Metagenomics to Bioremediation: Applications, Cutting Edge Tools, and Future Outlook

834 Pages·2022·23.76 MB·English

by  Vineet Kumar, Muhammad Bilal, Sushil Kumar Shahi, Vinod Kumar Garg

Metagenomics to Bioremediation
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Developments in Applied Microbiology and Biotechnology
Metagenomics to Bioremediation
Applications, Cutting-Edge Tools,
and Future Outlook
Edited by
Vineet Kumar
Department of Basic and Applied Sciences, School of Engineering and Sciences,
G D Goenka University, Gurugram, Haryana, India
Muhammad Bilal
School of Life Science and Food Engineering, Huaiyin Institute of Technology,
Huaian, China
Sushil Kumar Shahi
Department of Botany, Guru Ghasidas Vishwavidyalaya, Bilaspur, Chhattisgarh, India
Vinod Kumar Garg
Department of Environmental Science and Technology, Central University of Punjab,
Bathinda, Punjab, India
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Dedicated to my mentor, Prof. (Dr.) Ram Chandra, from whom I continue to
learn, and to my family for their unconditional support, patience, understanding,
encouragement, blessings, and love.
—Vineet Kumar
Dedicated to my family for their support, love, and educating me to date.
—Muhammad Bilal
Dedicated to my students, teachers, and mentors, from whom I continue to learn,
and to my family for their support, blessings, motivation, and love.
—Sushil Kumar Shahi
This book is truly dedicated to my family for their abundant and endless support,
love, and educating me to date; without them this book would not have been
possible.
—Vinod Kumar Garg
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Contents
Contributors....................................................................................................xxv
About the editors..........................................................................................xxxiii
Acknowledgments ........................................................................................xxxvii
SECTION 1: Introduction to bioremediation and metagenomics
Chapter 1: Bioremediation: A green technology for environmental cleanup...............3
PF Mishel, PF Steffi, B Thirumalaiyammal, and Rajeswari Anburaj
1 Introduction.............................................................................................................3
2 Agents of bioremediation.......................................................................................4
2.1 Bioremediation by bacteria...................................................................................4
2.2 Bioremediation by fungus.....................................................................................4
2.3 Bioremediation by algae........................................................................................4
3 Role of biotechnology in bioremediation..............................................................5
4 Microorganisms to clean up contaminated environments.....................................6
4.1 The role of microbes in bioremediation...............................................................6
4.2 How microbes destroy contaminants....................................................................7
4.3 Pollutants that are biodegradable..........................................................................7
5 Bacterial degradation..............................................................................................9
5.1 PGPR and PGPB degradation...............................................................................9
5.2 Microfungi and mycorrhiza degradation.............................................................10
5.3 Yeasts degradation...............................................................................................10
6 Degradative capacities of algae and protozoa.....................................................11
7 Plant-assisted bioremediation...............................................................................12
7.1 Mechanism of phytoremediation of contaminated soils.....................................12
8 Mycorrhiza assisted phytoremediation.................................................................16
9 Limitations of bioremediation..............................................................................16
10 Conclusion............................................................................................................16
References...................................................................................................................18
Further reading...........................................................................................................21
Chapter 2: Recent trends in bioremediation of heavy metals.................................23
Sirat Sandil
1 Introduction.............................................................................................................23
vii
Contents
2 Heavy metals: Sources and environmental effects................................................24
3 Effect of heavy metal toxicity on soil, microorganisms, and plants.....................27
4 Heavy metals toxicity in human beings.................................................................28
5 Bioremediation and its significance.......................................................................31
5.1 The need for bioremediation: Demerits of conventional remediation
methods..................................................................................................................31
5.2 What is bioremediation?........................................................................................32
5.3 Phytoremediation...................................................................................................33
5.4 Bioremediation with algae....................................................................................38
5.5 Microbial bioremediation......................................................................................39
6 Metagenomics and its application in bioremediation............................................44
6.1 Metagenomics methodology..................................................................................45
6.2 Application of metagenomics for the remediation of different
contaminated mediums..........................................................................................46
7 Conclusion..............................................................................................................48
References...................................................................................................................49
Chapter 3: Recent advances in bioremediation by metagenomics-based
approach for pharmaceutical derived pollutants...................................................55
S. Bhuvaneswari, K. Illakiya Bharathi, K. Rajakumari, and Vineet Kumar
1 Introduction.............................................................................................................55
2 Bioremediation.......................................................................................................56
2.1 Bioremediation methods involved in purifying air pollutants..............................56
2.2 Bioremediation in the removal of water pollutants..............................................57
3 Bioremediation techniques.....................................................................................57
3.1 Ex situ bioremediation technologies.....................................................................57
3.2 In situ bioremediation techniques.........................................................................61
4 Pharmaceutical wastes............................................................................................63
4.1 Different types of pharmaceutical wastes.............................................................64
5 Controlled drug wastes...........................................................................................65
5.1 Pharmaceuticals for veterinary use.......................................................................65
5.2 Agricultural use of pharmaceutical.......................................................................65
5.3 Sources of pharmaceutical waste products...........................................................65
5.4 Veterinary offices..................................................................................................67
6 Regulation of the disposal of pharmaceutical wastes............................................67
7 Characteristic hazardous wastes.............................................................................67
8 Remediation methods for pharmaceutical waste...................................................68
8.1 How bioremediation process helps in remediating pharmaceutical
wastes?...................................................................................................................68
8.2 Bioremediation of pharmaceutical wastes using cow
dung/gomeya..........................................................................................................70
8.3 Bioremediation of pharmaceuticals and pesticides...............................................72
8.4 Mycoremediation: A process to remediate pharmaceutical wastes......................73
8.5 Green approaches..................................................................................................75
9 Conclusion..............................................................................................................76
viii
Contents
References...................................................................................................................76
Further reading...........................................................................................................78
Chapter 4: Metagenomics in bioremediation: Recent advances, challenges,
and perspectives ..............................................................................................81
Aparna Gunjal, Shruti Gupta, Julius Eyiuche Nweze, and Justus Amuche Nweze
1 Introduction.............................................................................................................81
2 Microorganisms that are important in biosorption................................................82
3 Omics approach in bioremediation/biosorption.....................................................83
4 Application of metagenomics in bioremediation...................................................84
5 Exploring microbial communities using next-generation sequencing..................85
5.1 Shotgun sequencing...............................................................................................85
5.2 Sanger sequencing.................................................................................................85
6 Molecular biology approach in bioremediation.....................................................87
6.1 16S rRNA and other specific gene approaches....................................................88
6.2 PCR, RT-PCR, and qPCR technologies................................................................88
6.3 Temperature or denaturing gradient gel electrophoresis......................................89
6.4 Amplified ribosomal DNA restriction analysis and ribosomal
intergenic spacer analysis......................................................................................90
6.5 Terminal-restriction fragment length polymorphism (T-RFLP)..........................91
6.6 Fluorescent in situ hybridization (FISH)..............................................................91
6.7 Applications of DNA microarray technologies....................................................92
6.8 Nucleic acids based stable isotope probing (SIP).................................................93
6.9 Compound-specific isotope analysis (CSIA)........................................................94
7 Role of transcriptomics and metatranscriptomics in bioremediation....................94
8 Conclusion and future direction.............................................................................95
References...................................................................................................................95
Further reading.........................................................................................................101
Chapter 5: Metagenomicapproachesforunderstandingmicrobialcommunities
incontaminatedenvironments:Bioinformatictools,casestudiesandfutureoutlook......103
Arghya Mukherjee, Emilio D’Ugo, Roberto Giuseppetti, Fabio Magurano,
and Paul D. Cotter
1 Introduction...........................................................................................................103
2 Sequencing-based study of environmental microbiomes....................................104
2.1 Metataxonomics or amplicon sequence-based microbiome surveys..................105
2.2 Metagenomics......................................................................................................108
2.3 Metatranscriptomics.............................................................................................109
3 Bioinformatic analysis of high-throughput sequencing data...............................110
3.1 Quality control.....................................................................................................111
3.2 16S rRNA data analysis......................................................................................114
3.3 Metagenomic classification.................................................................................115
3.4 Metagenomic assembly.......................................................................................119
3.5 Binning and MAGs..............................................................................................121
3.6 Strain level metagenomic analysis......................................................................123
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