Genomics Approach to Bioremediation

Vineet Kumar is an Assistant Professor in the School of Engineering & Sciences at GD Goenka University, Gurugram, Haryana, India. He has published more than 110 scientific contributions in various fields of science and engineering, including bioremediation, phytoremediation, metagenomics, wastewater treatment, environmental monitoring, and waste management. Muhammad Bilal is an Assistant Professor in the Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Poznan, Poland. He has published widely in areas such as environmental biotechnology, environmental bioengineering, nanotechnology, bio-catalysis, enzyme engineering, and bioremediation of hazardous and emerging pollutants. Luiz Fernando Romanholo Ferreira is an Associate Professor at Tiradentes University and a researcher at the Institute for Technology and Research (ITP), Brazil. Dr. Ferreira serves on the editorial board of the World Journal of Microbiology and Biotechnology and is a Review Editor for Frontiers in Microbiology. Hafiz M.N. Iqbal is a Professor in the School of Engineering and Sciences at Tecnologico de Monterrey, Mexico. Dr. Iqbal’s research group is engaged in environmental engineering, bioengineering, biomedical engineering, materials science, enzyme engineering, bio catalysis, bioremediation, algal biotechnology, and applied biotechnology research.

• About the Editors xxiiiList of Contributors xxvPreface xxxiiiAcknowledgements xxxixPart 1 Fundamentals of Metagenomics and Bioremediation 11 Application of Bioremediation for Environmental Clean-Up: Issues, Recent Developments, and the Way Forward 3Sneha Bandyopadhyay, Vivek Rana, and Subodh Kumar Maiti1.1 Introduction 31.2 Bioremediation: A Sustainable Approach 41.3 Importance of Vegetation for Bioremediation 81.4 Application of Bioremediation to Clean Up Environmental Pollutants 81.5 Advantages and Disadvantages of Bioremediation Technology 91.6 Recent Advancements in Bioremediation Technology 101.7 Conclusion 12References 122 Omics in Biomethanation and Environmental Remediation 17Manan Kaur Ghai, Indu Shekhar Thakur, and Shaili Srivastava2.1 Introduction 172.2 Feedstocks Used 182.3 Microbiology and Biochemical Reactions in Anaerobic Digestions 212.4 Omics in Biomethanation and Bioremediation 232.5 Role of Factors in Anaerobic Digestions in Biomethanation 262.6 Inhibitory Substances for Anaerobic Digestion 282.7 Degradation and Bioremediation of Toxic Compounds for Enhanced Production of Biomethanation 292.8 Circular Economy Perspective in Biogas Production 302.9 Conclusion 32References 323 Enzyme Immobilization: An Effective Platform to Improve the Reusability and Catalytic Efficiency of Enzymes 35Nisha Bhardwaj, Komal Agrawal, and Pradeep Verma3.1 Introduction 353.2 Immobilization of Enzymes 363.3 Aspects Affecting the Performance of Immobilized Enzyme 373.4 Factors Contributing Toward the Immobilized Enzyme Activity Enhancement 403.5 Immobilized Enzyme Applications 443.6 Conclusion 44References 464 Biostimulation and Bioaugmentation: Case Studies 53Ana Maria Queijeiro López and Amanda Lys dos Santos Silva4.1 Introduction 534.2 Biostimulation 544.3 Bioagumentation 574.4 Commercially Available Bioremediation Agents 634.5 Conclusions 65References 655 Plant Microbe Synergism for Arsenic Stress Amelioration in Crop Plants 69Vandana Anand, Jasvinder Kaur, Sonal Srivastava, Varsha Dharmesh, Vidisha Bist, Akshita Maheshwari, Sumit Yadav, and Suchi Srivastava5.1 Introduction 695.2 Distribution of Arsenic in Soil and Water 705.3 Methods of Arsenic Remediation 715.4 Arsenic-Induced Toxicity in Crop Plants 735.5 Arsenic Remediation Through Mineral Fertilization 745.6 Bioremediation 765.7 Plant–Microbe Interaction and Their Role in Reducing As Toxicity in Crop Plants 805.8 Plant–Microbe Interaction as a Boon for Arsenic Remediation 825.9 Microbial Methylation of Arsenic in Soil and its Reduced Uptake in Plants 835.10 Conclusion 85References 856 Metagenomic Characterization and Applications of Microbial Surfactants in Remediation of Potentially Toxic Heavy Metals for Environmental Safety: Recent Advances and Challenges 89Geetansh Sharma, Kirti Shyam, Saurabh Thakur, Manu Yadav, Saransh Nair, Navneet Kumar, Himani Chandel, and Gaurav Saxena6.1 Introduction 896.2 Biosurfactants’ Characteristics 906.3 Classification of Biosurfactants 916.4 Screening of Microorganisms for Biosurfactants Production 966.5 Metagenomic Characterization of Biosurfactant-Producing Microorganisms 996.6 Biosynthesis of Biosurfactants 1006.7 Characterization of Biosurfactants 1016.8 Factors Influencing Biosurfactants Production 1046.9 Applications of Biosurfactants in Heavy Metals Environmental Remediation 1056.10 Challenges in Cost-Effective Production of Biosurfactants 1076.11 Future Research Needs 1106.12 Conclusions 110References 111Part 2 Metagenomics in Environmental Cleanup 1257 Metagenomic Approaches Applied to Bioremediation of Xenobiotics 127Júlia Ronzella Ottoni, Márcio Thomaz dos Santos Varjão, Aline Cavalcanti de Queiroz, Alysson Wagner Fernandes Duarte, and Michel Rodrigo Zambrano Passarini7.1 Introduction 1277.2 Metagenomic Approaches in Bioremediation Processes 1297.3 Metagenomics in the Hydrocarbon Degradation 1317.4 Metagenomic Approaches in the Drugs Degradation 1337.5 Metagenomic Approaches in the Dye Degradation 1347.6 Metagenomic Approaches in the Pesticides Degradation 1357.7 Metagenomics in Heavy Metal Biorremediation 136References 1378 Omics Approaches for Microalgal Applications in Wastewater Treatment 143Banani Ray Chowdhury, Sudip Das, Shreyan Bardhan, and Dibyajit Lahiri8.1 Introduction 1438.2 Concept on Microalgal Biofilms 1448.3 Factors Influencing Nutrient Extraction and Microalgal Growth 1488.4 Mechanism of Microalgal Remediation 1488.5 Multi-Omics Approach 1508.6 Conclusion 153References 1539 Microbial Community Profiling in Wastewater of Effluent Treatment Plant 157Hansa Mathur, Navneet Joshi, and Sarita Khaturia9.1 Source of Wastewater 1579.2 Wastewater Treatment Plant 1589.3 Wastewater Treatment Facilities Have a Wide Range of Microbial Diversity 1599.4 Microbial Composition in WWTPs 1619.5 Screening, Selection, and Identification of Microbial Communities 1659.6 Health Problem for Wastewater Treatment Employees 1729.7 Conclusion 1749.8 Future Prospective 174References 17510 Mining of Novel Microbial Enzymes Using Metagenomics Approach for Efficient Bioremediation: An Overview 183Shruti Dwivedi, Supriya Gupta, Aiman Tanveer, Gautam Anand, Sangeeta Yadav, and Dinesh Yadav10.1 Introduction 18310.2 Omics for Microbial Enzymes in Bioremediation 18410.3 Implementing Metagenomics for Énvironmental Remediations 18610.4 Metagenomics, Microbial Enzymes, and Bioremediation 18910.5 Meta –Omics Advances for Bioremediation 19210.6 Conclusion 194References 19511 Bioremediation Approaches for Genomic Microalgal Applications in Wastewater Treatment 199N. Nirmala, S.S. Dawn, and J. Arun11.1 Introduction 19911.2 Implantation of Microalgae in Wastewater Treatment 20011.3 Strategies to Enhance the Removal of Nutrients 20111.4 Mechanism of Nitrogen and Phosphorus Removal from Wastewater 20211.5 Biofuel Production with Simultaneous Wastewater Treatment 20311.6 Genetic Engineering and Bioremediation Approaches 20411.7 Bioremediation Approaches in Value-Added Products Formation 20511.8 Economic Feasibility of Nutrient Removal Methods 20611.9 Conclusion 206References 20712 Application of Microbial Enzymes in Wastewater Treatment 209Saloni Sahal, Sarita Khaturia, and Navneet Joshi12.1 Introduction 20912.2 Types and Functions of Microbial Enzymes 21112.3 Major Contaminants in Waste Water 21212.4 Technologies Used for Enzymatic Treatment of Waste Water 21612.5 Enzymatic Treatment Benefits 22012.6 Conclusion 22112.7 Future Perspectives 222References 22213 Microbial Biodegradation and Biotransformation of Petroleum Hydrocarbons: Progress, Prospects, and Challenges 229Kuruvalli Gouthami, A.M.M. Mallikarjunaswamy, Ram Naresh Bhargava, Luiz Fernando Romanholo Ferreira, Abbas Rahdar, Ganesh Dattatraya Saratale, Paul Olusegun Bankole, and Sikandar I. Mulla13.1 Introduction 22913.2 Pollution and Toxic Effect of Petroleum Hydrocarbons 23213.3 Taxonomic Relationships of Hydrocarbon-Utilizing Microorganisms 23413.4 Biotransformation 23513.5 Microbial-Mediated Remediation of Petroleum Hydrocarbons 23513.6 Metagenomics Approaches 24313.7 Current and Future Prospective 244Acknowledgments 245References 24514 Sewage Treatment System: Recent Trends, Challenges, and Opportunities 249Teow Yeit Haan, Ho Kah Chun, and Chien Hwa Chong14.1 Introduction 24914.2 Important Monitoring and Water Quality Parameters in Biological Sewage Treatment Systems 25114.3 Biological Treatment Option for Sewage Treatment Systems 25314.4 Challenges and Opportunities with Current Biological Sewage Treatment Processes 26214.5 Conclusion 264Acknowledgments 264Abbreviation 265References 26515 Omics Approach in Nano-Bioremediation of Persistent Organic Pollutants 271Jyoti, Nikita Yadav, Indu Shekhar, and Shaili Srivastava15.1 Introduction 27115.2 POP Into the Environment 27215.3 Nano-bioremediation of POPs 27315.4 Types of POPs and Their Degradation Pathways in the Environment 27415.5 Nanomaterial Used in Thermal Degradation of Persistent Organic Pollutants 28315.6 Conclusion 289References 29016 Application of Genetically Modified Microorganisms for Bioremediation of Heavy Metals from Wastewater 295Ankita Bhatt, Jugnu Shandilya, S.K. Singal, and Sanjeev Kumar Prajapati16.1 Introduction 29516.2 Bioremediation 29616.3 Genetically Modified Microorganisms (GMMs) for Bioremediation 30216.4 GMMs for Bioremediation of Heavy Metal-Contaminated Wastewater 30316.5 Case Studies 30516.6 Conclusions 312Acknowledgments 313References 31317 Biostimulation and Bioaugmentation of Petroleum Hydrocarbons: From Microbial Growth to Genomics 321Isabela Karina Della-Flora, Vanessa Kristine de Oliveira Schmidt, Karina Cesca, Maikon Kelbert, Débora de Oliveira, and Cristiano José de Andrade17.1 Introduction 32117.2 Impact of Petroleum Hydrocarbons on Microbial Diversity 32217.3 Genomic Approaches 32317.4 Soil Bioremediation 32817.5 Groundwater and Surface Water Bioremediation 33217.6 Organic and Inorganic Amendments to Biostimulation 33517.7 Conclusion 338References 33818 Omics Approach in Bioremediation of Heavy Metals (HMs) in Industrial Wastewater 343Nikita Yadav, Jyoti, Indu Shekhar, and Shaili Srivastava18.1 Introduction 34318.2 Nomenclature Used 34418.3 Heavy Metals as Pollutant Into the Water Environment: Sources and Pathways 34418.4 Toxicity and Physio-Biochemical Effects of Heavy Metals 34818.5 Existing Technologies for the Removal of Heavy Metals from the Environmental Matrices 35018.6 Omics Approach in the Bioremediation of Heavy Metals 35318.7 Nano-Bioremediation of Heavy Metals: An Emerging Approach 35618.8 Recent Advancement and Development of Nano-Bioremediation of HMs 35618.9 Conclusion 358References 358Part 3 Recent Trends and Future Outlook in Metagenomics to Bioremediation 36319 CRISPR/Cas Editing in Relation to Phytoremediation: Progress and Prospects 365Satarupa Dey, Uttpal Anand, Devendra Kumar Pandey, Mimosa Ghorai, Mahipal S.Shekhawat, Muddasarul Hoda, Potshangbam Nongdam, and Abhijit Dey19.1 Introduction 36519.2 Conventional Molecular Tools for Creating Genetically Modified Plants 36619.3 CRISPR-Mediated Gene Editing Technique 36719.4 Target Genes of CRISPR-Mediated Genetic Modification 36819.5 CRISPR-Mediated Strategies for Phytoremediation 37019.6 Role CRISPR-Mediated Strategies in Generating Stress Tolerant Plants 37119.7 Concluding Remarks and Future Perspectives 372References 37220 Biosensors as a Principal Tool for Bioremediation Monitoring 379Simranjeet Singh, Monika Thakur, Daljeet Singh Dhanjal, Ruby Angurana, Dhriti Kapoor, Vaidehi Katoch, Tunisha Verma, Joginder Singh, and Praveen C. Ramamurthy20.1 Introduction 37920.2 Types of Biosensors 38020.3 Biochemical Potential and Working of Different Biosensors 38320.4 Analysis Systems of Biosensors for Bioremediation Detection 38420.5 Using Biosensors to Detect Biochemical Potentials 38420.6 Biosensors 38620.7 Molecular-Based Methods 38620.8 Biosensors Based on Enzymes 38720.9 Bioaffinity-Based Biosensors 38720.10 Monitoring Bioremediation 38720.11 Parameters Monitored During Bioremediation 38820.12 Chemical Parameters 38820.13 Biological Parameters 38820.14 Toxicity Assessment 38920.15 Online Monitoring of Bioremediation 38920.16 Conclusion 389Acknowledgment 390References 39021 Integration of Pathway Analysis as a Powerful Tool for Microbial Remediation of Pollutants 397Parul Johri, Aditi Singh, Mala Trivedi, and Sachidanand Singh21.1 Introduction 39721.2 Microbial Approaches for Remediation of Pollutants 39821.3 Integration of Genetic and Metabolic Engineering in Remediation Process 39921.4 Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology 40321.5 Using Bacteria as Whole Cell Bacterial Catalysis 40721.6 Ecological Safety and Risk Assessment 40921.7 Future Perspective and Challenges 41021.8 Conclusion 411References 41222 Oxidative Catalytic Potential of Lignin-Modifying Enzymes in the Treatment of Emerging Contaminants 417Sthefany Araujo Bomfim, Gabriela Pereira Barros, Ram Naresh Bharagava, Vineet Kumar, Katlin Ivon Barrios Eguiluz, and Luiz Fernando Romanholo Ferreira22.1 Introduction 41722.2 Ligninolytic Enzymes 41822.3 Conclusion and Perspectives 425References 42523 Omics Technologies in Environmental Microbiology and Microbial Ecology: Insightful Applications in Bioremediation Research 433Kirti Shyam, Navneet Kumar, Himani Chandel, Abhinav Singh Dogra, Geetansh Sharma, and Gaurav Saxena23.1 Introduction 43323.2 Basics of Bioremediation 43423.3 Limitations of Conventional Molecular Sequencing Technologies 43723.4 Omics Technologies: An Overview 43723.5 Applications of Omics in Bioremediation Research 44023.6 Computational, Bioinformatics, and Biostatistics Tools in Omics Approaches 44423.7 Challenges and Opportunities 44823.8 Conclusions 449References 44924 Bioinformatics and Its Contribution to Bioremediation and Genomics: Recent Trends and Advancement 455Sonal Nigam and Surbhi Sinha24.1 Introduction 45524.2 Bioinformatics Tools for Bioremediation 45624.3 Application of Omics Technology in Bioremediation 46224.4 Conclusion 464References 46425 Genetically Modified Bacteria for Arsenic Bioremediation 467Sougata Ghosh and Bishwarup Sarkar25.1 Introduction 46725.2 Genetically Modified Bacteria for Arsenic Bioremediation 46825.3 Conclusions and Future Perspectives 481References 48126 Proteomics and Bioremediation Using Prokaryotes 485Ana Maria Queijeiro López and Amanda Lys dos Santos Silva26.1 Introduction 48526.2 Prokaryotic Membranes, Proteins, and Adaptation to Biodegradation Dynamics 48626.3 Stimuli to Biodegradation 48826.4 Protein Contribution of Subcellular Components to Biodegradation 48926.5 Expression of Proteins and Proteomic Steps 49126.6 Strategies for Identifying and Quantifying Proteins by Mass Spectrometry (MS) 49326.7 Posttranslational Modifications of Proteins 49526.8 Improvements Required to Proteomic Techniques 49726.9 Conclusions 499References 499Index 503