Metagenomics to Bioremediation: Applications, Cutting Edge Tools, and Future Outlook PDF
Preview Metagenomics to Bioremediation: Applications, Cutting Edge Tools, and Future Outlook
Metagenomics to Bioremediation This page intentionally left blank 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 AcademicPressisanimprintofElsevier 125LondonWall,LondonEC2Y5AS,UnitedKingdom 525BStreet,Suite1650,SanDiego,CA92101,UnitedStates 50HampshireStreet,5thFloor,Cambridge,MA02139,UnitedStates TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UnitedKingdom Copyright©2023ElsevierInc.Allrightsreserved. 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ISBN978-0-323-96113-4 ForinformationonallAcademicPresspublications visitourwebsiteathttps://www.elsevier.com/books-and-journals Publisher:StacyMasucci AcquisitionsEditor:LindaVersteeg-Buschman EditorialProjectManager:MariaElaineDDesamero ProductionProjectManager:SwapnaSrinivasan CoverDesigner:ChristianJ.Bilbow TypesetbySTRAIVE,India 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 This page intentionally left blank 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 ix
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