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Genomics Approach to Bioremediation

Principles, Tools, and Emerging Technologies

Kumar, Vineet / Bilal, Muhammad / Romanholo Ferreira, Luiz Fernando / Iqbal, Hafiz M. N. (Herausgeber)


1. Auflage Januar 2023
560 Seiten, Hardcover
Wiley & Sons Ltd

ISBN: 978-1-119-85210-0
John Wiley & Sons

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Genomics Approach to Bioremediation

Provides insights into the various aspects of microbial genomics and biotechnology for environmental cleanup

In recent years, the application of genomics to biodegradation and bioremediation research has led to a better understanding of the metabolic capabilities of microorganisms, their interactions with hazardous and toxic chemical compounds, and their adaptability to changing environmental conditions.

Genomics Approach to Bioremediation: Principles, Tools, and Emerging Technologies provides comprehensive and up-to-date information on cutting-edge technologies and approaches in bioremediation and biodegradation of environmental pollutants. Edited by prominent researchers in the field, this authoritative reference examines advanced genomics technologies, next-generation sequencing (NGS), and state-of-the-art bioinformatics tools while offering valuable insights into the unique functional attributes of different microbial communities and their impact on the removal of chemical contaminants.

Each chapter includes numerous high-quality illustrations, detailed tables, extensive references, and step-by-step descriptions of various microbial metabolic pathways of degradation and biotransformation of environments containing various inorganic, metallic, organometallic, and organic hydrocarbon contaminants.

* Describes methodologies and underlying theory for the remediation, detoxification, and

degradation of contaminated environments

* Covers new genomics technologies that address nutrient removal, resource recovery, and

other major trends in environmental cleanup

* Highlights recent advances in microbial biotechnological approaches including the latest

description of the relationship between microbes and the environment focusing on their impact

on ecosystem services.

* Offers perspectives on energy saving, production, sustainability, and community involvement

* Discusses current challenges and future directions in the field of bioremediation

Genomics Approach to Bioremediation: Principles, Tools, and Emerging Technologies is an essential resource for biochemical and environmental engineers, environmental microbiologists, academic researchers, process and treatment plant managers, policymakers, and industry professionals working in the areas of microbial degradation, bioremediation, and phytoremediation.

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
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.

V. Kumar, GD Goenka University, Haryana, India; M. Bilal, Poznan University of Technology, Poznan, Poland; L. F. Romanholo Ferreira, Tiradentes University Aracaju, Brazil; H. M. N. Iqbal, Tecnologico de Monterrey Monterrey, Mexico