Genomics Approach to Bioremediation

About the Editors xxiii List of Contributors xxv Preface xxxiii Acknowledgements xxxix Part 1 Fundamentals of Metagenomics and Bioremediation 1 1 Application of Bioremediation for Environmental Clean-Up: Issues, Recent Developments, and the Way Forward 3 Sneha Bandyopadhyay, Vivek Rana, and Subodh Kumar Maiti 1.1 Introduction 3 1.2 Bioremediation: A Sustainable Approach 4 1.3 Importance of Vegetation for Bioremediation 8 1.4 Application of Bioremediation to Clean Up Environmental Pollutants 8 1.5 Advantages and Disadvantages of Bioremediation Technology 9 1.6 Recent Advancements in Bioremediation Technology 10 1.7 Conclusion 12 References 12 2 Omics in Biomethanation and Environmental Remediation 17 Manan Kaur Ghai, Indu Shekhar Thakur, and Shaili Srivastava 2.1 Introduction 17 2.2 Feedstocks Used 18 2.3 Microbiology and Biochemical Reactions in Anaerobic Digestions 21 2.4 Omics in Biomethanation and Bioremediation 23 2.5 Role of Factors in Anaerobic Digestions in Biomethanation 26 2.6 Inhibitory Substances for Anaerobic Digestion 28 2.7 Degradation and Bioremediation of Toxic Compounds for Enhanced Production of Biomethanation 29 2.8 Circular Economy Perspective in Biogas Production 30 2.9 Conclusion 32 References 32 3 Enzyme Immobilization: An Effective Platform to Improve the Reusability and Catalytic Efficiency of Enzymes 35 Nisha Bhardwaj, Komal Agrawal, and Pradeep Verma 3.1 Introduction 35 3.2 Immobilization of Enzymes 36 3.3 Aspects Affecting the Performance of Immobilized Enzyme 37 3.4 Factors Contributing Toward the Immobilized Enzyme Activity Enhancement 40 3.5 Immobilized Enzyme Applications 44 3.6 Conclusion 44 References 46 4 Biostimulation and Bioaugmentation: Case Studies 53 Ana Maria Queijeiro López and Amanda Lys dos Santos Silva 4.1 Introduction 53 4.2 Biostimulation 54 4.3 Bioagumentation 57 4.4 Commercially Available Bioremediation Agents 63 4.5 Conclusions 65 References 65 5 Plant Microbe Synergism for Arsenic Stress Amelioration in Crop Plants 69 Vandana Anand, Jasvinder Kaur, Sonal Srivastava, Varsha Dharmesh, Vidisha Bist, Akshita Maheshwari, Sumit Yadav, and Suchi Srivastava 5.1 Introduction 69 5.2 Distribution of Arsenic in Soil and Water 70 5.3 Methods of Arsenic Remediation 71 5.4 Arsenic-Induced Toxicity in Crop Plants 73 5.5 Arsenic Remediation Through Mineral Fertilization 74 5.6 Bioremediation 76 5.7 Plant–Microbe Interaction and Their Role in Reducing As Toxicity in Crop Plants 80 5.8 Plant–Microbe Interaction as a Boon for Arsenic Remediation 82 5.9 Microbial Methylation of Arsenic in Soil and its Reduced Uptake in Plants 83 5.10 Conclusion 85 References 85 6 Metagenomic Characterization and Applications of Microbial Surfactants in Remediation of Potentially Toxic Heavy Metals for Environmental Safety: Recent Advances and Challenges 89 Geetansh Sharma, Kirti Shyam, Saurabh Thakur, Manu Yadav, Saransh Nair, Navneet Kumar, Himani Chandel, and Gaurav Saxena 6.1 Introduction 89 6.2 Biosurfactants’ Characteristics 90 6.3 Classification of Biosurfactants 91 6.4 Screening of Microorganisms for Biosurfactants Production 96 6.5 Metagenomic Characterization of Biosurfactant-Producing Microorganisms 99 6.6 Biosynthesis of Biosurfactants 100 6.7 Characterization of Biosurfactants 101 6.8 Factors Influencing Biosurfactants Production 104 6.9 Applications of Biosurfactants in Heavy Metals Environmental Remediation 105 6.10 Challenges in Cost-Effective Production of Biosurfactants 107 6.11 Future Research Needs 110 6.12 Conclusions 110 References 111 Part 2 Metagenomics in Environmental Cleanup 125 7 Metagenomic Approaches Applied to Bioremediation of Xenobiotics 127 Júlia Ronzella Ottoni, Márcio Thomaz dos Santos Varjão, Aline Cavalcanti de Queiroz, Alysson Wagner Fernandes Duarte, and Michel Rodrigo Zambrano Passarini 7.1 Introduction 127 7.2 Metagenomic Approaches in Bioremediation Processes 129 7.3 Metagenomics in the Hydrocarbon Degradation 131 7.4 Metagenomic Approaches in the Drugs Degradation 133 7.5 Metagenomic Approaches in the Dye Degradation 134 7.6 Metagenomic Approaches in the Pesticides Degradation 135 7.7 Metagenomics in Heavy Metal Biorremediation 136 References 137 8 Omics Approaches for Microalgal Applications in Wastewater Treatment 143 Banani Ray Chowdhury, Sudip Das, Shreyan Bardhan, and Dibyajit Lahiri 8.1 Introduction 143 8.2 Concept on Microalgal Biofilms 144 8.3 Factors Influencing Nutrient Extraction and Microalgal Growth 148 8.4 Mechanism of Microalgal Remediation 148 8.5 Multi-Omics Approach 150 8.6 Conclusion 153 References 153 9 Microbial Community Profiling in Wastewater of Effluent Treatment Plant 157 Hansa Mathur, Navneet Joshi, and Sarita Khaturia 9.1 Source of Wastewater 157 9.2 Wastewater Treatment Plant 158 9.3 Wastewater Treatment Facilities Have a Wide Range of Microbial Diversity 159 9.4 Microbial Composition in WWTPs 161 9.5 Screening, Selection, and Identification of Microbial Communities 165 9.6 Health Problem for Wastewater Treatment Employees 172 9.7 Conclusion 174 9.8 Future Prospective 174 References 175 10 Mining of Novel Microbial Enzymes Using Metagenomics Approach for Efficient Bioremediation: An Overview 183 Shruti Dwivedi, Supriya Gupta, Aiman Tanveer, Gautam Anand, Sangeeta Yadav, and Dinesh Yadav 10.1 Introduction 183 10.2 Omics for Microbial Enzymes in Bioremediation 184 10.3 Implementing Metagenomics for Énvironmental Remediations 186 10.4 Metagenomics, Microbial Enzymes, and Bioremediation 189 10.5 Meta –Omics Advances for Bioremediation 192 10.6 Conclusion 194 References 195 11 Bioremediation Approaches for Genomic Microalgal Applications in Wastewater Treatment 199 N. Nirmala, S.S. Dawn, and J. Arun 11.1 Introduction 199 11.2 Implantation of Microalgae in Wastewater Treatment 200 11.3 Strategies to Enhance the Removal of Nutrients 201 11.4 Mechanism of Nitrogen and Phosphorus Removal from Wastewater 202 11.5 Biofuel Production with Simultaneous Wastewater Treatment 203 11.6 Genetic Engineering and Bioremediation Approaches 204 11.7 Bioremediation Approaches in Value-Added Products Formation 205 11.8 Economic Feasibility of Nutrient Removal Methods 206 11.9 Conclusion 206 References 207 12 Application of Microbial Enzymes in Wastewater Treatment 209 Saloni Sahal, Sarita Khaturia, and Navneet Joshi 12.1 Introduction 209 12.2 Types and Functions of Microbial Enzymes 211 12.3 Major Contaminants in Waste Water 212 12.4 Technologies Used for Enzymatic Treatment of Waste Water 216 12.5 Enzymatic Treatment Benefits 220 12.6 Conclusion 221 12.7 Future Perspectives 222 References 222 13 Microbial Biodegradation and Biotransformation of Petroleum Hydrocarbons: Progress, Prospects, and Challenges 229 Kuruvalli Gouthami, A.M.M. Mallikarjunaswamy, Ram Naresh Bhargava, Luiz Fernando Romanholo Ferreira, Abbas Rahdar, Ganesh Dattatraya Saratale, Paul Olusegun Bankole, and Sikandar I. Mulla 13.1 Introduction 229 13.2 Pollution and Toxic Effect of Petroleum Hydrocarbons 232 13.3 Taxonomic Relationships of Hydrocarbon-Utilizing Microorganisms 234 13.4 Biotransformation 235 13.5 Microbial-Mediated Remediation of Petroleum Hydrocarbons 235 13.6 Metagenomics Approaches 243 13.7 Current and Future Prospective 244 Acknowledgments 245 References 245 14 Sewage Treatment System: Recent Trends, Challenges, and Opportunities 249 Teow Yeit Haan, Ho Kah Chun, and Chien Hwa Chong 14.1 Introduction 249 14.2 Important Monitoring and Water Quality Parameters in Biological Sewage Treatment Systems 251 14.3 Biological Treatment Option for Sewage Treatment Systems 253 14.4 Challenges and Opportunities with Current Biological Sewage Treatment Processes 262 14.5 Conclusion 264 Acknowledgments 264 Abbreviation 265 References 265 15 Omics Approach in Nano-Bioremediation of Persistent Organic Pollutants 271 Jyoti, Nikita Yadav, Indu Shekhar, and Shaili Srivastava 15.1 Introduction 271 15.2 POP Into the Environment 272 15.3 Nano-bioremediation of POPs 273 15.4 Types of POPs and Their Degradation Pathways in the Environment 274 15.5 Nanomaterial Used in Thermal Degradation of Persistent Organic Pollutants 283 15.6 Conclusion 289 References 290 16 Application of Genetically Modified Microorganisms for Bioremediation of Heavy Metals from Wastewater 295 Ankita Bhatt, Jugnu Shandilya, S.K. Singal, and Sanjeev Kumar Prajapati 16.1 Introduction 295 16.2 Bioremediation 296 16.3 Genetically Modified Microorganisms (GMMs) for Bioremediation 302 16.4 GMMs for Bioremediation of Heavy Metal-Contaminated Wastewater 303 16.5 Case Studies 305 16.6 Conclusions 312 Acknowledgments 313 References 313 17 Biostimulation and Bioaugmentation of Petroleum Hydrocarbons: From Microbial Growth to Genomics 321 Isabela Karina Della-Flora, Vanessa Kristine de Oliveira Schmidt, Karina Cesca, Maikon Kelbert, Débora de Oliveira, and Cristiano José de Andrade 17.1 Introduction 321 17.2 Impact of Petroleum Hydrocarbons on Microbial Diversity 322 17.3 Genomic Approaches 323 17.4 Soil Bioremediation 328 17.5 Groundwater and Surface Water Bioremediation 332 17.6 Organic and Inorganic Amendments to Biostimulation 335 17.7 Conclusion 338 References 338 18 Omics Approach in Bioremediation of Heavy Metals (HMs) in Industrial Wastewater 343 Nikita Yadav, Jyoti, Indu Shekhar, and Shaili Srivastava 18.1 Introduction 343 18.2 Nomenclature Used 344 18.3 Heavy Metals as Pollutant Into the Water Environment: Sources and Pathways 344 18.4 Toxicity and Physio-Biochemical Effects of Heavy Metals 348 18.5 Existing Technologies for the Removal of Heavy Metals from the Environmental Matrices 350 18.6 Omics Approach in the Bioremediation of Heavy Metals 353 18.7 Nano-Bioremediation of Heavy Metals: An Emerging Approach 356 18.8 Recent Advancement and Development of Nano-Bioremediation of HMs 356 18.9 Conclusion 358 References 358 Part 3 Recent Trends and Future Outlook in Metagenomics to Bioremediation 363 19 CRISPR/Cas Editing in Relation to Phytoremediation: Progress and Prospects 365 Satarupa Dey, Uttpal Anand, Devendra Kumar Pandey, Mimosa Ghorai, Mahipal S.Shekhawat, Muddasarul Hoda, Potshangbam Nongdam, and Abhijit Dey 19.1 Introduction 365 19.2 Conventional Molecular Tools for Creating Genetically Modified Plants 366 19.3 CRISPR-Mediated Gene Editing Technique 367 19.4 Target Genes of CRISPR-Mediated Genetic Modification 368 19.5 CRISPR-Mediated Strategies for Phytoremediation 370 19.6 Role CRISPR-Mediated Strategies in Generating Stress Tolerant Plants 371 19.7 Concluding Remarks and Future Perspectives 372 References 372 20 Biosensors as a Principal Tool for Bioremediation Monitoring 379 Simranjeet Singh, Monika Thakur, Daljeet Singh Dhanjal, Ruby Angurana, Dhriti Kapoor, Vaidehi Katoch, Tunisha Verma, Joginder Singh, and Praveen C. Ramamurthy 20.1 Introduction 379 20.2 Types of Biosensors 380 20.3 Biochemical Potential and Working of Different Biosensors 383 20.4 Analysis Systems of Biosensors for Bioremediation Detection 384 20.5 Using Biosensors to Detect Biochemical Potentials 384 20.6 Biosensors 386 20.7 Molecular-Based Methods 386 20.8 Biosensors Based on Enzymes 387 20.9 Bioaffinity-Based Biosensors 387 20.10 Monitoring Bioremediation 387 20.11 Parameters Monitored During Bioremediation 388 20.12 Chemical Parameters 388 20.13 Biological Parameters 388 20.14 Toxicity Assessment 389 20.15 Online Monitoring of Bioremediation 389 20.16 Conclusion 389 Acknowledgment 390 References 390 21 Integration of Pathway Analysis as a Powerful Tool for Microbial Remediation of Pollutants 397 Parul Johri, Aditi Singh, Mala Trivedi, and Sachidanand Singh 21.1 Introduction 397 21.2 Microbial Approaches for Remediation of Pollutants 398 21.3 Integration of Genetic and Metabolic Engineering in Remediation Process 399 21.4 Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology 403 21.5 Using Bacteria as Whole Cell Bacterial Catalysis 407 21.6 Ecological Safety and Risk Assessment 409 21.7 Future Perspective and Challenges 410 21.8 Conclusion 411 References 412 22 Oxidative Catalytic Potential of Lignin-Modifying Enzymes in the Treatment of Emerging Contaminants 417 Sthefany Araujo Bomfim, Gabriela Pereira Barros, Ram Naresh Bharagava, Vineet Kumar, Katlin Ivon Barrios Eguiluz, and Luiz Fernando Romanholo Ferreira 22.1 Introduction 417 22.2 Ligninolytic Enzymes 418 22.3 Conclusion and Perspectives 425 References 425 23 Omics Technologies in Environmental Microbiology and Microbial Ecology: Insightful Applications in Bioremediation Research 433 Kirti Shyam, Navneet Kumar, Himani Chandel, Abhinav Singh Dogra, Geetansh Sharma, and Gaurav Saxena 23.1 Introduction 433 23.2 Basics of Bioremediation 434 23.3 Limitations of Conventional Molecular Sequencing Technologies 437 23.4 Omics Technologies: An Overview 437 23.5 Applications of Omics in Bioremediation Research 440 23.6 Computational, Bioinformatics, and Biostatistics Tools in Omics Approaches 444 23.7 Challenges and Opportunities 448 23.8 Conclusions 449 References 449 24 Bioinformatics and Its Contribution to Bioremediation and Genomics: Recent Trends and Advancement 455 Sonal Nigam and Surbhi Sinha 24.1 Introduction 455 24.2 Bioinformatics Tools for Bioremediation 456 24.3 Application of Omics Technology in Bioremediation 462 24.4 Conclusion 464 References 464 25 Genetically Modified Bacteria for Arsenic Bioremediation 467 Sougata Ghosh and Bishwarup Sarkar 25.1 Introduction 467 25.2 Genetically Modified Bacteria for Arsenic Bioremediation 468 25.3 Conclusions and Future Perspectives 481 References 481 26 Proteomics and Bioremediation Using Prokaryotes 485 Ana Maria Queijeiro López and Amanda Lys dos Santos Silva 26.1 Introduction 485 26.2 Prokaryotic Membranes, Proteins, and Adaptation to Biodegradation Dynamics 486 26.3 Stimuli to Biodegradation 488 26.4 Protein Contribution of Subcellular Components to Biodegradation 489 26.5 Expression of Proteins and Proteomic Steps 491 26.6 Strategies for Identifying and Quantifying Proteins by Mass Spectrometry (MS) 493 26.7 Posttranslational Modifications of Proteins 495 26.8 Improvements Required to Proteomic Techniques 497 26.9 Conclusions 499 References 499 Index 503