Microbes Based Approaches for the Management of Hazardous Contaminants

Ajay Kumar, PhD, is currently working as an assistant professor at Amity Institute of Biotechnology, Amity University, Noida, India. Livleen Shukla, PhD, is currently working as Principal Scientist at the Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India. Joginder Singh, PhD, is working as a Professor at the Department of Botany, Nagaland University, Nagaland, India. Luiz Fernando R. Ferreira, PhD, is an Associate Professor at the Catholic University of Brassilia, Brasilia, Brazil, focused on Environmental Engineering, Microbiotechnology, Biotechnology, and Biomedical Engineering.

List of Contributors xix

Preface xxvii

1 Mycobial Nanotechnology in Bioremediation of Wastewater 1
Vikanksha Thakur, Arun Kumar, and Jatinder Singh

1.1 Fungi 1

1.2 Nanotechnology Aspects 2

1.3 The Production of Nanoparticles Using an Origin of Fungi 2

1.4 Categories and Characteristics of Synthesized Nanoparticles 4

1.5 Various Usage of Nanomaterials 6

1.6 Mycobial Bioremediation of Heavy Metals from Wastewater 7

1.7 Benefits of Mycobial Bioremediation 8

1.8 Constraints of Mycobial Bioremediation 9

1.9 Conclusion and Future Prospects 9

References 9

2 Microbial Enzymes in Biodegradation of Organic Pollutants: Mechanisms and Applications 12
Bharati Lap, Ashim Debnath, Gourav Kumar Singh, Priyank Chaturvedi, Joy Kumar Dey, and Sajal Saha

2.1 Introduction 12

2.2 Conclusion 18

References 18

3 Microbe Assisted Remediation of Xenobiotics: A Sustainable Solution 20
Azha Ufaq Nabi, Faamiya Shajar, and Reiaz Ul Rehman

3.1 Introduction 20

3.2 Bioremediation 24

3.3 Environmental Factors 25

3.4 Ex Situ Bioremediation Strategies 27

3.5 Genetic Engineering Approaches 28

3.6 The Beneficial Role of Microbes in Degradation of Different Pollutants 29

3.7 Mechanism of Heavy Metal Detoxification by Microbes 30

3.8 Intracellular Sequestration 30

3.9 Extracellular Sequestration 30

3.10 Reduction of Heavy Metal Ions by Microbial Cell 31

3.11 The Degradation Mechanism of the Complex Dye Structure by Microbes 31

3.12 In Domestic and Agricultural Lignocellulose Wastes Remediation 33

3.13 Conclusion 34

References 34

4 Bioremediation Strategies as Sustainable Bio-Tools for Mitigation of Emerging Pollutants 42
Hamza Rafeeq, Zainab Riaz, Anum Shahzadi, Shazaf Gul, Fatima Idress, Sidra Ashraf, and Asim Hussain

4.1 Introduction 42

4.2 Bioremediation by Microbial Strains 43

4.3 Factors Affecting Microbial Bioremediation 44

4.4 Classification of Bioremediations 46

4.5 Bioremediation of Various Pollutants 50

4.6 Recent Advancement and Challenges in Bioremediation 53

4.7 Advantages and Disadvantages 57

4.8 Conclusion 58

4.9 Future Perspective 58

References 58

5 How Can Plant-microbe Interactions be used for the Bioremediation of Metals in Water Bodies? 65
Gabriela Petroceli-Mota, Emilane Pinheiro da Cruz Lima, Mariana Miranda de Abreu, Glacielen Ribeiro de Souza, Jussara Tamires de Souza Silva, Gabriel Quintanilha-Peixoto, Alessandro Coutinho Ramos, Rachel Ann Hauser-Davis, and Aline Chaves Intorne

5.1 Water Contamination Issues 65

5.2 Metal Contamination Effects 66

5.3 Metal Bioremediation 69

5.4 Aquatic Macrophytes in Metal Phytoremediation Processes 70

5.5 Microorganisms in Metal Remediation 72

5.6 Interaction Between Aquatic Macrophytes and Microorganisms 74

5.7 Conclusion 76

References 76

6 Extremophilic Microorganisms for Environmental Bioremediation 82
Nazim Hussain, Mehvish Mumtaz, Warda Perveez, and Hafsa

6.1 Introduction 82

6.2 Extremophiles 82

6.3 Extremophilic Microorganisms Under Extreme Conditions 83

6.4 Extremophiles Applications for Environmental Bioremediation 90

6.5 Bioremediation of Petroleum Product 92

6.6 Conclusion and Future Perspective 99

References 99

7 Bacterial/Fungal Inoculants: Application as Bio Stimulants 108
V. Mamtha, Swati, K. Sowmiya, and Haralakal Keerthi Kumari

7.1 Introduction 108

7.2 Arbuscular Mycorrhizal Fungi (AMF) 111

7.3 Conclusion 114

References 114

8 Microbial Inoculants and Their Potential Application in Bioremediation: Emphasis on Agrochemicals 118
Shriniketan Puranik, Kallinkal Sobha Sruthy, Menpadi Manoj, Konaghatta Vijayakumar Vikram, Praveen Karijadar, Sandeep Kumar Singh, and Livleen Shukla

8.1 Introduction 118

8.2 Pollution of Different Matrices by Agrochemicals 119

8.3 Different Strategies Employed in Bioremediation 122

8.4 Microbe-Mediated Bioremediation and Recent Advances 127

8.5 Novel Enzymes or Genes Involved in Bioremediation of Pollutants 131

8.6 Conclusion 135

References 135

9 Porous Nanomaterials for Enzyme Immobilization and Bioremediation Applications 146
Nazim Hussain, Areej Shahbaz, Hafiza Ayesha Malik, Farhana Ehsan, José Cleiton Sousa dos Santos, and Aldona Balčiūnaitė

9.1 Introduction 146

9.2 Enzyme Immobilization 147

9.3 Model Enzymes With Multifunctional Attributes 149

9.4 Supports for Enzyme Immobilization 150

9.5 Inorganic Materials as Support Matrices 150

9.6 Organic Materials as Support Matrices 152

9.7 Synthetic Polymers as Support Matrices 152

9.8 Nanomaterials as Supports for Enzyme Immobilization 153

9.9 Porous Nanomaterials as Supports for Enzyme Immobilization 154

9.10 Advantages of Enzyme Immobilization 154

9.11 Metal–Organic Frameworks as Supports for Enzyme Immobilization 155

9.12 Bioremediation Applications of Enzyme Immobilized Porous Nanomaterials 156

9.13 Future Directions 156

9.14 Conclusion 157

References 157

10 Effects of Microbial Inoculants on Soil Nutrients and Microorganisms 162
D. Vijaysri, Konderu Niteesh Varma, Haralkal Keerthi Kumari, D. Sai Srinivas, S.T.M. Aravindharajan, Dilbag Singh, Livleen Shukla, T. Kavya, and Sandeep Kumar Singh

10.1 Introduction 162

10.2 Microbial Inoculants and Soil Nutrients 163

10.3 Influence of Microbial Inoculants on Soil Nutrient Quality 163

10.4 Impact of Microbial Inoculants on Natural Soil Microbial Communities 166

10.5 Microbial Inoculants: Mechanisms Involved in Affecting the Resident Microbial Community 166

10.6 Effect of Monoinoculation Versus Coinoculation 167

10.7 Conclusion 168

References 168

11 Bacterial Treatment of Industrial Wastewaters: Applications and Challenges 171
Christina Saran, Anuradha Devi, Ganesh Dattatraya Saratale, Rijuta Ganesh Saratale, Luiz Fernando R. Ferreira, Sikandar I. Mulla, and Ram Naresh Bharagava

11.1 Introduction 171

11.2 Composition and Nature of Various Industrial Wastewater 172

11.3 Role of Bacteria in Biodegradation of Specific Pollutant Found in Wastewater 174

11.4 Different Approaches and Mechanism of Bacterial Bioremediation in Industrial Wastewater 177

11.5 Factors Influencing Bacterial Degradation Efficiency 182

11.6 Conclusion and Future Prospects 185

References 185

12 Sustainable Algal Industrial Wastewater Treatment: Applications and Challenges 190
Anuradha Devi, Christina Saran, Ganesh Dattatraya Saratale, Rijuta Ganesh Saratale, Luiz Fernando R. Ferreira, Sikandar I. Mulla, and Ram Naresh Bharagava

12.1 Introduction 190

12.2 Characteristics and Composition of Industrial Wastewater (IWW) 191

12.3 Perks of Microalgae in Wastewater Treatment (WWT) 193

12.4 Cultivation System for IWW Treatment 194

12.5 Algal Nutrient Uptake Mechanisms 195

12.6 Bioremediation of Industrial Effluents 198

12.7 Recovery of Valuable Nutrients 200

12.8 Future Directions and Research Frontiers 201

12.9 Conclusion 202

References 202

13 Immobilization of Microbial Inoculants for Improving Soil Nutrient Bioavailability 206
Swati, V. Mamtha, and Haralakal Keerthi Kumari

13.1 Introduction 206

13.2 History of Immobilization 207

13.3 Support Material Selection 207

13.4 Support Materials Used for Immobilization of Microbes 207

13.5 Conclusion 211

References 211

14 Insight Into the Factors Inhibiting the Anammox Process in Wastewater 213
Surbhi Sinha, Anamika Singh, and Rachana Singh

14.1 Introduction 213

14.2 Substrate Inhibition 214

14.3 Heavy Metals Inhibition 214

14.4 Organic Matter Inhibition 215

14.5 Salinity Inhibition 216

14.6 Microplastic Inhibition 216

14.7 Nanoparticle (NPs) Inhibition 217

14.8 Control Strategies 217

14.9 Conclusion and Prospects 220

References 220

15 Chitinolytic Microbes for Pest Management in Organic Agriculture: Challenges and Strategies 224
Vikram Poria, Sandeep Kumar, Babett Greff, Pawan Kumar, Prakriti Jhilta, Balkar Singh, and Surender Singh

15.1 Introduction 224

15.2 Alternatives to Agrochemicals in Organic Agriculture for Pest Management 225

15.3 Pest Management in Organic Agriculture Using Chitinolytic Microbial Agents 228

15.4 Challenges Associated With the Use of Chitinolytic Microorganisms 230

15.5 Strategies for Sustainable Use of Chitinolytic Microorganisms in Organic Agriculture 232

15.6 Conclusion and Prospects 233

Acknowledgments 233

References 234

16 Microbial Bioremediation of Metals and Radionuclides: Approaches and Advancements 242
Sobia Riaz, Muhammad Sohail, and Rashba Sahar

16.1 Introduction 242

16.2 Sources and Effects of Heavy Metals 243

16.3 Biotic and Abiotic Factors Affecting Microbial Bioremediation 244

16.4 Approaches for Bioremediation of Heavy Metals Through Microbial Processes: An Introduction 245

16.5 Approaches for the Bioremediation of Radionuclide 247

16.6 Novel Technologies in Bioremediation 249

16.7 Future Perspectives and Conclusions 250

References 251

17 Chapter Role of Microbial Biofilms in Bioremediation: Current Perspectives 257
Sahaya Nadar and Tabassum Khan

17.1 Introduction 257

17.2 Formation of Biofilm 258

17.3 Microbes Forming Biofilm 259

17.4 Biofilms in Bioremediation 261

17.5 Emerging Opportunities 264

17.6 Challenges in Bioremediation Using Biofilms 266

17.7 Conclusions 266

References 267

18 Green Nanoparticles for Textile Wastewater Treatment: The Current Insights 277
Irfan Haidri, Aneeza Ishfaq, Muhammad Shahid, Tanvir Shahzad, Sabir Hussain, and Faisal Mahmood

18.1 Introduction 277

18.2 Sources and Composition of Textile Wastewater 278

18.3 Environmental Effects of Textile Wastewater 278

18.4 Nanotechnology in Environmental Pollution Remediation 278

18.5 Types of Biologically Synthesized Nanoparticles Used in the Treatment of Textile Wastewater 279

18.6 Green Synthesis Methods 280

18.7 Treatment of Textile Wastewater by Different Process 283

18.8 Degradation of Dyes by Green Synthesized Nanoparticles 285

18.9 Removal Efficiency of Green Synthesized Nanoparticles for the Treatment of Textile Wastewater 285

18.10 Toxicity and Safety Considerations for the Treatment of Textile Wastewater Using Green Synthesized Nanoparticles 286

18.11 Cost-effectiveness 287

18.12 Challenges and Limitations 287

18.13 Future Trends and Research Directions 288

18.14 Conclusion 288

References 288

19 Microbial Inoculants: Application in the Management of Metal Stress 293
Poulomi Ghosh and Saprativ P. Das

19.1 Introduction 293

19.2 Microbial Inoculants 293

19.3 Factors Influencing Microbial Inoculants’ Efficacy 295

19.4 Sources of Heavy Metals 298

19.5 Effects of Heavy Metals 300

19.6 Microbial Mechanisms of Metal Tolerance and Remediation 302

19.7 Other Remediation Approaches 304

19.8 Metal Remediation in Co-contaminated Soils 305

19.9 Concomitant Strategies for Metal Stress Management 306

19.10 Challenges, Impending Visions, and Conclusions 308

References 309

20 Harnessing In Silico Techniques for Bioremediation Solutions 312
Nischal Pradhan and Ajay Kumar

20.1 Introduction 312

20.2 Emergence of In Silico Approaches 313

20.3 Genome-Scale Models 314

20.4 Molecular Modeling 315

20.5 QSAR Models 316

20.6 Metabolic Modeling for Engineering Microbes 317

20.7 Development of In Silico Platforms for Bioremediation Research 318

20.8 Challenges and Limitations 318

20.9 Conclusion 319

References 319

21 Microbial Inoculants and Their Potential Application in Bioremediation 321
Ankita Agrawal, Jitesh Kumar Maharana, and Amiya Kumar Patel

21.1 Introduction 321

21.2 Overview of Bioremediation 322

21.3 Microbial Inoculants: Concept and Types 325

21.4 Mode of Action of Microbial Inoculants in Bioremediation 328

21.5 Applications of Microbial Inoculants 329

21.6 Process Optimization for Enhanced Bioremediation 330

21.7 Challenges and Future Prospects of Microbial Inoculants 331

21.8 Ecological Consequences 331

21.9 Assessment and Implementation of Microbial Inoculants 332

21.10 Case Studies and Success of Restoration Efforts 333

21.11 Conclusion 336

21.12 Future Perspectives 336

Acknowledgment 336

References 337

22 Microbial Inoculant Approaches for Disease Management 345
S.T.M. Aravindharajan, Sivaprakasam Navarasu, Velmurugan Shanmugam, S.S. Deepti Varsha, D. Vijaysri, Sandeep Kumar Singh, and Livleen Shukla

22.1 Introduction 345

22.2 Approaches of Various Microbial Inoculants for Controlling the Economically Important Disease 346

22.3 Central Role of Micro Organisms to Induced the Innate Immunity 351

22.4 Synthetic Microbial Communities in Plant Disease Management 355

22.5 Recent Trends of Biocontrol Agent 356

22.6 Conclusion 357

References 358

23 Impact of Microbial Inoculants on the Secondary Metabolites Production of Medicinal Plants 367
Haralakal Keerthi Kumari, D. Vijaysri, T. Chethan, Swati, and V. Mamtha

23.1 Introduction 367

23.2 Biosynthesis of Plant Secondary Phytochemicals and Their Classification 367

23.3 General Mechanism of Microbial Inoculants-Induced Production of Secondary Compounds 369

23.4 Determinants of Secondary Phytochemical Synthesis 370

23.5 Ideal Characteristics of Microbial Inoculants 370

23.6 Fungi 370

23.7 Mechanism of Fungal Elicitors 371

23.8 Advantages of Microbial Inoculants over Chemical Inoculants for Metabolite Production 374

23.9 Applications of Plant Secondary Metabolites 374

23.10 Conclusion 374

References 375

24 Bioremediation of High Molecular Weight Polycyclic Aromatic Hydrocarbons 378
Fahad S. Alotaibi, Abdullah Alrajhi, and Saif Alharbi

24.1 Introduction 378

24.2 Polycyclic Aromatic Hydrocarbons (PAHs): Sources, Pollution, and Exposure Routes 379

24.3 Biodegradation Pathways 380

24.4 Challenges and Future Directions 384

List of Abbreviations 385

References 385

25 Microbial Indicators for Monitoring Pollution and Bioremediation 390
Vijay Kumar, Ashok Chhetri, Joy Kumar Dey, and Ashim Debnath

25.1 Introduction 390

25.2 Biosensors for Microbial Remediation 393

References 394

26 PGPRs: Toward a Better Greener Future in Sustainable Agriculture 397
Soham Das, V.H.S. Vaishnavee, Anshika Dedha, Priya Yadav, Rahul Prasad Singh, and Ajay Kumar

26.1 Introduction 397

26.2 Brief Introduction of PGPRs 398

26.3 Role of PGPRs 398

26.4 Social and Economic Impact of PGPRs 404

26.5 Challenges, Future Perspectives and Conclusion 405

References 406

27 Role of MATE Transporters in Xenobiotics Tolerance 411
Arathi Radhakrishnan, Shakshi, Raj Nandini, Ajay Kumar, Raj Kishor Kapardar, and Rajpal Srivastav

27.1 Introduction 411

27.2 Degradation and Management of Xenobiotics 411

27.3 Role of MATE in Xenobiotics’ Extrusion and Metabolism 413

27.4 OMIC-Based Analysis for Xenobiotics Degradation and Metabolism 416

27.5 Conclusive Remarks 417

Acknowledgments 417

References 417

Index 421