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Emerging Technologies in Environmental
Bioremediation
 Emerging Technologies in
Environmental Bioremediation

Edited by
Maulin P. Shah
Industrial Waste Water Research Lab, Division of Applied & Environmental
Microbiology, Enviro Technology Limited, India

Susana Rodriguez-Couto
Ikerbasque, Basque Foundation for Science,
Maria Diaz de Haro 3, Bilbao, Spain

S. Sevinç Şengör
Middle East Technical University, Department of
Environmental Engineering, Ankara, Turkey
Elsevier
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The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom
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To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any
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A catalogue record for this book is available from the British Library
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ISBN: 978-0-12-819860-5

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Publisher: Susan Dennis

Acquisition Editor: Kostas Marinakis
Editorial Project Manager: Vincent Gabrielle
Production Project Manager: Omer Mukthar
Cover Designer:
Typeset by MPS Limited, Chennai, India
Contents
List of contributors ............................................................................................... xv
Preface.................................................................................................................xix

Chapter 1: Immobilization of anaerobic ammonium oxidation bacteria for

nitrogen-rich wastewater treatment ........................................................ 1
Shou-Qing Ni, Hafiz Adeel Ahmad and Shakeel Ahmad
1.1 Introduction .......................................................................................................... 1
1.2 Anammox bacteria and their metabolic process ................................................. 3
1.3 Cell immobilization: a strategy to improve microbial wastewater treatment .... 5
1.3.1 What is cell immobilization? ...................................................................... 5
1.3.2 Different approaches for cell immobilization .............................................. 5
1.4 Why is gel immobilization advantageous?.......................................................... 8
1.5 Gel materials used for the immobilization of anammox..................................... 9
1.5.1 Polyvinyl alcohol and polyvinyl alcohol/sodium alginate ......................... 10
1.5.2 Waterborne polyurethane .......................................................................... 10
1.5.3 Polyethylene glycol gel............................................................................. 11
1.6 Application of cell immobilization in anammox and partial nitrification........ 12
1.6.1 Application of immobilized anammox ...................................................... 12
1.7 Commercialization of immobilizing technology ............................................... 13
1.8 Conclusion .......................................................................................................... 17
Acknowledgments....................................................................................................... 18
References................................................................................................................... 18

Chapter 2: Accelerated bioremediation of petroleum refinery sludge through

biostimulation and bioaugmentation of native microbiome...................... 23
Jayeeta Sarkar, Ajoy Roy, Pinaki Sar and Sufia K. Kazy
2.1 Introduction ........................................................................................................ 23
2.2 Petroleum refinery waste: composition and hazard .......................................... 26
2.3 Microbiology of hydrocarbon-associated environments ................................... 28

v
vi Contents

2.4 Microbial bioremediation of waste sludge ........................................................ 43

2.4.1 Accelerated bioremediation ...................................................................... 44
2.5 Factors affecting bioremediation ....................................................................... 49
2.6 Future scope ....................................................................................................... 51
References................................................................................................................... 51
Further reading............................................................................................................ 64

Chapter 3: Degradation and detoxification of waste via bioremediation: a step

toward sustainable environment ........................................................... 67
Komal Agrawal and Pradeep Verma
3.1 Introduction ........................................................................................................ 67
3.2 Bioremediation and the role of bioavailability.................................................. 68
3.2.1 Surfactants ................................................................................................ 68
3.2.2 Biodegradation ......................................................................................... 69
3.2.3 In situ and ex situ bioremediation ............................................................. 70
3.3 The degradation and/or detoxification of pollutants ......................................... 70
3.3.1 Heavy metal pollutant............................................................................... 70
3.3.2 Dyes ......................................................................................................... 73
3.4 Role of genetic engineering in bioremediation ................................................. 76
3.4.1 Bioremediation through microbial systems biology .................................. 77
3.5 Limitations and future prospect ......................................................................... 78
Acknowledgment ........................................................................................................ 78
Competing interests .................................................................................................... 78
References................................................................................................................... 79
Further reading............................................................................................................ 83

Chapter 4: Fungal laccases: versatile green catalyst for bioremediation of

organopollutants ................................................................................. 85
Ajit Patel, Vanita Patel, Radhika Patel, Ujjval Trivedi and Kamlesh Patel
4.1 Introduction ........................................................................................................ 85
4.2 Distribution and physiological functions of laccases ........................................ 87
4.3 Production of laccases........................................................................................ 88
4.3.1 Screening of laccase-producing fungi ....................................................... 88
4.3.2 Cultural and nutritional conditions for laccase production ........................ 89
4.3.3 Heterologous production of laccases ......................................................... 91
4.3.4 Biochemical properties of laccases ........................................................... 94
4.3.5 Mode of action of laccases ....................................................................... 97
4.3.6 Classification of laccases according to substrate specificity .................... 100
 Contents vii

4.3.7 Laccase mediator system ........................................................................ 101

4.3.8 Immobilization of laccase ....................................................................... 104
4.4 Application of laccases for bioremediation of environmental pollutants ....... 106
4.4.1 Degradation of xenobiotic compounds .................................................... 107
4.4.2 Decolorization of synthetic dyes ............................................................. 110
4.4.3 Treatment of industrial effluent .............................................................. 113
4.4.4 Potential applications in pulp and paper industry .................................... 113
4.4.5 Applications of laccases to develop ecofriendly processes ...................... 114
4.5 Limitations and future prospects...................................................................... 115
References................................................................................................................. 116

Chapter 5: Emerging bioremediation technologies for the treatment of

wastewater containing synthetic organic compounds .............................131
Kunal Jain, Jenny Johnson, Neelam Devpura, Rohit Rathour, Chirayu Desai,
Onkar Tiwari and Datta Madamwar
5.1 Introduction ...................................................................................................... 131
5.2 Electrobioremediation ...................................................................................... 134
5.3 Bioelectrochemical systems/technology .......................................................... 135
5.4 Phytotechnology (phytoremediation)............................................................... 138
5.4.1 Phytoreactors and constructed wetlands .................................................. 138
5.4.2 Plant microbe phytoremediation ........................................................... 139
5.4.3 Plant enzymes and metabolites ............................................................... 140
5.4.4 Hydroponic systems................................................................................ 141
5.4.5 Plant tissue culturing .............................................................................. 141
5.5 Electron beam irradiation................................................................................. 142
5.6 Conclusion: unresolved challenges and future perspectives ........................... 144
Acknowledgments..................................................................................................... 146
References................................................................................................................. 146

Chapter 6: Bacterial quorum sensing in environmental biotechnology: a new

approach for the detection and remediation of emerging pollutants .......151
Debapriya Sarkar, Kasturi Poddar, Nishchay Verma, Sayantani Biswas
and Angana Sarkar
6.1 Introduction ...................................................................................................... 151
6.2 Mechanisms of bacterial quorum sensing ....................................................... 152
6.2.1 Two-component system in Gram-positive bacteria ................................. 153
6.2.2 Acyl homoserine lactone in Gram-negative bacteria ............................... 153
6.3 Quorum sensing in environmental biotechnology........................................... 154
viii Contents

6.3.1 Heavy metal detection ............................................................................ 154

6.3.2 Pathogen detection .................................................................................. 158
6.3.3 Bioremediation ....................................................................................... 158
6.3.4 Biofilm formation ................................................................................... 159
6.3.5 Hydrocarbon remediation ....................................................................... 160
6.4 Limitations of microbial quorum sensing........................................................ 161
6.5 Conclusion........................................................................................................ 161
References................................................................................................................. 161

Chapter 7: Bioremediation: an effective technology toward a sustainable

environment via the remediation of emerging environmental pollutants ...165
Komal Agrawal, Ankita Bhatt, Venkatesh Chaturvedi and Pradeep Verma
7.1 Introduction ...................................................................................................... 165
7.2 Emerging pollutants ......................................................................................... 166
7.2.1 Bisphenol A ............................................................................................ 166
7.2.2 Polycyclic aromatic hydrocarbons .......................................................... 168
7.2.3 Polychlorinated biphenyls ....................................................................... 169
7.2.4 Pharmaceutical wastes ............................................................................ 170
7.2.5 Hospital effluents as source of emerging pollutants ................................ 171
7.2.6 Other emerging pollutants ...................................................................... 172
7.3 Types of bioremediation .................................................................................. 173
7.3.1 Microbial bioremediation........................................................................ 173
7.3.2 Phycoremediation ................................................................................... 175
7.3.3 Mixed cell culture system ....................................................................... 176
7.3.4 Phytoremediation .................................................................................... 176
7.3.5 Enzymatic bioremediation ...................................................................... 179
7.3.6 Zooremediation....................................................................................... 179
7.3.7 Vermiremediation ................................................................................... 179
7.4 Emerging techniques ........................................................................................ 180
7.4.1 Application of biosurfactants ................................................................ 180
7.4.2 Immobilization techniques .................................................................... 181
7.4.3 Adsorption and electrostatic binding ..................................................... 181
7.4.4 Entrapment in porous matrix and encapsulation ................................... 181
7.4.5 Electrokinetic remediation .................................................................... 182
7.4.6 Metagenomics....................................................................................... 182
7.4.7 Protein engineering ............................................................................... 183
7.4.8 Bioinformatics ...................................................................................... 183
7.4.9 Nanotechnology .................................................................................... 183
7.4.10 Genetic engineering .............................................................................. 184
7.4.11 Designer microbe and plant approach ................................................... 184
 Contents ix

7.4.12 Rhizosphere engineering ....................................................................... 185

7.4.13 Manipulation of plant microbe symbiosis ........................................... 185
7.4.14 Cometabolic bioremediation ................................................................. 186
7.5 Conclusion ........................................................................................................ 186
Acknowledgment ...................................................................................................... 186
Competing interests .................................................................................................. 186
References................................................................................................................. 187

Chapter 8: Application of metagenomics in remediation of contaminated sites and

environmental restoration ...................................................................197
Vineet Kumar, Indu Shekhar Thakur, Ajay Kumar Singh and Maulin P. Shah
8.1 Introduction ...................................................................................................... 197
8.2 Mechanism of bioremediation ......................................................................... 200
8.3 Approaches used to study microbial communities involved in in situ
and ex situ bioremediation............................................................................... 202
8.3.1 Culture-based techniques ........................................................................ 203
8.3.2 Culture-independent techniques .............................................................. 203
8.4 Metagenomics: a culture-independent insight ................................................. 215
8.4.1 Functional-based metagenomics ............................................................. 216
8.4.2 Sequence-based metagenomics ............................................................... 217
8.4.3 Metatranscriptomics................................................................................ 218
8.4.4 Metaproteomics ...................................................................................... 218
8.4.5 Metabolomics ......................................................................................... 219
8.4.6 Metagenomics sequencing strategies....................................................... 220
8.5 Next-generation sequencing technologies to explore structure and
function of microbial communities.................................................................. 220
8.6 Conclusion ........................................................................................................ 224
References................................................................................................................. 225
Further reading.......................................................................................................... 232

Chapter 9: In situ bioremediation techniques for the removal of emerging

contaminants and heavy metals using hybrid microbial
electrochemical technologies ................................................................233
M.M. Ghangrekar, S.M. Sathe and I. Chakraborty
9.1 Introduction ...................................................................................................... 233
9.1.1 Bioremediation for pollution control and classification of
bioremediation techniques ...................................................................... 234
9.1.2 Microbial electrochemical technology .................................................... 235
x Contents

9.2 In situ bioremediation using microbial electrochemical technologies............ 235

9.2.1 Constructed wetlands-microbial fuel cells............................................... 235
9.2.2 Sediment-microbial fuel cells ................................................................. 241
9.2.3 Soil-microbial fuel cells .......................................................................... 243
9.2.4 Plant-microbial fuel cells ........................................................................ 246
9.3 Future scope of research .................................................................................. 250
9.4 Summary............................................................................................................. 251
References................................................................................................................. 251

Chapter 10: Gene-targeted metagenomics approach for the degradation of

organic pollutants ..........................................................................257
Raghawendra Kumar, Dinesh Kumar, Labdhi Pandya, Priti Raj Pandit,
Zarna Patel, Shivarudrappa Bhairappanavar and Jayashankar Das
10.1 Introduction .................................................................................................... 257
10.2 Gene-targeted metagenomics ......................................................................... 258
10.3 Methods used for metagenomics studies ....................................................... 259
10.4 Bacterial community abundance.................................................................... 262
10.4.1 Biodegradation pathway involved in the degradation of organic
compounds ........................................................................................... 262
10.4.2 Functional metagenomics ..................................................................... 265
10.5 Conclusion...................................................................................................... 268
10.6 Future perspective .......................................................................................... 269
References................................................................................................................. 269
Further reading.......................................................................................................... 273

Chapter 11: Current status of toxic wastewater control strategies .......................275

Sushma Chityala, Dharanidaran Jayachandran, Ashish A. Prabhu and
Veeranki Venkata Dasu
11.1 Introduction .................................................................................................... 275
11.2 Causes and effects of toxic wastewater pollution ......................................... 276
11.3 Current interventions in toxic wastewater control ........................................ 277
11.3.1 Treatment using aquatic systems .......................................................... 277
11.3.2 Treatment using microalgae .................................................................. 278
11.3.3 Treatment using vermifiltration ............................................................ 278
11.3.4 Other interventions in toxic wastewater control .................................... 279
11.4 Wastewater reuse............................................................................................ 281
11.5 Conclusion...................................................................................................... 282
Acknowledgments..................................................................................................... 282
References................................................................................................................. 282
 Contents xi

Chapter 12: Latest innovations in bacterial degradation of textile azo dyes ..........285
Shantkriti Srinivasan, Kanyaga Parameswari M and Siranjeevi Nagaraj
12.1 Introduction .................................................................................................... 285
12.2 Bacteria in degradation of azo dyes .............................................................. 287
12.2.1 Bacteria as source ................................................................................. 287
12.2.2 Mechanism of azo dye degradation by bacteria .................................... 288
12.2.3 Phases of treatment ............................................................................... 289
12.2.4 Recent studies in bacterial mediated azo dye degradation..................... 290
12.2.5 Analytical methods in azo dye degradation .......................................... 294
12.2.6 Analysis of efficiency of bacterial dye degradation by toxicity tests .... 295
12.3 Computational inputs in enhancing biodegradation ...................................... 296
12.3.1 Choice of strains: adapted versus nonadapted strains ............................ 296
12.3.2 In silico analysis as a valuable tool....................................................... 298
12.4 Alternative front-runners: fungi, yeast, and algae-mediated azo dye
degradation ..................................................................................................... 300
12.5 Future perspective .......................................................................................... 301
References................................................................................................................. 302

Chapter 13: Development in wastewater treatment plant design .........................311

Bapi Mandal, Anwesha Purkayastha, Ashish A. Prabhu and Veeranki Venkata Dasu
13.1 Introduction .................................................................................................... 311
13.1.1 Conventional wastewater treatment technology .................................... 312
13.1.2 Recent advances achieved in wastewater treatment plant ..................... 315
13.2 Tertiary treatment........................................................................................... 320
13.3 Conclusion ...................................................................................................... 320
References................................................................................................................. 320

Chapter 14: Engineering biomaterials for the bioremediation: advances in

nanotechnological approaches for heavy metals removal from
natural resources ...........................................................................323
Magapu Solomon Sudhakar, Aakriti Aggarwal and Mahesh Kumar Sah
14.1 Introduction .................................................................................................... 323
14.2 Bioremediation ............................................................................................... 325
14.3 Nanotechnology and bioremediation ............................................................. 325
14.3.1 Nanomaterials used for removing pollutants ......................................... 326
14.3.2 Bioremediation of soil .......................................................................... 332
14.4 Conclusion ...................................................................................................... 333
Acknowledgement .................................................................................................... 334
References................................................................................................................. 334
xii Contents

Chapter 15: Algal bacterial symbiosis and its application in wastewater

treatment ......................................................................................341
Inigo Johnson, Sudeeptha Girijan, Binay Kumar Tripathy,
Mohammad Abubakar Sithik Ali and Mathava Kumar
15.1 Introduction .................................................................................................... 341
15.2 The symbiotic process.................................................................................... 342
15.2.1 Exchange of information in the form of bioactive compounds for
symbiosis .............................................................................................. 343
15.2.2 Exudates that can inhibit the microbes in the vicinity........................... 345
15.2.3 Exudates that can stimulate the microbes in the vicinity....................... 346
15.2.4 Factors affecting symbiotic systems...................................................... 349
15.3 Applications in wastewater treatment............................................................ 351
15.3.1 Types of reactors .................................................................................. 351
15.3.2 Nutrients removal ................................................................................. 353
15.3.3 Metal removal ...................................................................................... 356
15.3.4 Organic matter removal ........................................................................ 357
15.3.5 Emerging contaminants removal ........................................................... 359
15.3.6 Removal of refractory compounds ........................................................ 361
15.4 Energy generation .......................................................................................... 362
15.4.1 Algal biohydrogen production .............................................................. 363
15.4.2 Algal lipid production ........................................................................... 363
15.4.3 Microbial fuel cell reactor using algal bacteria interaction.................. 364
15.5 Conclusion and future directions ................................................................... 365
References................................................................................................................. 366

Chapter 16: Role of plant growth promoting rhizobacteria in mitigation of

heavy metals toxicity to Oryza sativa L. .........................................373
Vishnu Kumar, Gayatri Singh, Rajveer Singh Chauhan and Geetgovind Sinam
16.1 Introduction .................................................................................................... 373
16.2 Different genera of plant growth promoting rhizobacteria ......................... 374
16.3 Plant growth promoting rhizobacteria role in heavy metals dynamics
in the soil ........................................................................................................ 377
16.4 Plant growth promoting rhizobacteria’s role in controlling pathogens
in rice.............................................................................................................. 379
16.5 Plant growth promoting rhizobacteria in remediation of the
environment.................................................................................................... 380
16.6 Conclusion and future prospect ..................................................................... 384
References................................................................................................................. 384
Further reading.......................................................................................................... 389
 Contents xiii

Chapter 17: Study of transport models for arsenic removal using nanofiltration
process: recent perspectives ............................................................391
Robin Marlar Rajendran, Sangeeta Garg and Shailendra Bajpai
17.1 Introduction .................................................................................................... 391
17.1.1 Sources ................................................................................................. 391
17.1.2 Health effects ....................................................................................... 393
17.1.3 Permissible limit ................................................................................... 393
17.2 Chemistry of arsenic ...................................................................................... 395
17.3 Methods of arsenic removal from water/wastewater .................................... 395
17.3.1 Membrane technology .......................................................................... 396
17.4 Nanofiltration of arsenic ................................................................................ 397
17.4.1 Modeling of nanofiltration membranes for arsenic removal .................. 397
17.5 Conclusion and future perspective................................................................. 401
Nomenclature............................................................................................................ 401
Greek symbols .......................................................................................................... 402
Abbreviations ............................................................................................................ 402
References................................................................................................................. 402
Further Reading ........................................................................................................ 405

Chapter 18: Bioremediation and biorecovery of aqueous lead by local

lead-resistant organisms .................................................................407
B. van Veenhuyzen, C. Hörstmann, J. Peens and H.G. Brink
18.1 Introduction .................................................................................................... 407
18.2 Remediation of Pb.......................................................................................... 408
18.2.1 Conventional methods for Pb remediation or recovery ......................... 408
18.2.2 Bioremediation of Pb ............................................................................ 408
18.2.3 Mechanisms of bioremediation ............................................................. 409
18.3 Case study of aqueous Pb biorecovery by local Pb-resistant organisms...... 411
18.3.1 Characterization of bacterial consortia .................................................. 411
18.3.2 Precipitate identification ....................................................................... 412
18.3.3 Microbiological and kinetic study ......................................................... 413
18.3.4 Case studies of varied operating conditions .......................................... 417
18.4 Conclusion and outlook ................................................................................. 421
Acknowledgment ...................................................................................................... 422
References................................................................................................................. 422
xiv Contents

Chapter 19: Microbial bioremediation of azo dye through microbiological

approach .......................................................................................425
Celia Vargas-de la Cruz and Daniela Landa-Acuña
19.1 Introduction .................................................................................................... 425
19.2 Classification of dyes ..................................................................................... 426
19.3 Role of environmental parameters on microbial biodegradation and
bioremediation of azo dye.............................................................................. 427
19.4 Effects of environmental parameters on azo dye degradation...................... 432
19.4.1 Temperature ......................................................................................... 433
19.4.2 Oxygen ................................................................................................. 433
19.4.3 Dye concentration ................................................................................. 434
19.4.4 Electron donor ...................................................................................... 435
19.4.5 pH ........................................................................................................ 435
19.4.6 Dye structure ........................................................................................ 435
19.4.7 Redox potential..................................................................................... 436
19.4.8 Redox mediator .................................................................................... 437
19.4.9 Decolorization by genetically modified organisms ............................... 438
19.5 Conclusion...................................................................................................... 438
References................................................................................................................. 438
Further reading.......................................................................................................... 441

Chapter 20: Novel process of ellagic acid synthesis from waste generated
from mango pulp processing industries ............................................443
Murugan Athiappan, Shantkriti Srinivasan, Rubavathi Anandan and
Janani Rajaram
20.1 Introduction .................................................................................................... 443
20.1.1 Waste from mango pulp processing industries ...................................... 443
20.2 Composition of mango wastes ....................................................................... 444
20.3 Types of tannins ............................................................................................. 444
20.4 Bioconversion of tannin to ellagic acid......................................................... 445
20.5 Microbes involved in the production of ellagic acid .................................... 447
20.6 Applications of ellagic acid ........................................................................... 448
20.7 Conclusion...................................................................................................... 451
References................................................................................................................. 451
Further reading.......................................................................................................... 454
Index ............................................................................................................ 455
List of contributors

Aakriti Aggarwal Department of Biotechnology, Dr. B. R. Ambedkar National Institute of

Technology, Jalandhar, India
Komal Agrawal Bioprocess and Bioenergy Laboratory, Department of Microbiology, Central
University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, India
Hafiz Adeel Ahmad Shandong Provincial Key Laboratory of Water Pollution Control and
Resource Reuse, School of Environmental Science and Engineering, Shandong University,
Shandong, P.R. China
Shakeel Ahmad Department of Soil and Environmental Sciences, Muhammad Nawaz Shareef
University of Agriculture, Multan, Pakistan
Mohammad Abubakar Sithik Ali Environmental and Water Resource Engineering Division,
Department of Civil Engineering, IIT Madras, Chennai, India
Rubavathi Anandan Department of Microbiology, Periyar University, Salem, India
Murugan Athiappan Department of Microbiology, Periyar University, Salem, India
Shailendra Bajpai Department of Chemical Engineering, Dr B R Ambedkar National Institute of
Technology, Jalandhar, India
Shivarudrappa Bhairappanavar Gujarat Biotechnology Research Centre (GBRC), Department of
Science and Technology (DST), Government of Gujarat, Gandhinagar, India
Ankita Bhatt Bioprocess and Bioenergy Laboratory, Department of Microbiology, Central
University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, India
Sayantani Biswas Department of Biotechnology and Medical Engineering, National Institute of
Technology Rourkela, Odisha, India
H.G. Brink Department of Chemical Engineering, Faculty of Engineering, Built Environment and
Information Technology, University of Pretoria, Hatfield, Pretoria, South Africa
I. Chakraborty Department of Civil Engineering, Indian Institute of Technology Kharagpur,
Kharagpur, India
Venkatesh Chaturvedi SMW College, MG Kashi Vidyapeeth, Varanasi, India
Rajveer Singh Chauhan Department of Botany, Deen Dayal Upadhyaya Gorakhpur University,
Gorakhpur, India
Sushma Chityala Biochemical Engineering Laboratory, Department of Biosciences and
Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
Jayashankar Das Gujarat Biotechnology Research Centre (GBRC), Department of Science and
Technology (DST), Government of Gujarat, Gandhinagar, India

xv
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