Microbial Biodegradation and Bioremediation: Techniques and Case Studies for Environmental Pollution

Microbial Biodegradation and Bioremediation: Techniques and Case Studies for Environmental Pollution, Second Edition describes the successful application of microbes and their derivatives for bioremediation of potentially toxic and relatively novel compounds in the environment. Our natural biodiversity and environment is in danger due to the release of continuously emerging potential pollutants by anthropogenic activities. Though many attempts have been made to eradicate and remediate these noxious elements, thousands of xenobiotics of relatively new entities emerge every day, thus worsening the situation. Primitive microorganisms are highly adaptable to toxic environments, and can reduce the load of toxic elements by their successful transformation and remediation.

This completely updated new edition presents many new technologies and techniques and includes theoretical context and case studies in every chapter. Microbial Biodegradation and Bioremediation: Techniques and Case Studies for Environmental Pollution, Second Edition serves as a single-source reference and encompasses all categories of pollutants and their applications in a convenient, comprehensive format for researchers in environmental science and engineering, pollution, environmental microbiology, and biotechnology.

• Describes many novel approaches of microbial bioremediation including genetic engineering, metagenomics, microbial fuel cell technology, biosurfactants and biofilm-based bioremediation
• Introduces relatively new hazardous elements and their bioremediation practices including oil spills, military waste water, greenhouse gases, polythene wastes, and more
• Provides the most advanced techniques in the field of bioremediation, including insilico approach, microbes as pollution indicators, use of bioreactors, techniques of pollution monitoring, and more
• Completely updated and expanded to include topics and techniques such as genetically engineered bacteria, environmental health, nanoremediation, heavy metals, contaminant transport, and in situ and ex situ methods
• Includes theoretical context and case studies within each chapter

• Language: English
• Publisher: Elsevier Science
• Release date: Nov 24, 2021
• ISBN: 9780323900133

Book preview

Microbial Biodegradation and Bioremediation

Techniques and Case Studies for Environmental Pollution

Second Edition

Edited by

Surajit Das

Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, India

Hirak Ranjan Dash

DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, India

Table of Contents

Cover image

Title page

Copyright

List of contributors

Preface

Part I: Toxicity of various pollutants and introduction to bioremediation

Chapter 1. Prospects and scope of microbial bioremediation for the restoration of the contaminated sites

Abstract

1.1 Introduction

1.2 Recent advances in conventional remediation technologies

1.3 Biological treatment of pollutants: bioremediation

1.4 Selection criteria of microorganisms for the bioremediation

1.5 Applications of microorganisms for environmental restoration

1.6 Factors influencing the efficiency of bioremediation

1.7 Microbial bioremediation strategies

1.8 Future perspectives and challenges

Acknowledgments

References

Chapter 2. Mechanism of toxicity and adverse health effects of environmental pollutants

Abstract

2.1 Introduction

2.2 Types of pollutants

2.3 Sources and fate of pollutants in the environment

2.4 Human exposure to pollutants

2.5 Metabolic response of pollutants in the human body

2.6 Toxic effects of pollutants on human health

2.7 Conclusion

References

Chapter 3. The use of molecular tools to characterize functional microbial communities in contaminated areas

Abstract

3.1 Introduction

3.2 Elucidating structure of microbial communities

3.3 Functional analysis of microbial communities

3.4 Determination of in situ abundance of microorganisms

3.5 Conclusion

References

Chapter 4. Fate and consequences of microplastics in the environment and their impact on biological organisms

Abstract

4.1 Introduction

4.2 Residence time of microplastics in the environment

4.3 Impact on terrestrial organisms

4.4 Impact on aquatic organisms

4.5 Impact on human beings

4.6 Conclusion

References

Chapter 5. Metagenomic approaches to study the culture-independent bacterial diversity of a polluted environment—a case study on north-eastern coast of Bay of Bengal, India

Abstract

5.1 Introduction

5.2 Metagenomics-based methodology for microbial diversity analysis

5.3 Bacterial diversity of natural versus polluted coastal ecosystem

5.4 Bacterial community composition in north-eastern coast of Bay of Bengal: the case study

5.5 Scope of metagenomic tools in the diversity analysis

5.6 Conclusion

References

Chapter 6. Constructing thermodynamic models of toxic metal biosorption

Abstract

6.1 Introduction

6.2 Single species isotherms

6.3 Multisorption

6.4 Site-specific interactions

6.5 Electrical potential correction

6.6 Continuum approaches

References

Chapter 7. Biodegradation of organophosphates: biology and biotechnology

Abstract

7.1 Introduction

Acknowledgments

References

Further reading

Chapter 8. Pollutants in the coral environment and strategies to lower their impact on the functioning of reef ecosystem

Abstract

8.1 Introduction

8.2 Pollutants and their impact on the reef ecosystem

8.3 Current and advance strategies for protecting reef ecosystem from pollution

8.5 Conclusion

Acknowledgements

References

Part II: Role of diverse microorganisms in bioremediation

Chapter 9. Biology, genetic aspects and oxidative stress response of actinobacteria and strategies for bioremediation of toxic metals

Abstract

9.1 Introduction

9.2 Actinobacteria: biology and genetic systems

9.3 Regulation of oxidative stress in actinobacteria

9.4 Metal detoxification and bioremediation

9.5 Bioremediation strategies using actinobacteria

9.6 Conclusion

References

Chapter 10. Bacterial and fungal bioremediation strategies

Abstract

10.1 Introduction

10.2 Bioremediation considerations

10.3 Advantages and disadvantages of bioremediation

10.4 Microbial mechanisms of transformation of xenobiotic compounds

10.5 Screening of bacteria and white rot fungi for bioremediation applications for pesticides and crude oil

10.6 Degradation of pesticide mixtures and crude oil by bacteria and fungi

10.7 Inoculant production for soil incorporation of bioremedial fungi

10.8 Use of spent mushroom composts

10.9 Conclusions and future strategies

References

Chapter 11. Current trends in algal biotechnology for the generation of sustainable biobased products

Abstract

11.1 Introduction

11.2 What is bioprospecting?

11.3 Phycoremediation, microalgae, and bioprospecting

11.4 Isolation methods

11.5 Culturing the target strain(s)

11.6 Information garnered from the whole genome sequencing of lipid-producing microalgae

11.7 Bioinformatics resources to study lipid metabolic pathways in microalgae

References

Chapter 12. A review on microbial potential of toxic azo dyes bioremediation in aquatic system

Abstract

12.1 Introduction

12.2 Bioremediation of azo dyes

12.3 Cyanobacterial remediation of azo dyes

12.4 Application of cyanobacteria derived nanoparticles to remove azo dye from aquatic phase

12.5 Limitations

12.6 Conclusion

References

Chapter 13. Role of rhizosphere microbiome during phytoremediation of heavy metals

Abstract

13.1 Introduction

13.2 Coping mechanism of microorganism to high concentrations of metals

13.3 The physiological effect of heavy metals in plants

13.4 Plant mechanisms to withstand with high concentrations of heavy metals

13.5 Plants with the ability to tolerate high concentrations of heavy metals: natural cases

13.6 Biotechnological contribution

13.7 Omics tools to understand plant–microorganism association during phytoremediation

13.8 Functional and taxonomic diversity of root-associated bacteria in heavy metal hyperaccumulating plants: a case study

References

Chapter 14. Recent advancements in microbial bioremediation of industrial effluents: challenges and future outlook

Abstract

14.1 Introduction

14.2 Industrial effluents and toxicity

14.3 Remediation: a microbial perspective

14.4 Emerging strategies for bioremediation of industrial effluents

14.5 Conclusion

References

Chapter 15. Potential of anaerobic bacteria in bioremediation of metal-contaminated marine and estuarine environment

Abstract

15.1 Introduction

15.2 Principle and biochemistry of bioremediation

15.3 Mechanisms of metal remediation by microorganism

15.4 Metal degradation by bacteria

15.5 Genetically modified bacteria in metal bioremediation

15.6 Bioremediation of metals in marine and estuarine environments

15.7 Bioremediation of mercury—a case study

15.8 Significance of anaerobic bacteria in mercury bioremediation

15.9 Biosorption by mercury-resistant anaerobic bacteria—case study from a tropical estuary

15.10 Discussion

15.11 Conclusion

Acknowledgments

References

Chapter 16. Plant growth-promoting rhizobacteria-assisted bioremediation of toxic contaminant: recent advancements and applications

Abstract

16.1 Introduction

16.2 Pesticides

16.3 Environmental fate of pesticides

16.4 Plant growth-promoting rhizobacteria

16.5 Bioremediation of pesticides by plant growth-promoting rhizobacteria

16.6 Conclusion and future prospects

Acknowledgment

References

Chapter 17. Cyanobacterial and microalgal bioremediation: an efficient and eco-friendly approach toward industrial wastewater treatment and value-addition

Abstract

17.1 Introduction

17.2 General characteristics

17.3 Cyanobacteria in bioremediation

17.4 Microalgae in bioremediation

17.5 Cyanobacterial bioremediation of various industrial wastewaters

17.6 Phycoremediation of industrial wastewater

17.7 Cyanobacteria: value-added products

17.8 Microalgae: value-added products

17.9 Merits and demerits of algal bioremediation technology

17.10 Case studies

17.11 Future prospective and conclusions

References

Part III: Various pollutants and their bioremediation strategies

Chapter 18. Microbial degradation of aromatic pollutants: metabolic routes, pathway diversity, and strategies for bioremediation

Abstract

18.1 Introduction

18.2 Aromatic compounds: properties and sources

18.3 Impact of aromatic pollutants on planetary health

18.4 Microbes involved in aromatic compound degradation

18.5 Bacterial metabolism of aromatic compounds

18.6 Bioremediation: strategies to remove pollutants

18.7 Roadblocks/factors affecting bioremediation

18.8 Future directions

Acknowledgments

References

Chapter 19. Microbial bioremediation of Cr(VI)-contaminated soil for sustainable agriculture

Abstract

19.1 Introduction

19.2 Chromium production and toxicity

19.3 Microbial bioremediation of Cr(VI) toxicity

19.4 Impact of Cr(VI)-contaminated soil in agriculture

19.5 Case study

19.6 Conclusion

References

Chapter 20. Microbial bioremediation of aquaculture effluents

Abstract

20.1 Introduction

20.2 Microbes as bioremediators

20.3 Limitations of microbial bioremediation

20.4 Multitrophic bioremediation systems: a sustainable alternative

20.5 Conclusion

References

Chapter 21. Transport and disposal of radioactive wastes in nuclear industry

Abstract

21.1 Introduction

21.2 The nuclear fuel cycle

21.3 Classification of radioactive wastes

21.4 Radioactive waste management or treatment of radioactive waste

21.5 Transport of radioactive wastes in the environment

21.6 Decontamination of radioactive waste

21.7 Biological decontamination of radioactive waste

21.8 Conclusion

References

Chapter 22. Biofilm-mediated biodegradation of hydrophobic organic compounds in the presence of metals as co-contaminants

Abstract

22.1 Introduction

22.2 Hydrophobic organic compounds: a class of persistent organic pollutants

22.3 Metals: as coexisting contaminant

22.4 Microbial interactions with HOCs and metal contaminants

22.5 Biofilms for the rescue

22.6 Remedial mechanism for combined pollutants

22.7 Engineered biofilms and genomic approaches

22.8 Factors affecting biofilm-mediated remediation for mixed pollutants

22.9 Conclusion

22.10 Challenges and future perspectives

Acknowledgments

References

Chapter 23. Factors affecting the bioremediation of industrial and domestic wastewaters

Abstract

23.1 Introduction

23.2 Factors affecting bioremediation of domestic/industrial wastewater: analysis

23.3 Main aspects influencing the bioremediation of domestic and industrial wastewater

23.4 Effectiveness of contaminants removal mechanisms

23.5 Type of microorganisms

23.6 Conclusion

References

Chapter 24. Organophosphate pesticide: usage, environmental exposure, health effects, and microbial bioremediation

Abstract

24.1 Introduction

24.2 Usages and associated health risks

24.3 Human population’s exposure to organophosphorus pesticide

24.4 Pharmacology and toxicology

24.5 Clinical effects: toxicological analyses and biomedical investigations

24.6 Removal of organophosphorus pesticides from the environment

24.7 Microbial mediated organophosphorus pesticide biodegradation

24.8 Evaluating the significance of organophosphorus pesticide degrading enzymes

24.9 Conclusion

References

Part IV: Advanced bioremediation strategies

Chapter 25. Feasibility of using bioelectrochemical systems for bioremediation

Abstract

25.1 Introduction

25.2 Bioelectrochemical system configurations, microbial processes, and remediation

25.3 Anodic remediation

25.4 Cathodic remediation

25.5 Current state and challenges

References

Chapter 26. Electrochemical biosensors for monitoring of bioorganic and inorganic chemical pollutants in biological and environmental matrices

Abstract

26.1 Introduction

26.2 Types of inorganic pollutants and their source

26.3 Electrochemical biosensor for ammonia detection

26.4 Electrochemical biosensors for SO2, HSO3−, and SO3−

26.5 Electrochemical biosensors for hydrogen sulfide detection

26.6 Electrochemical biosensors for chloride and fluoride ion determination

26.7 Organic pollutants and electrochemical biosensors for their quantification

26.8 Electrochemical biosensors for azo dyes

26.9 Electrochemical biosensors for aromatics nitro compounds

26.10 Electrochemical biosensors for phenolic compounds

26.11 Electrochemical biosensors for pesticide detection

26.12 Conclusion

Acknowledgments

Declaration of competing interest

References

Chapter 27. Bioelectrochemical system for environmental remediation of toxicants

Abstract

27.1 Bioelectrochemical system for bioremediation

27.2 Configurations of bioelectrochemical system for environmental remediation

27.3 Microbial community and biocompatible electrodes for bioelectrochemical system

27.4 Principle of remediation by bioelectrochemical system

27.5 Bioelectrochemical system for treatment of wastewater

27.6 Bioelectrochemical system for treatment of solid waste and semisolid waste

27.7 BES for carbon capture and flue gas treatment

27.8 Conclusion

References

Chapter 28. Biofilm-mediated bioremediation of polycyclic aromatic hydrocarbons: current status and future perspectives

Abstract

28.1 Introduction

28.2 Polycyclic aromatic hydrocarbons: sources and toxicity

28.3 Polycyclic aromatic hydrocarbons biodegradation: metabolic and genomic aspect

28.4 Bacterial biofilms

28.5 Fidelity of biofilms in polycyclic aromatic hydrocarbons bioremediation

28.6 Biofilm omics insights into polycyclic aromatic hydrocarbons bioremediation

28.7 Conclusion

References

Chapter 29. Extremophilic nature of microbial ligninolytic enzymes and their role in biodegradation

Abstract

29.1 Introduction

29.2 Extremophilic ligninolytic enzymes

29.3 Role of extremophilic ligninolytic enzymes in bioremediation

29.4 Conclusion and future prospects

Acknowledgments

References

Chapter 30. Marine hydrocarbon-degrading bacteria: their role and application in oil-spill response and enhanced oil recovery

Abstract

30.1 Introduction

30.2 Diversity of marine hydrocarbon-degrading bacteria

30.3 Use of marine hydrocarbon-degrading bacteria in oil spill cleanup

30.4 Use of marine hydrocarbon-degrading bacteria in enhanced oil recovery

30.5 Research needs

References

Chapter 31. Nanoremediation of toxic contaminants from the environment: challenges and scopes

Abstract

31.1 Introduction

31.2 Different kinds of remediation

31.3 Limitations of traditional remediation methods

31.4 Nanoremediation: an alternative for traditional remediation processes

31.5 Nanotoxicity and fate of nanomaterials in the environment

31.6 Conclusion

References

Index

Copyright

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List of contributors

Uday Pratap Azad,     School of Physical Sciences, Department of Chemistry, Guru Ghasidas Vishwavidyalaya, Bilaspur, India

A.C. Bastos,     Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal

Himadri Tanaya Behera,     School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India

Punyasloke Bhadury,     Integrative Taxonomy and Microbial Ecology Research Group, Department of Biological Sciences & Centre for Climate and Environmental Studies, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, India

M.B. Binish,     School of Environmental Sciences, Mahatma Gandhi University, Kottayam, India

P. Binu,     School of Environmental Sciences, Mahatma Gandhi University, Kottayam, India

L. Breton-Deval,     Cátedras Conacyt—Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico

J.K. Bwapwa,     Faculty of Engineering, Department of Civil Engineering, Mangosuthu University of Technology, Umlazi, South Africa

Jaya Chakraborty,     Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, India

Sukalyan Chakraborty,     Department of Civil and Environmental Engineering, Birla Institute of Technology, Mesra, India

Shalini Chandel,     Department of Microbiology, College of Basic Sciences, CSK Himachal Pradesh Agricultural University, Palampur, India

Pranjal Chandra,     Laboratory of Bio-Physio Sensors and Nanobioengineering, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India

Ram Chandra,     Department of Environmental Microbiology, School of Earth and Environmental Science, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, India

Shreosi Chatterjee,     Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, India

Subhankar Chatterjee,     Bioremediation and Metabolomics Research Group, Department of Environmental Sciences, Central University of Himachal Pradesh, Kangra, India

Punarbasu Chaudhuri,     Department of Environmental Science, University of Calcutta, Kolkata, India

Ashvini Chauhan,     Environmental Biotechnology Laboratory, School of the Environment, Florida A&M University, Tallahassee, FL, United States

Khushboo Choudhary,     Department of Microbiology, Central University of Rajasthan, Bandarsindri, India

Santanu Chowdhury,     Department of Environmental Science, Asutosh College, Kolkata, India

Surajit Das,     Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, India

Debashis Dash,     Department of Botany, Odisha University of Agriculture and Technology, Bhubaneswar, India

Deepika Devadarshini,     Department of Microbiology, Odisha University of Agriculture and Technology, Bhubaneswar, India

Tushar Dhamale,     Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India

Divya,     Laboratory of Bio-Physio Sensors and Nanobioengineering, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India

Nelson Duran,     Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), Santo André, Brazil

Bobby Edwards III,     Environmental Biotechnology Laboratory, School of the Environment, Florida A&M University, Tallahassee, FL, United States

Paul H. Fallgren,     Advanced Environmental Technologies, LLC, Fort Collins, CO, United States

S. Fragoeiro,     Global Animal Health Science and Technology, MSD Animal Health, Milton Keynes, United Kingdom

Aniket Gade,     Department of Biotechnology, Sant Gadge Baba Amravati University, Amravati, India

Priyanka Gehlot,     Department of Microbiology, Central University of Rajasthan, Bandarsindri, India

Anwesha Ghosh,     Centre for Climate and Environmental Studies, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, India

V.G. Gopikrishna,     School of Environmental Sciences, Mahatma Gandhi University, Kottayam, India

S. Gouma,     Technical Educational Institute, Heraklion, Crete

A. Guevara-García,     Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico

Indarchand Gupta,     Department of Biotechnology, Institute of Science, Aurangabad, India

Pratishtha Gupta,     Laboratory of Applied Microbiology, Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, India

Tony Gutierrez,     Institute of Mechanical, Process and Energy Engineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, United Kingdom

Soumya Haldar,     Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India

Avinash Ingle

Department of Biotechnology, Sant Gadge Baba Amravati University, Amravati, India

Biotechnology Centre, Department of Agriculture Botany, Dr. Panjabrao Deshmukh Agriculture University, Akola, India

Rajneesh Jaswal,     Environmental Biotechnology Laboratory, School of the Environment, Florida A&M University, Tallahassee, FL, United States

Song Jin

Department of Civil and Architectural Engineering, University of Wyoming, Laramie, WY, United States

Advanced Environmental Technologies, LLC, Fort Collins, CO, United States

K. Juarez,     Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico

Adarsh Kumar,     Department of Environmental Microbiology, School of Earth and Environmental Science, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, India

Vipin Kumar,     Laboratory of Applied Microbiology, Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, India

Swetambari Kumari,     Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, India

Neelam Kungwani,     Pediatric Associates, Ahmedabad, India

P. Lara,     Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico

N. Magan,     Applied Mycology Group, Cranfield Soil and AgriFood Institute, Cranfield University, Bedford, United Kingdom

Rishi Mahajan,     Department of Microbiology, College of Basic Sciences, CSK Himachal Pradesh Agricultural University, Palampur, India

Supratim Mahapatra,     Laboratory of Bio-Physio Sensors and Nanobioengineering, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India

Uma Mahto,     Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, India

Raya Majumdar,     Department of Environmental Science, Asutosh College, Kolkata, India

Luis Rafael Martínez-Córdova,     Department of Scientific and Technological Research of the University of Sonora (DICTUS), Hermosillo, Mexico

Marcel Martínez-Porchas,     Center for Research in Food and Development (CIAD), Biology of Aquatic Organisms, Hermosillo, Mexico

Bibhuti Bhusan Mishra,     Department of Microbiology, Odisha University of Agriculture and Technology, Bhubaneswar, India

Mahesh Mohan,     School of Environmental Sciences, Mahatma Gandhi University, Kottayam, India

Balaram Mohapatra,     Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India

Swati Mohapatra,     Department of Infection Biology, School of Medicine, Wankwong University, Iskan, South Korea

Abhik Mojumdar,     School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India

Christina Nikolova,     Institute of Mechanical, Process and Energy Engineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, United Kingdom

Krishna Palit,     Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, India

S. Panigrahi,     Radiological and Environmental Safety Division, Indira Gandhi Centre for Atomic Research, Kalpakkam, India

Nidhi Pareek,     Department of Microbiology, Central University of Rajasthan, Bandarsindri, India

Sunil Parthasarathy

Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India

Biocatalysis Group, Almac Sciences Limited, Craigavon, United Kingdom

Kristofer G. Paso,     Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway

Neha P. Patel,     Analytical and Environmental Science Division and Centralized Instrument Facility (AESD & CIF), CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Bhavnagar, India

Ashish Pathak,     Environmental Biotechnology Laboratory, School of the Environment, Florida A&M University, Tallahassee, FL, United States

Swayamsidha Pati,     Department of Microbiology, Odisha University of Agriculture and Technology, Bhubaneswar, India

Swati Pattnaik,     Department of Microbiology, Odisha University of Agriculture and Technology, Bhubaneswar, India

Prashant S. Phale,     Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India

Marco Antonio Porchas-Cornejo,     Northwest Biological Research Center (CIBNOR), Guaymas, Mexico

Monika Priyadarshanee,     Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, India

Hemant J. Purohit,     Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, India

Asifa Qureshi

Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, India

Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India

Mahendra Rai

Department of Biotechnology, Sant Gadge Baba Amravati University, Amravati, India

Department of Microbiology, Nicolaus Copernicus University, Toruń, Poland

Rupa Rani,     Laboratory of Applied Microbiology, Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, India

Sonalin Rath,     Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, India

Lopamudra Ray

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India

School of Law, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India

Arijit Reeves,     Department of Environmental Science, University of Calcutta, Kolkata, India

Glen Ricardo Robles-Porchas,     Center for Research in Food and Development (CIAD), Biology of Aquatic Organisms, Hermosillo, Mexico

D. Rubio-Noguez,     Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico

Annapoorni Lakshman Sagar,     Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India

Braja Kishor Saha,     Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India

Deviprasad Samantaray,     Department of Microbiology, Odisha University of Agriculture and Technology, Bhubaneswar, India

Amedea B. Seabra,     Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), Santo André, Brazil

Wasim Akram Shaikh,     Department of Civil and Environmental Engineering, Birla Institute of Technology, Mesra, India

Nagaraj P. Shetti,     School of Advanced Sciences, KLE Technological University, Vidyanagar, Hubballi, Karnataka, India

M.E. Shuaib,     Applied Mycology Group, Cranfield Soil and AgriFood Institute, Cranfield University, Bedford, United Kingdom

Sudhir K. Shukla,     Biofouling & Biofilm Processes Section, Water & Steam Chemistry Division, BARC Facilities, Kalpakkam, India

Dayananda Siddavattam,     Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India

Ankur Singh,     Laboratory of Applied Microbiology, Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, India

Ananya Srivastava,     Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Guwahati, India

T. Subba Rao

Biofouling & Biofilm Processes Section, Water & Steam Chemistry Division, BARC Facilities, Kalpakkam, India

Water & Steam Chemistry Division, Bhabha Atomic Research Centre, Kalpakkam, India

Homi Bhabha National Institute, Anushakthi Nagar, Mumbai, India

Ksheerabdi Tanaya,     Department of Microbiology, Odisha University of Agriculture and Technology, Bhubaneswar, India

E. Tovar-Sanchez,     Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico

Vandana,     Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, India

Francisco Vargas-Albores,     Center for Research in Food and Development (CIAD), Biology of Aquatic Organisms, Hermosillo, Mexico

P. Velraj

Water & Steam Chemistry Division, Bhabha Atomic Research Centre, Kalpakkam, India

Homi Bhabha National Institute, Anushakthi Nagar, Mumbai, India

Shalini Verma,     Bioremediation and Metabolomics Research Group, Department of Environmental Sciences, Central University of Himachal Pradesh, Kangra, India

Vivekanand Vivekanand,     Centre for Energy and Environment, Malaviya National Institute of Technology, Jaipur, India

Prerna J. Yesankar

Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, India

Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India

Preface

Anthropogenic activities have increased loads of toxic compounds in the environment over the years. The gradual increase of these xenobiotic compounds has placed significant pressure on the environment threatening the dynamics of nature besides having a detrimental effect on the existing flora and fauna. The United Nations has also taken cognizance of this alarming situation, and most of the countries are being directed to minimize their pollution level by various means. With this, an immediate global demand arises to develop strategies to combat such noxious pollutants. Advanced techniques for the disposal and treatment of these xenobiotic compounds are the primary concern, but the recently developed treatment strategies are very costly and lead to the production of toxic intermediates, which can adversely affect living organisms. Over time, microbial remediation processes have been accelerated to produce better, more eco-friendly, safer, and more biodegradable measures for the complete dissemination of these toxic xenobiotic compounds. Bioremediation is the process of the usage of living organisms such as plants (phytoremediation) and microbes such as bacteria, algae, and fungi (microbial remediation) and their enzymes to detoxify toxic xenobiotic compounds. Some toxic xenobiotics include synthetic organochlorides, such as plastics and pesticides, and naturally occurring organic chemicals, such as polyaromatic hydrocarbons, and some crude oil and coal fractions. The evolution of new metabolic pathways from natural metabolic cycles has enabled the microorganisms to degrade almost all the different complex and resistant xenobiotics found on Earth. This is an imperative, efficient, green, and economical new alternative to conventional treatment technologies.

The previous edition of the book "Microbial Biodegradation and Bioremediation" comprised chapters dealing with various bioremediation strategies with the help of different groups of microorganisms, along with detailed diagrammatic representations. We have received an overwhelming response from the readers. Keeping the research advancements in microbial bioremediation in mind, we have come out with the second edition of this book to meet the global awareness of the detrimental effects of these xenobiotic compounds and approaches to their remediation. A few more chapters have been added in the second edition of this book. Besides, other chapters have been amended substantially with recent research outcomes to update the knowledge of the readers. This second edition will be helpful both for the beginners and experts in the field of microbial bioremediation. We hope to instill the present status and implications of microbial bioremediation to academicians, students, teachers, researchers, environmentalists, agriculturalists, industrialists, professional engineers, and other enthusiastic people are wholeheartedly devoted to conserving nature. We thank all the contributors who have expertise in this field of research for their advanced, timely chapters and their help in making this a successful endeavor.

Part I

Toxicity of various pollutants and introduction to bioremediation

Outline

Chapter 1 Prospects and scope of microbial bioremediation for the restoration of the contaminated sites

Chapter 2 Mechanism of toxicity and adverse health effects of environmental pollutants

Chapter 3 The use of molecular tools to characterize functional microbial communities in contaminated areas

Chapter 4 Fate and consequences of microplastics in the environment and their impact on biological organisms

Chapter 5 Metagenomic approaches to study the culture-independent bacterial diversity of a polluted environment—a case study on north-eastern coast of Bay of Bengal, India

Chapter 6 Constructing thermodynamic models of toxic metal biosorption

Chapter 7 Biodegradation of organophosphates: biology and biotechnology

Chapter 8 Pollutants in the coral environment and strategies to lower their impact on the functioning of reef ecosystem

Chapter 1

Prospects and scope of microbial bioremediation for the restoration of the contaminated sites

Shreosi Chatterjee, Swetambari Kumari, Sonalin Rath and Surajit Das,    Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, India

Abstract

Industrialization and large-scale anthropogenic activities have led to environmental pollution. Dust, smoke, fumes, and toxic gas emissions occur because of highly polluting industries such as thermal power plants, coal mines, cement, sponge iron, steel and ferroalloys, petroleum, and chemicals. Besides, a copious amount of organic and inorganic substances are released which are highly toxic and cause irreparable damage to our ecology and environment, often breaching carrying capacity of environment. Therefore adequate and effective pollution control measures should be adopted to minimize adverse effects. Though many remediation techniques are available, microorganisms in the remediation technique are advantageous over other techniques based on certain parameters like cost-effectiveness, less or no by-products, reusability, etc. Microorganisms are omnipresent, highly diverse, readily available, and can use many of the pollutants as a source of the nutrient. Microorganisms-mediated remediation of polluted sites could be achieved in extreme environmental conditions, including in situ and ex situ conditions. Alternative bioremediation technologies are also employed, which, together with the traditional one, can exploit the natural metabolic functionalities of microorganisms to convert them into novel biological entities of interest. In this chapter, the role of microbes in bioremediation and their mechanism and how effectively they are applied to remove the pollutants from the environment have been discussed.

Keywords

Bioremediation; microorganism; genetic manipulation; extreme environment

1.1 Introduction

The advancement of modern agriculture and industrialization intentionally and accidentally introduce a profuse amount of organic and inorganic toxicants leading to a severe ecological imbalance between biotic and abiotic components in the biosphere. Almost every environmental element is being hindered with the large quantum of recalcitrant contaminants, including plastics, heavy metal pollutants, petroleum-derived products, fossil fuel refinery, exhaust gas from automobiles, domestic and agricultural activities, and chemical seeping from the industries, etc. These persistent pollutants have accumulated in various parts of the biosphere for several years, contributing to soil, water, and air pollutions. Moreover, most of these recalcitrants possess high residence time and travel a long distance from the pollution source. For instance, Arctic regions are getting polluted by persistent organic pollutants (POP) without any primary contamination source (Lehmann-Konera, Ruman, Franczak, & Polkowska, 2020). This phenomenon is known as the grasshopper effect, where POPs originated from the warmer zone are evaporated and precipitated in the arctic region due to low temperature. The subsequent cycle of evaporation and condensation intensifies POP pollution, eradicating the ecosystem functioning in the polar region.

The presence of these pollutants in the earth beyond the threshold value rigorously hampers natural microbial activities involving nutrient cycling and ecosystem productivity, which eventually jeopardize human health (Grath, Chaudri, & Giller, 1994). It is also noteworthy that their accumulation and degree of toxicity crucially depend on the chemical environment of the contaminated site. For example, alteration in the soil environment, such as acidification or variation in redox potential, can lead to the transformation of chemical form and the specific binding property of heavy metals (Sutherland, Tack, Tolosa, & Verloo, 2000). This phenomenon results in the leaching of toxic metals from soil matrix to groundwater, severely affecting the aquatic ecosystem. Though these pollutants primarily accumulate in nonliving elements, they can move to biotic components in the ecosystem and enter the food chain resulting in bioaccumulation and biomagnification. The human can be exposed to these pollutants via inhalation of toxic gas, absorption through the respiratory epithelium, cornea, skin, and contaminated food ingestion through the gut. Many vital organs such as the gastrointestinal tract, nervous system, respiratory system, skeletal muscles, etc., get damaged upon exposure to these pollutants (Fig. 1.1) (Gaur, Narasimhulu, & PydiSetty, 2018; Pehkonen & Zhang, 2002; Rahimi & Abdollahi, 2007). Most of these pollutants are teratogenic, thus affect fetuses and embryos too. The contaminants are observed in humans beyond any age limit but are often found in high concentrations in aged persons (Scheringer, 2009). Continuous exposure of the living body to these pollutants can lead to significant health issues like obesity, neurological problems, diabetes, reproductive issues, hormonal disruption, even cancer (Harrad, 2010; Rajmohan, Gopinath, & Chetty, 2018).

Figure 1.1 The movement of pollutants and their impacts on human health and the environment.

Since the degree of pollution increases exponentially over time, environmental remediation has emerged as a significant global issue to overcome the obnoxious effect of pollutants on the ecosystem. Several different physicochemical and biological processes have been employed for decades to mitigate environmental pollution. The conventional physiological treatment includes ion exchange, osmosis, precipitation, electrochemical treatment, sorption, and evaporation. However, such traditional remediations are not often economically and environmentally sustainable (Kadirvelu, Senthilkumar, Thamaraiselvi, & Subburam, 2002; Mulligan, Yong, & Gibbs, 2001). Based on multiple biological levels, the recovery of contaminated sites could be achieved by considering various paradigms driven by complex processes (Duarte et al., 2015). The present scenario focuses more on utilizing naturally available microbial systems rather than the application of physicochemical techniques. Recent findings reported that microbe-based bioremediation could employ the combination of the physiological, ecological, genomic, biochemical, and metagenomic bases of microorganisms with a various phenomenon such as photosynthesis, anaerobic oxidation of methane, uptake of nutrients such as sulfur, nitrogen, and phosphorous (Bae et al., 2018; Varjani, 2017). The advances in environmental biotechnology provide a relatively easy and simple means to understand the characterization of naturally occurring complex microbial communities for the bioremediation process that thrive in the soil, air, and water.

Bioremediation is comparatively ecocompatible and economically feasible approach, thus gaining much attention in recent years. This cleanup process employs either the whole organism or the metabolic pathway for the degradation of organic and inorganic pollutants. As microbial cells are susceptible to any change in environmental conditions, this process is highly sensitive and efficient even in low concentration of contaminants. The bioremediation approach can be applied in situ and ex situ methods like biostimulation and bioaugmentation process. Biostimulation involves using specific nutrients into the contamination site, which encourages the growth of specific naive microbiota, leading to the metabolism of xenobiotic compounds. A slightly different approach is applied in the bioaugmentation method, where native or foreign microbes are allowed to acquaint with a polluted environment for the degradation of pollutants. Besides, microbial catabolic genes, intercellular and extracellular proteins, metabolites, and different metabolic pathways can also be used for enhanced bioremediation targeting specific pollutants. This book chapter covers an in-depth description of the bioremediation of organic and inorganic pollutants, including heavy metals, polyaromatic hydrocarbons, petroleum derivatives, pesticides, plastic, dyes, and other synthetic chemicals. This chapter highlights the factors influencing the bioremediation process. Additionally, this chapter elucidates different bioremediation strategies employed in recent years.

1.2 Recent advances in conventional remediation technologies

Restoration of the ecosystem can be achieved with proper disposal and suitable treatment of waste materials laden with toxic metals and organic pollutants. Several physicochemical treatments, such as chemical oxidation, precipitation, flocculation, ion exchange, reverse osmosis, filtration, etc., have been practiced for years to mitigate environmental pollution (Table 1.1). These technologies convert pollutants into less toxic compounds or remove them from the target site by selective manipulation of the critical physicochemical properties required for toxicity and bioavailability. The setup of these technologies can be established either locally applied in situ or industrial plant-based ex situ treatment. The success of these remediation technologies critically depends on the transportation of efficient remediation materials to the target medium and searching for favorable conditions for remediation. Different physicochemical remediation technologies frequently used in waste treatment are described below.

Table 1.1

DSA, dimensionally stable anode; PAH, polycyclic aromatic hydrocarbon; PMMA, polymethyl methacrylate; PVDF, polyvinylidene fluoride; TCE, trichloroethylene.

1.2.1 Chemical oxidation

In wastewater treatment, the chemical oxidation process is one of the most frequently used techniques for cleaning up large-scale industrial effluent contaminated with organic pollutants (Tunay & Kabdasli, 2010). This process utilizes different oxidants like hydrogen peroxides, ozone, potassium permanganate, chlorine, hypochlorite, etc., which destroy the organic pollutants by oxidizing the chemical groups present in pollutants required for toxicity, mobility, and bioavailability. In recent years, the advanced oxidation process (AOP) has emerged as a promising tool for the treatment of xenobiotics, which successfully utilizes highly reactive hydroxyl radicals as strong oxidants. Depending on the source of oxidants, Fenton reaction, ozonation, incineration, and wet air oxidation (WAO) are the standard technologies involved in the AOP.

During the Fenton reaction, ferrous ion (Fe²+) reacts with hydrogen peroxide to generate hydroxyl molecule in an acidic environment, which in turn catalyzes the organic pollutant degradation. Here Fe²+ ion serves as a catalyst and regenerates to initiate another cycle of Fenton reaction. In contrast to the Fenton reaction, ozonation is carried out in an alkaline environment generating hydroxyl and superoxide radicals for rapid degradation of organic pollutants. In case of incineration and WAO, pollutants are oxidized at a very high temperature utilizing atmospheric oxygen under dry and aqueous phases, respectively. Although the chemical oxidation process is a very rapid and efficient technique for the remediation of environmental pollutants, it has certain disadvantages. This process exploits oxidants like chlorine, ozone, hydrogen peroxides, potassium permanganates, etc., which are highly toxic, thus affecting the normal flora of the adjacent environment. Moreover, the types of equipment for generating ozone are comparatively expensive. In wastewater, several scavengers are present, which capture radical species reducing the effectiveness of the process. Additionally, incineration and WAO method demand extensively high temperature for oxidation, thus requiring high energy. These methods produce secondary pollutants like furans and dioxins from chlorinated pollutants.

1.2.2 Chemical reduction

Similar to chemical oxidation, the chemical reduction process modifies the oxidation state of the target pollutant, converting them into less toxic and immobilized compounds (Ibanez, Hernandez-Esparza, Doria-Serrano, Fregoso-Infante, & Singh, 2007). Industrial waste laden with heavy metals is often precipitated by chemical reduction to their elemental state. Sulfur-based reducing agents like sulfur dioxide and sulfite ions are most frequently used as reducing agents for the treatment of chlorinated pollutants and hexavalent chromium reduction. However, excessive use of these reagents elevates the concentration of sulfur in the environment leading to secondary environmental pollution. In recent years, metal-based nanoparticles like zero-valent metals and iron oxide nanoparticles have emerged as the most promising reductants for their unique physicochemical properties. They successfully catalyze the dehalogenation of organic pollutants and reduction of Cr-contaminated waste. Despite possessing excellent reducing properties, nanoparticles are extremely unstable and promote ecotoxicity affecting normal microflora of the surrounding environment (Yan, Lien, Koel, & Zhang, 2013). Besides sulfur-based and metal-based reductants, hydrazine, hydroxylamine, thiosulfate, borohydride, activated charcoal, and aldehydes can also be used for the chemical reduction of organic pollutants.

1.2.3 Photocatalysis

The photocatalysis process obeys the basic principle of the AOP generating reactive radical species with UV radiation to catalyze organic pollutant degradation (Zhu & Wang, 2017). In this process, a semiconducting material like TiO2 is irradiated with UV rays resulting in the excitation of an electron from its valence band to the conducting band. This process creates an electron hole in the valence band, which further reacts with water to generate hydroxyl radicals. These reactive radical species breakdown the complex structure of organic pollutants into simpler form. The major drawback of this process is the presence of bicarbonate and carbonate ions in wastewater, which neutralize hydroxyl radicals thereby reducing the efficiency of the process. Further, the target pollutant also contains various light scattering and absorbing compounds, which significantly interfere with the excitation process. Finally, intermediates generating from this process retain the toxicity of the parent compounds.

1.2.4 Chemical precipitation

Removal of heavy metal contamination from the aqueous phase is effectively accomplished by precipitation of metal ions from the target medium (United States Environmental Protection Agency, 2000). The stability and toxicity of metal ions in an aqueous medium crucially depend on the pH of the medium. For instance, Pb²+ is highly stable in an acidic environment. With the rise in pH, Pb²+ ions get precipitated by forming Pb(OH)2. In another example, the pH of the target medium regulates the speciation of Cr ions, which in turn confers the degree of toxicity on the environment. Change in the pH of the target medium from acidic to basic condition triggers the speciation of Cr(VI) to Cr(III), thus reducing the toxicity of the pollutant. The addition of commercial bases like calcium hydroxide, sodium hydroxide, sodium carbonate, etc., in the heavy metal amended aqueous solution potentially removed the metal ions by forming insoluble metal hydroxides and carbonates. Although this process is relatively simple and inexpensive, it requires a surplus amount of chemical precipitants to settle metal ions at a suitable level. Moreover, it is operated under high basic environment and produces an enormous volume of sludge, which needs additional treatments, thus increasing the cost of waste disposal. Disposal of sludge without prior treatment adversely affects the environment imparting long-term impacts on living beings.

1.2.5 Coagulation–flocculation

The coagulation–flocculation process is widely employed in wastewater treatment to remove the turbidity, color compounds, suspended solids, phosphoric substances, heavy metal ions, and organic contaminants under alkaline condition (Duan & Gregory, 2003). In this process, ferric/alum salts are mostly utilized as chemical coagulants, which destabilize the physical state of suspended particles and increase the size of particles by the formation of unstable and bulky floccules. The formation of floccules involves complexation, charge neutralization, adsorption, and entrapment inside the coagulants, which facilitate easy separation of contaminants through filtration and sedimentation (Li, Zhu, Wang, Yao, & Tang, 2006). This process also helps to remove pathogenic microorganisms from drinking water. However, the major limitations of this technique include expensive operational cost, production of a large amount of putrescible sludge, and possible leaching of metal ions from the sludge, promoting secondary environmental pollution.

1.2.6 Ion exchange

The ion exchange process exclusively serves the purpose of selective metal ion separation from an aqueous environment and removes undesirable substances such as nitrate, ammonia, and silicate from drinking water. This technique potentially recovers valuable heavy metals from industrial effluent (Da¸browski, Hubicki, Podkościelny, & Robens, 2004). Both cationic and anionic contaminants can be separated depending on the active chemical groups anchored to the surface of polymeric resin. For example, carboxylate and sulfonic groups are widely employed for the separation of cations, while quaternary ammonium groups selectively remove anions from the target medium. Natural exchangers such as synthetic zeolite and clinoptilolite are also used for the purification of heavy metal contaminated wastewater. This process involves the reversible interchange of ions between the ion exchanger and target solution (sorption) followed by releasing an equivalent amount of charged ions (cation/anion exchange). For the recovery of metals, adsorbed ions are eluted in concentrated form using suitable reagents, which in turn regenerates the ion exchangers. Unlike other physicochemical treatments, ion exchange does not produce any sludge, thus facilitates easy and low-cost disposal. However, this process is highly expensive, demanding sophisticated equipment for operation. Prior to ion exchange, metal amended wastewater is subjected to suitable pretreatment for removal of suspended solids, increasing operational cost. Additionally, specific ion exchangers for all heavy metals are not commercially available, thus unable to treat multimetal solution.

1.2.7 Electrochemical technique

In recent years, electrochemical techniques such as electrochemical precipitation, electrodialysis, membrane electrolysis, and electrocoagulation have gained significant attention for in situ wastewater treatment due to reliability and safety in operation (Janssen & Koene, 2002). These techniques utilize the electrolytic potential to remove metal ions and other ionic contaminants from the effluent. Electrochemical precipitation follows the basic principle of conventional chemical precipitation, generating hydroxyl molecules in an electrochemical cell by hydrolyzing water molecules. Electrodialysis technique efficiently removes and recovers metal ions from wastewater using an ion-exchange membrane. When an electric field is applied to a target ionic solution, target ions cross the ion-exchange membrane and migrate toward their respective electrode depending on their charge. This process is not applicable to the purification of wastewater with high metal concentrations. This problem can be overcome by membrane electrolysis, where redox reaction in electrodes is driven by the electrolytic potential, which assists the removal of metal contaminants from wastewater. In case of electrocoagulation, that is, Fe²+ or Al³+ ions are generated by electrical dissolution from iron or aluminum electrodes. These nascent cations serve as excellent coagulants instigating particulates flocculation. Hydrogen gas released from the cathode eliminates the floccules from the target medium by flotation (Chen, 2004). Although these treatments produce less amount of secondary contaminants and exhibit some degree of ecocompatibility, these techniques require high energy consumption and precious materials to construct suitable electrodes. Moreover, electrode rapidly corrodes due to subsequent chemical reactions reducing the metal removal efficiency.

1.2.8 Adsorption

In the field of advanced wastewater treatment, the adsorption process is the most robust technique for the removal of both organic and inorganic contaminants. This process involves the entrapment of a substance with a definite mass on the surface of a highly porous particle called adsorbent through physical or chemical interaction (Kurniawan & Babel, 2003). Since adsorption is a surface phenomenon, an increase in the surface area significantly enhances the removal of contaminants from the target medium. This process is also applicable for removal of gaseous pollutants. Different types of natural adsorbent like clay, mineral, activated carbon, zeolites, etc. are commercially available and frequently used in this cleanup treatment. Due to having high surface reactivity and adsorption capacity, activated carbon is employed as a universal adsorbent for the removal of synthetic dyes, phenolic compounds, pesticides, and heavy metal ions from the target medium. Recently, with the advent of nanotechnology, nanomaterials like carbon nanotubes, graphene nanotube, zero-valent metal, and metal oxide nanoparticles are extensively studied for the adsorption of heavy metal and chlorinated organic pollutants from industrial effluent and groundwater. The presence of unique physicochemical properties like smaller size, higher surface to volume ratio, and high surface reactivity makes nanomaterials the most promising and potential adsorbents (Amin, Alazba, & Manzoor, 2014). However, this process requires a controlled environment. Several environmental parameters like pH, temperature, and the concentration of adsorbents critically regulate the adsorption process. Alteration in any factors may either hamper the adsorption process or instigate the release of adsorbed compounds from the active sites of the adsorbent.

1.2.9 Membrane filtration

The membrane filtration process has emerged as a potential technique to remove organic and inorganic contaminants from effluent, supporting the reuse of wastewater. Sometimes, this process is employed with the conjugation of other physicochemical treatments to remove suspended solids from an aqueous system. Different classes of membrane filtration such as microfiltration, ultrafiltration, nanofiltration, and reverse osmosis are frequently used based on the particle size retained by the membrane. In general, membranes are made up of both organic and inorganic materials such as polysulfone, cellulose acetate, polyvinylidene fluoride, polyethersulfone, polyamide, sintered metals, and porous alumina. Microfiltration, a pressure-driven separation technique, efficiently separates macromolecules, suspended solids, and colloids with a membrane having pore size of 0.1–1.0 µm. This process is usually employed as pretreatment of wastewater separating solids from the liquid phase. However, this process is unable to remove organic matter, dissolved solids, and viruses from the target medium. Additionally, membrane fouling is another major limitation of this technique. The ultrafiltration process effectively filters pathogenic microorganisms, including viruses, macromolecules, and suspended particles, with a size range between 0.005 and 10 µm. This technique demands lesser pressure than microfiltration. The major drawbacks of this process include regular maintenance and inadequate removal of dissolved materials (Krüger, Vial, Arifin, Weber, & Heijnen, 2016).

Nanofiltration is widely used in the removal of organic matter, synthetic dyes, and heavy metal ions from industrial effluent. Unique properties of the membrane, that is, smaller pore size and surface charge, aid filtration of charged solutes having a size smaller than membrane pores along with macroparticles. The filtration mechanism implicates both steric and electrical effects where an electric potential is created between the charged ions in the target medium and the charged groups attached to the surface of the membrane leading to the removal of ions from industrial effluent (Van der Bruggen & Vandecasteele, 2003). As compared to other filtration techniques, reverse osmosis is considered as the most promising tool for removing heavy metal ions and dissolved particles from industrial wastewater (Bodalo-Santoyo, Gómez-Carrasco, Gomez-Gomez, Maximo-Martin, & Hidalgo-Montesinos, 2003). It has several advantages such as high rejection rate, excellent mechanical strength, high chemical and thermal stability, resistance to biofouling, and high water flux rate. When an amount of wastewater is fed to the filtration unit, a permeable membrane allows only water molecules to pass driven by high hydrostatic pressure and retain the contaminants. However, this process is highly expensive and consumes high energy for filtration.

1.3 Biological treatment of pollutants: bioremediation

In the present scenario, when environmental protection is an utmost concern, switching to biological treatment of contaminants seems a suitable alternative to physicochemical techniques. These conventional technologies are relatively expensive and consume high energy for operation. Most of them are ineffective for the complete degradation of organic pollutants and often generate noxious intermediates during treatment. Moreover, these treatments utilize toxic chemicals for treatment, which leads to secondary environmental pollution. However, the treatment of hazardous waste by applying biological inventions under controlled environmental conditions offers several advantages over conventional physicochemical technologies in terms of economic sustainability and environmental safety (Fulekar, 2012). The emerging trend of biotechnological approaches has been proved beneficial for hazardous waste generating industries. The bioremediation approach extensively utilizes biological systems like plants, bacteria, fungi, algae, etc., for the ecofriendly and sustainable degradation of environmental pollutants.

Phytoremediation, that is, the use of green plants and plant-associated microflora, can be adapted to control the environmental pollution caused by the contamination of soil or surface/groundwater. Various aquatic and terrestrial plants can be applied to cleanup pesticides, solvents, metals, explosives, crude oil, and other contaminants. Plants exhibit several mechanisms such as accumulation, stabilization, degradation, volatilization, and hydraulic control involved in the bioremediation process (Muthusaravanan et al., 2018). Moreover, plant roots release various exudates into the soil matrix, which facilitates the microbial activities, enhancing degradation rate. Followed by phytoremediation, the plant that has absorbed/accumulated contaminants must be harvested and discarded. The most common method used for the disposal of plants is incineration. The resultant ashes can then be disposed of at appropriate waste discarding sites. With the development of genetic engineering and molecular biology, the transgenic plant can be developed by inserting a specific gene of interest in the plant cell to expedite the bioremediation process. For instance, metal absorption regulation in plants is suspected to be controlled by many different genes. These genes duly carry out metal solubilization in soils surrounding the roots and the movement of these absorbed metals into the root cells followed by plant shoot. Genetically modified plants that show enhanced tolerance to metal contamination have been developed by successfully identifying and cloning these genes at the laboratory. However, the phytoremediation approach is not feasible for large-scale applications and has a substantial risk of contaminating the food chain.

Microbe-based bioremediation offers several advantages over phytoremediation such as ease of cultivation, larger biomass, requires a cheap source of nutrients, and ease of genetic manipulation, thus considered as the best suitable approach for environmental restoration. Microorganisms are the most primitive biotic element that bridges between abiotic and biotic components in the biosphere. They have a diverse range of habitats and can easily adapt the extreme condition. Importantly, microbes act as decomposers in the ecosystem and involve in biogeochemical cycles of nutrients, minerals, and metals. They quickly respond to any environmental changes and exhibit excellent resilient properties to mitigate environmental stressors. The bioremediation approach utilizes microbial defense mechanisms such as, bioaccumulation, biotransformation, volatilization, immobilization, and degradation to remove organic and inorganic toxicants (Abatenh, Gizaw, Tsegaye, & Wassie, 2017). In nature, microorganism often exists as sessile community sheltered inside a hydrophobic gelatinous extracellular polymeric substance, instead of free-living cells known as biofilm. This structure protects bacterial cells from environmental stressors as well as aids the bioremediation process by solubilizing, immobilizing, and accumulating the pollutants inside the matrix. In recent years, biofilm-mediated bioremediation has gained significant attention in the metal removal process (Gupta & Diwan, 2017). The presence of specific microorganisms in the correct amount and combination is a prerequisite to carry out bioremediation in suitable environmental conditions. The pre-existing microbes in the contaminated site are well adapted to toxicants and the prevailing environmental conditions, including temperature, pH, and oxidation/reduction potential. Bioremediation is a combination of both biotransformation and biodegradation, which is carried out by transforming pollutants into nonhazardous or comparatively less hazardous chemicals. Often this combination results in the release of carbon dioxide, methane, biomass, and water as a result of the metabolism of contamination carried out by microorganisms.

1.4 Selection criteria of microorganisms for the bioremediation

A plethora of factors, including the indigenous microbial population, their phenotypic characteristics, a wide range of environmental parameters, and the introduction process cumulatively determine the activity, persistence, and performance of bioaugmented strains, which ultimately decide the fate of bioremediation. Due to the negligence in considering certain factors such as redox and pH, the existence of toxic contaminants, the absence of crucial cosubstrates, and the isolation of dynamic microbial strains serve as the root cause behind the failure of bioremediation. Before inoculation, the strain selection stage, ecological distribution, that is, the relative spatial and temporal abundance of potential source populations and their ability to tolerate the prevailing conditions in target habitats, play a crucial role in the degradation process.

The relevance of bioremediation critically depends on the successful isolation and identification of the most suitable microbial strains and their subsequent survival followed by activity once released into the target habitat. For years, isolation of microbial strains became easy using selective enrichment media (Beijerinck, 1901). Relative to the indigenous community, microbial strains from polluted samples are subjected to enrichment by providing the target contaminant as the sole source of carbon, nitrogen, and other minerals. The specific enrichment culture condition helps the microbial strain retaining the degradation ability outside their natural habitat. This enrichment procedure serves the microbial strain to adopt the fluctuating environmental condition (e.g., nutrients, moisture, pH, redox, and osmotic factors) to compete with indigenous microbial populations. This approach proved essential to derive superior strains, and it is necessary to obtain exploitable strains (Singer, van der Gast, & Thompson, 2005). However, it downregulates other characteristics required by the strains to act as competitive and convenient for the target pollutant, thus not effectively serving the purpose of the bioremediation (England, Lee, & Trevors, 1993; Recorbet, Steinberg, & Faurie, 1992). The selection of strains should be done on prior knowledge of the ubiquity, population dynamics, and based on spatial and temporal distribution of microbial communities present in the source habitat, and preferably with some understanding of the type of organisms that are prevalent and usual in the target habitat.

The recent advancement in molecular microbial ecology and analytical chemistry facilitated us with identifying in situ populations and even individual cells responsible for carrying out specific processes. A more comprehensive assessment of the identification, composition, and structure of microbial communities in the environment has been achieved by utilizing microbial approaches such as fluorescent in situ hybridization (DeLong et al., 1989), terminal restriction fragment length polymorphism (Liu, Marsh, Cheng, & Forney, 1997), denaturing gradient gel electrophoresis (Muyzer et al., 1993), length-heterogeneity polymerase chain reaction (Suzuki, Rappé, & Giovannoni, 1998), and stable isotope probing (Boschker et al., 1998; Radajewski, Ineson, Parekh, & Murrell, 2000). All these techniques are not utilized routinely and widely. So, before finding the suitable strain with improved bioremediation capacity for a specific contaminant at a particular site, the triple selection criteria should be checked first. These include: (1) the relative abundance of source populations in the target habitat, (2) tolerance to cocontaminants, and (3) the ability to degrade components of the contaminated site along with the accessibility of contaminants to the microbial cells.

1.5 Applications of microorganisms for environmental restoration

Over a decade, microbial-based bioremediation of various toxic pollutants has gained profound attention worldwide due to ecofriendly and economically feasible remediation technology. Microorganisms like bacteria, fungi, and microalgae are widely used as promising tools for detoxifying organic pollutants such as polyaromatic hydrocarbons, synthetic dyes, petroleum derivatives, and other xenobiotics, as well as inorganic heavy metal pollutants from contaminated soil and water. It is noteworthy that the biological treatment of pollutants has exploited the natural ability of the microorganisms either to breakdown toxic compounds into less toxic forms or to eliminate them from the polluted site (Fig. 1.3) (Abatenh et al., 2017). A large number of catabolic genes have been reported in various microorganisms that are found responsible for the degradation of xenobiotic compounds (Table 1.2). The bioremediation process aims to stimulate microorganisms to thrive in contaminated sites with nutrients and minerals that enable them to survive in the extreme environment and subsequently destroy the contaminants. Microorganisms often utilize these pollutants in metabolic or other cellular reactions to generate energy for building more cells. However, the bioremediation approach requires basic knowledge of the toxic effects of various pollutants on microbial populations. Besides indigenous species, in some particular cases, allochthonous microorganisms and genetically modified microbes could be efficiently utilized for enhanced degradation of contaminated sites that is a matter of extensive research.

Table 1.2

PAH, polycyclic aromatic hydrocarbon; RBRR, Remazol Brilliant Blue R.

1.5.1 Mitigation of inorganic pollutants

1.5.1.1 Heavy metal sequestration

The naturally occurring metals with a density greater than 5 g cm−3 are known as heavy metals. Rapid industrialization and various anthropogenic activities like burning of fossil fuels, unmanaged use of agrochemicals, and dumping of sewage sludge account for the degradation of soil and water quality with the release of heavy metals. A few of the heavy metals like manganese (Mn), iron (Fe), copper (Cu), nickel (Ni), molybdenum (Mo), and zinc (Zn) act as micronutrients. On the contrary, heavy metals like aluminum (Al), lead (Pb), cadmium (Cd), gold (Au), mercury (Hg), and silver (Ag) are not having any biological importance; instead, they are toxic to living organisms. Since these heavy metals are nonbiodegradable, they can bioaccumulate and biomagnify along with the trophic levels inside tissues and persist in the environment. Implementing bioremediation could help avoid heavy metal leaching and mobilization into the environmental segments, facilitate their extraction, and protect the living beings from its hazardous impact.

Bacteria mainly adapt two mechanisms for developing resistance against heavy metals. One is detoxification, that is, the transformation of the toxic metal state and depriving its availability, and the other is active efflux pumping of the toxic metal from the cells (Silver & Phung, 1996). The interaction between the metal contaminated soil and microorganisms involves the basic redox (oxidation and reduction) reaction, which involves microorganisms as the oxidizing agent of heavy metals. The electron so released is accepted by alternative electron acceptors like nitrate, sulfate, and ferric oxides. The growth of microorganisms occurs, utilizing the energy released from the oxidation of organic compounds in the presence of electron acceptors Fe (III) and Mn (IV) (Lovley & Phillips, 1988).

The removal of these heavy metals occurs with the adaptation of different physicochemical mechanisms as a bioremediation approach. Biosorption is one of the processes involving a higher affinity biosorbent toward sorbate (metal ions) until equilibrium occurs between the two components (Das, Vimala, & Karthika, 2008). Accession and transformation of heavy metals into less toxic compounds occur by considering fungi as a potent biocatalyst (Pinedo-Rivilla, Aleu, & Collado, 2009). Algae also possess bioaccumulation, that is, taking up toxic heavy metals from the environment, which leads to its high concentration than that in the surrounding water (Megharaj, Ragusa, & Naidu, 2003). Microalgae synthesized posttranscriptionally class III metallothioneins or phytochelatins, which effectively bind to heavy metal (Dwivedi, 2012). The expression of these metallothioneins and phytochelatins (metal-binding proteins and peptides) provides a way to study the microbial-mediated accumulation of heavy metals (Cobbett & Goldsbrough, 2002). Apart from these binding proteins, microorganisms adapt various other mechanisms to remove heavy metals like heavy metal volatilization, precipitation, etc.

Saccharomyces cerevisiae as a biosorbent carried out the removal of Zn (II) and Cd (II) following ion-exchange