	17.4.4 Phytovolatilization	375
	17.4.5 Phytodegradation or Phytotransformation	376
	17.4.6 Rhizodegradation/Phytostimulation	376
	17.4.7 Biotransformation of Pollutants by Plants	377
	17.5 Factors Affecting the uptake Mechanisms of Contaminants in Phytoremediation	377
	17.6 Characterization of the Textiles Dyes and Effluents After Phytoremediation	378
	17.7 Toxicity Analysis of Dye Products in Dye Effluents (Kabra et al. 2013)	379
	17.8 Various Physiochemical Factors Affecting the Phytoremediation of Textile Dyes and Effluents (Pilon-Smits 2005)	379
	17.9 Advantages Of Phytoremediation	379
	17.10 Disadvantages of Phytoremediation	380
	17.11 Conclusions	380
	18 Role of Biosurfactants in Enhancing the Microbial Degradation of Pyrene	383
	Abstract	383
	18.1 Introduction	383
	18.2 Occurrence and Physical Properties of Pyrene	384
	18.3 Toxic Effects Caused Due to Pyrene Exposure	385
	18.4 Pyrene Degradation by Single Microbial Species and Microbial Consortium	386
	18.5 Pyrene Degradation Pathway by Microbes	389
	18.6 Surfactant-Enhanced Degradation of Pyrene	389
	18.7 Conclusions and Future Scope	391
	References	391
	19 Bioremediation of Nitrate-Contaminated Wastewater and Soil	395
	Abstract	395
	19.1 Introduction	396
	19.2 Sources of Nitrate-Contaminated Wastewater	396
	19.3 Environmental and Health Concerns Due to Nitrate Contamination	397
	19.4 Technologies Available for Nitrate Removal	397
	19.5 Biological Denitrification	398
	19.6 Heterotrophic and Autotrophic Denitrification	400
	19.7 Suspended Growth Process and Fixed Film Process	401
	19.8 Denitrification Microbiology	402
	19.9 Organic Compounds for Denitrification	402
	19.10 Factors Affecting Nitrate Removal Efficiency	404
	19.10.1 Effect of Hydraulic Residence Time (HRT)	404
	19.10.2 Effect of Temperature	404
	19.10.3 Effect of Grain Size	405
	19.10.4 Effect of Dissolved Oxygen (DO)	405
	19.10.5 Effect of Initial Nitrate Concentration (C0)	406
	19.10.6 Effect of Salinity	406
	19.10.7 Effect of PH	407
	19.10.8 Effect of Other Trace Elements	407
	19.10.9 Effect of Free Ammonia Concentration	407
	19.11 Reactors for Denitrification	407
	19.12 Limitations of Denitrification	411
	19.13 Denitrification in Soil	412
	19.14 Future Scope	413
	19.15 Summary	414
	References	414
	Author Index	418