Bioremediation of Environmental Pollutants: Emerging Trends and Strategies

Preface
Contents
Chapter 1: Waste Management: Challenges and Opportunities
	1.1 Introduction
	1.2 Classification of the Solid Waste
	1.3 Solid Waste Status and Problems
	1.4 Solid Waste Management
		1.4.1 Collection
		1.4.2 Segregation and Secondary Storage
		1.4.3 Transportation
		1.4.4 Treatment
			1.4.4.1 Landfill
			1.4.4.2 Incineration
			1.4.4.3 Pyrolysis
			1.4.4.4 Gasification
			1.4.4.5 Recycling
			1.4.4.6 Pulverization
			1.4.4.7 Mechanical Biological Treatment
		1.4.5 Final Disposal
	1.5 Circular Economy and 9 R´s Principle
	1.6 Solid Waste as a Resource: Seeking Opportunities
		1.6.1 Solid Waste as a Fuel
		1.6.2 Solid Waste as Construction Materials
		1.6.3 Geopolymer
		1.6.4 Biogas
		1.6.5 Compositing
		1.6.6 Plasma Arc Recycling
	1.7 Challenges
		1.7.1 Population
		1.7.2 Consumerism
		1.7.3 Plastic Production
		1.7.4 Growing Waste Management Cost
		1.7.5 Poor Waste Management Facilities
		1.7.6 Lack of Legal and Basic Framework
		1.7.7 Impact of Pandemic
	1.8 Status of Waste Management in India
	1.9 Conclusion
	References
Chapter 2: Microbes Assisted Bioremediation: A Green Technology to Remediate Pollutants
	2.1 Introduction
	2.2 Bioremediation and Its Methods
		2.2.1 Biostimulation
		2.2.2 Bioaugmentation
		2.2.3 Bioattenutaion
		2.2.4 Biosparging
		2.2.5 Bioventing
	2.3 Mechanism of Microbial Bioremediation
	2.4 Applications of Microbial Bioremediation
		2.4.1 Remediation of Heavy Metals by Microbes
			2.4.1.1 Mechanism of Heavy Metals Detoxification by Microbes
		2.4.2 Treatment of Solid, Liquid and Gaseous Waste
			2.4.2.1 Microbial Degradation of Solid Waste
			2.4.2.2 Microbial Degradation of Liquid Waste
		2.4.3 Microbial Degradation of Hydrocarbons
		2.4.4 Microbial Bioremediation of Dyes
		2.4.5 Microbial Bioremediation of Agricultural Chemicals
	2.5 Genetic Engineering of Microbial Cultures for Environmental Pollution Regulation
	2.6 Conclusion and Future Prospective
	References
Chapter 3: Microbial Fuel Cells for Wastewater Treatment
	3.1 Introduction
	3.2 Characteristics of the MFCs
	3.3 Types of Microbial Fuel Cells
		3.3.1 Single Chambered MFC or Air-Cathode MFC
		3.3.2 Two-Chambered MFC
		3.3.3 Benthic MFC (BMFC)
		3.3.4 Stacked MFC (SFMC)
	3.4 Principles of Waste Management by the Use of Microbial Fuel Cells
	3.5 Advantages of MFCs
	3.6 MFCs in Wastewater Management
	3.7 Redox Reactions in MFCs (Metabolic Mechanism)
		3.7.1 Metabolism in the Anode Chamber
		3.7.2 Metabolism in Cathode Chamber
			3.7.2.1 Abiotic Cathodes
			3.7.2.2 Biocathodes
			3.7.2.3 Reaction in Biocathode Chamber (Reduction Reaction)
			3.7.2.4 Performance of Microbial Fuel Cells in Agriculture Wastewater Management
	3.8 Organic Substrate Removal by MFCs
	3.9 Removal of Nitrogen and Phosphorous in MFCs
	3.10 Removal of Heavy Metals by MFCs
	3.11 Current Difficulties in Microbial Fuel Cells
		3.11.1 COD Expulsion Rates
		3.11.2 Low Power Densities
		3.11.3 Biocathode and Air Cathode Advancement
		3.11.4 Integration with Other Valuable Cycles
	3.12 Cost Analysis in Microbial Fuel Cells
	3.13 Conclusion and Future Perspectives
	References
Chapter 4: Critical Process Parameters and Their Optimization Strategies for Enhanced Bioremediation
	4.1 Introduction
	4.2 Optimization Approaches in Environmental Bioremediation Processes
		4.2.1 In-situ Bioremediation Processes Optimization
			4.2.1.1 Phytoremediation
			4.2.1.2 Bioaugmentation
			4.2.1.3 Biostimulation
		4.2.2 Ex-situ Bioremediation Processes Optimization
			4.2.2.1 Bioremediation in Bioreactor
			4.2.2.2 Biosorption
			4.2.2.3 Enzymatic Bioremediation
	4.3 Concluding Remarks
	References
Chapter 5: Microbial Biosensors for Real-Time Monitoring of the Bioremediation Processes
	5.1 Bioremediation: An Eco-friendly Tool for Environmental Rehabilitation
	5.2 Quantification of Pollutant Degradation by Non-microbial Tools
	5.3 Limitations Associated with Conventional Monitoring Techniques
	5.4 Eco-toxicity Assessment
	5.5 Biosensors as a Powerful and Innovative Analytical Tool
		5.5.1 Design and Fabrication of a Microbial Biosensor
		5.5.2 Host Strain
		5.5.3 Reporter Genes
		5.5.4 Regulatory Proteins
		5.5.5 Microbial Immobilization Techniques
	5.6 Diversity of Microbial Biosensors
		5.6.1 Electrochemical Microbial Biosensors
			5.6.1.1 Types of Electrochemical Biosensors
			5.6.1.2 Application of Electrochemical Biosensors in Environmental Monitoring
		5.6.2 Optical Microbial Biosensors
			5.6.2.1 Bioluminescent Microbial Biosensors
			5.6.2.2 Fluorescent Microbial Biosensors
			5.6.2.3 Colourimetric Microbial Biosensors
			5.6.2.4 Optical Microbial Biosensors in Environmental Monitoring
		5.6.3 Microbial Fuel-Cell Type Biosensors
			5.6.3.1 Microbial Fuel-Cell Biosensors in Environmental Monitoring
	5.7 Advantages, Limitations and Future Challenges of Biosensors
		5.7.1 Environmental Safety Concerns
		5.7.2 Non-target Interaction and Poor Signal Quality
		5.7.3 Reliance on Genetic Manipulation When Designing
		5.7.4 The High Cost of Development and Maintenance
	5.8 Future of Microbial Biosensors
	References
Chapter 6: Recent Advancements in Mycoremediation
	6.1 Introduction
	6.2 Impact of the Agrochemicals on the Ecosystem
		6.2.1 Eutrophication and Algal Blooms in the Lakes
	6.3 Mycoremediation of Pesticides
	6.4 Mycoremediation of Herbicides
	6.5 Mycoremediation of Heavy Metals
		6.5.1 Toxicity of Heavy Metals
		6.5.2 Remediation of Heavy Metals by Fungi
		6.5.3 Mycoremediation of Hydrocarbon Pollution
	6.6 Petroleum Biodegradation by Fungi
	6.7 Myconanoparticles
	6.8 Biodegradation in Soils by Fungi
	6.9 Conclusions
	References
Chapter 7: Genetically Modified Organisms for Bioremediation: Current Research and Advancements
	7.1 Introduction
	7.2 Bioremediation
	7.3 Bioremediation by Extremophilic Organisms
	7.4 Designer Organisms for a Cleaner Tomorrow
		7.4.1 Gene Transfer
		7.4.2 Genetic Mutations Improve Biodegradation of Pollutants
		7.4.3 Genetically Engineered Enzymes in Bioremediation
		7.4.4 Genetically Modified Plants for Improved Phytoremediation
	7.5 Impact and Challenges of Using Genetically Modified Organisms for Bioremediation
	7.6 Future Perspectives
	References
Chapter 8: Understanding the Role of Genetic and Protein Networking Involved in Microbial Bioremediation
	8.1 Introduction
	8.2 Unraveling the Potential of Culturable Microorganism
		8.2.1 Genomic Approaches
			8.2.1.1 Understanding Phylogeny Through 16S rRNA
			8.2.1.2 Mining the Physiology Through Whole Genome Sequencing
			8.2.1.3 Applying Omics in Bioremediation
		8.2.2 Transcriptomics
		8.2.3 Proteomics
			8.2.3.1 Tracing the Developments on Bioremediation Using Proteomics Tools
		8.2.4 Interactomics
	8.3 Metaomics for Unraveling the Unculturable Microorganism
		8.3.1 Metagenomics
			8.3.1.1 Case Studies of Metagenomic Approaches for Bioremediation
			8.3.1.2 Tools Involved in Metagenomic Approach
		8.3.2 Metatranscriptomics
		8.3.3 Metaproteomics
	8.4 Metabolomics and Fluxomics
	8.5 Prediction and Reconstruction of Bioremediation Pathways
	8.6 In-Silico Tools Used for Pathway Reconstruction
	8.7 Gene Editing
	8.8 Synthetic Biology for Application in Bioremediation
	8.9 Future Prospects
	8.10 Conclusion
	References
Chapter 9: In Silico Approaches in Bioremediation Research and Advancements
	9.1 Introduction
	9.2 Microbes and Plants: An Asset in Bioremediation
	9.3 Environmental Factors Affecting Microbes and Plants
	9.4 Omics Experimentation for Bioremediation
		9.4.1 In Silico Analysis of Omics Data and Their Integration for Bioremediation
			9.4.1.1 Genome Assembly and Data Analysis
			9.4.1.2 16S rRNA Based Approach in Bioremediation
			9.4.1.3 Transcriptome Data Analysis
			9.4.1.4 Proteomics Data Analysis
			9.4.1.5 Metabolomics Data Analysis
			9.4.1.6 NMR Spectroscopy and Metabolite Profiling During Bioremediation
		9.4.2 Computational Systems Biology for Omics Data Integration and Novel Discovery
		9.4.3 Pathway Modeling
		9.4.4 Network Analysis
		9.4.5 Target Structure Modeling, Validation and Visualization
		9.4.6 Molecular Docking, Virtual Screening and Molecular Dynamics Simulation
	9.5 Development of In Silico Platforms for Bioremediation Research
		9.5.1 Database Development
		9.5.2 Software/Tool Development
	9.6 Limitation of In Silico Approaches
	9.7 Future Prospects
	9.8 Conclusion
	References
Chapter 10: Modern Landfilling Approaches for Waste Disposal and Management
	10.1 Introduction
	10.2 Solid Waste Composition
	10.3 Management of Solid Waste
		10.3.1 Decentralization of MSWs Management
		10.3.2 Separation of MSWs at Sites
		10.3.3 Disinfected and Secure Management of MSWs
		10.3.4 Combustible Gases from Landfills
		10.3.5 Soil Salinity from Compost Application
	10.4 Sustainable Landfill Management
	10.5 Optional Marketing of Products from MSWs
	10.6 Application of ``Pay as You Throw´´ Scheme
	10.7 Conclusion
	References
Chapter 11: Aerobic Granular Technology: Current Perspective and Developments
	11.1 Introduction
	11.2 What Is Aerobic Granular Sludge?
	11.3 Granule Formation and Characterization
		11.3.1 Granule Formation
			11.3.1.1 Seed Sludge
			11.3.1.2 Feed Composition
			11.3.1.3 SBR Operation
		11.3.2 Granule Characterization
			11.3.2.1 Physical Parameters
			11.3.2.2 Chemical Parameters
			11.3.2.3 Biological Parameters
	11.4 Mechanism of Aerobic Granulation
	11.5 Applications of Aerobic Granulation Technology
		11.5.1 Nutrient Removal by Aerobic Granules
		11.5.2 Degradation of Pollutants
		11.5.3 Heavy Metal Elimination Using Aerobic Granules
		11.5.4 Wastewater/Sewage Treatment
	11.6 Challenges Ahead
	11.7 Future Prospects
	11.8 Conclusion
	References
Chapter 12: Recent Perspectives of Immobilized Enzyme Reactors Used for Wastewater Treatment
	12.1 Introduction
	12.2 Modes of Immobilization
	12.3 Enzyme Reactors
		12.3.1 Batch Mode Reactor
		12.3.2 Continuous Mode Reactor
		12.3.3 Membrane Reactor (MR)
	12.4 Factors Important for Choosing Immobilized Enzyme Reactors
	12.5 Conclusions
	References
Chapter 13: Role of Chelating Compounds in Biodegradation and Bioremediation
	13.1 Introduction
	13.2 Chelator-Assisted Phytoextraction
		13.2.1 Natural Chelating Agents
			13.2.1.1 Aminopolycarboxylates as Chelating Agents
				Nitrilotriacetic Acid (NTA)
				Ethylenediaminedisuccinic Acid (EDDS)
			13.2.1.2 Low Molecular Weight Organic Acids as Chelating Agents
				Citric Acid
				Tartaric Acid
				Oxalic Acid
		13.2.2 Synthetic Chelating Agents
			13.2.2.1 Aminopolycarboxylic Acids as Chelating Agents
				Ethylenediaminetetraacetic Acid (EDTA)
				Diethylenetriaminepentaacetic Acid (DTPA)
	13.3 Soil Washing Using Chelating Agents
	13.4 Chelant Enhanced Electrokinetic Extraction
	13.5 Conclusion
	References
Chapter 14: Spectroscopy and Its Advancements for Environmental Sustainability
	14.1 Introduction
	14.2 UV-Visible (UV/VIS) Spectroscopy
	14.3 Applications of UV-Vis Spectroscopy
	14.4 NMR Spectroscopy
		14.4.1 Solution-State NMR
		14.4.2 Solid-State NMR
		14.4.3 High-Resolution Magic Angle Spinning NMR
		14.4.4 Comprehensive Multiphase NMR
		14.4.5 Hyphenated NMR
		14.4.6 Low Field NMR
		14.4.7 Magnetic Resonance Imaging (MRI)
	14.5 Study of Non-covalent Interaction
	14.6 Study of Metabolite
	14.7 X-Ray Fluorescence (XRF)
		14.7.1 Use of XRF in Environmental Application
		14.7.2 Detection of Heavy Metals in Water by XRF
	14.8 Inductively Coupled Plasma (ICP)
		14.8.1 Application of ICP-MS in Environments
	14.9 Future Perspectives
	14.10 Conclusion
	References
Chapter 15: Role of Biochar in Wastewater Treatment and Sustainability
	15.1 Introduction
	15.2 Organic Contaminants
	15.3 Inorganic Contaminants
	15.4 Application of Biochar for Wastewater Treatment
	15.5 Removal of the Pesticides by Biochar
	15.6 Biochar for Heavy Metal Contaminated Soils
	15.7 Mechanism of Removal of Contaminants by Modified Biochar
	15.8 Conclusion
	References
Chapter 16: Bio-inoculants for Biodegradation and Bioconversion of Agrowaste: Status and Prospects
	16.1 Introduction
	16.2 Agro-Waste
		16.2.1 Crop Waste
		16.2.2 Animal Waste
	16.3 Biodegradation of Agrowaste
		16.3.1 Enzymes Responsible for Biodegradation
	16.4 Bioinoculants for Biodegradation and Bioconversion of Agro Waste
		16.4.1 Importance of Bio-inoculants in Agrowaste Degradation
		16.4.2 Renewable Energy Generation
			16.4.2.1 Bioethanol Production
			16.4.2.2 Biogas Production
		16.4.3 Compost Production
	16.5 Conclusion
	References
Chapter 17: Biochemical Parameters and Their Optimization Strategies for Microbial Bioremediation of Wastewater
	17.1 Introduction
	17.2 Factors Affecting Microbial Growth and Bioremediation Process
		17.2.1 Nutrient/Substrate Content
		17.2.2 Temperature
		17.2.3 pH
		17.2.4 Oxygen Level
		17.2.5 Enzymes
	17.3 Process Optimization
	17.4 Bioremediation Process Optimization
	17.5 Conclusion and Future Perspectives
	References
Chapter 18: Advanced Molecular Technologies for Environmental Restoration and Sustainability
	18.1 Introduction
	18.2 Genomic Methods
	18.3 Specific Genotyping Methodologies
		18.3.1 Fingerprinting-Based Methodologies
		18.3.2 Sequence-Based Methodologies
	18.4 The Genomic Future
	18.5 Proteomics Technologies in Bacterial Identification and Characterization
		18.5.1 Mass Spectrometry-Based Bacterial Characterization and Identification
			18.5.1.1 Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry
			18.5.1.2 Electrospray Ionization Mass Spectrometry
			18.5.1.3 Surface-Enhanced Laser Desorption/Ionization
		18.5.2 Gel-Based Method
			18.5.2.1 Two-Dimensional Gel Electrophoresis (2DE)
	18.6 Databases
	18.7 Conclusion
	References