Extremophiles: Diversity, Adaptation and Applications 9815080369, 9789815080360

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Extremophiles: Diversity, Adaptation and Applications Edited by Masrure Alam

Department of Biological Sciences Aliah University India

& Bipransh Kumar Tiwary

Department of Microbiology North Bengal St. Xavier’s College India

Extremophiles: Diversity, Adaptation and Applications Editors: Masrure Alam and Bipransh Kumar Tiwary ISBN (Online): 978-981-5080-35-3 ISBN (Print): 978-981-5080-36-0 ISBN (Paperback): 978-981-5080-37-7 © 2022, Bentham Books imprint. Published by Bentham Science Publishers Pte. Ltd. Singapore. All Rights Reserved. First published in 2022.

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CONTENTS FOREWORD ........................................................................................................................................... i PREFACE ................................................................................................................................................ ii ABOUT THE EDITORS ........................................................................................................................ iv LIST OF CONTRIBUTORS .................................................................................................................. v CHAPTER 1 EXTREMOPHILES: AN OVERVIEW ...................................................................... Bipransh Kumar Tiwary and Masrure Alam INTRODUCTION .......................................................................................................................... HYPERTHERMOPHILES ........................................................................................................... Diversity .................................................................................................................................. Mechanisms of Adaptation ..................................................................................................... PSYCHROPHILES ........................................................................................................................ Diversity .................................................................................................................................. Mechanisms of Adaptation ..................................................................................................... ACIDOPHILES .............................................................................................................................. Diversity .................................................................................................................................. Mechanisms of Adaptation ..................................................................................................... ALKALIPHILES ............................................................................................................................ Diversity .................................................................................................................................. Mechanisms of Adaptation ..................................................................................................... HALOPHILES ................................................................................................................................ Diversity .................................................................................................................................. Mechanisms of Adaptation ..................................................................................................... RADIATION RESISTANT MICROORGANISMS ................................................................... Diversity .................................................................................................................................. Mechanisms of Adaptation ..................................................................................................... PIEZOPHILES ............................................................................................................................... Diversity .................................................................................................................................. Mechanisms of Adaptation ..................................................................................................... ANAEROBIC MICROORGANISMS .......................................................................................... Diversity .................................................................................................................................. Mechanisms of Adaptation ..................................................................................................... CONCLUSION AND FUTURE PROSPECTS ............................................................................ CONSENT FOR PUBLICATION ................................................................................................ CONFLICT OF INTEREST ......................................................................................................... ACKNOWLEDGEMENT ............................................................................................................. REFERENCES ...............................................................................................................................

1

CHAPTER 2 HYPERTHERMOPHILES: DIVERSITY, ADAPTATION AND APPLICATIONS Masrure Alam and Baishali Pandit INTRODUCTION .......................................................................................................................... HYPERTHERMAL ENVIRONMENTS ...................................................................................... Terrestrial Hot Springs ............................................................................................................ Marine Hydrothermal Vents ................................................................................................... Other Hyperthermal Environments ......................................................................................... DIVERSITY OF HYPERTHERMOPHILES .............................................................................. Diversity of Cultured Hyperthermophiles .............................................................................. Diversity of Uncultivated Hyperthermophiles: Information Obtained From Metagenomic Analysis of High-Temperature Environments ........................................................................

24

2 3 3 4 5 5 5 6 6 7 7 7 8 9 9 10 11 11 12 13 13 13 14 14 15 16 16 16 16 17

25 28 28 29 30 30 31 34

MECHANISMS OF ADAPTATION OF HYPERTHERMOPHILES ..................................... Adaptations of the Membrane Structures ............................................................................... Maintenance of the Nucleic Acid Structures .......................................................................... Maintenance of the Structure of Proteins ................................................................................ APPLICATIONS OF HYPERTHERMOPHILES ...................................................................... Thermophilic and Hyperthermophilic Enzymes with Industrial Applications ....................... Enzymes with Molecular Biological Applications ................................................................. Biofuel Production .................................................................................................................. Reduction of Antibiotic Residues and Other Uses ................................................................. CONCLUDING REMARKS ......................................................................................................... CONSENT FOR PUBLICATION ................................................................................................ CONFLICT OF INTEREST ......................................................................................................... ACKNOWLEDGEMENT ............................................................................................................. REFERENCES ...............................................................................................................................

36 36 38 41 43 43 46 46 47 48 48 48 49 49

CHAPTER 3 PSYCHROPHILES ....................................................................................................... Mazharul Abbasi INTRODUCTION .......................................................................................................................... DIVERSITY OF PSYCHROPHILES .......................................................................................... MECHANISMS OF ADAPTATION ............................................................................................ Changes in the Cellular Envelopes ......................................................................................... Cryoprotection ........................................................................................................................ Enzymes .................................................................................................................................. Energy Conservation and Metabolic Pathways ...................................................................... Cold Shock Proteins (CSPS) ................................................................................................... Chaperones .............................................................................................................................. Other Adaptations ................................................................................................................... APPLICATIONS ............................................................................................................................ Enzymes .................................................................................................................................. Applications in Molecular Biology ......................................................................................... In Detergent Industry .............................................................................................................. In Food and Beverage Industries ............................................................................................ In Bioremediation ................................................................................................................... Production of Polyhydroxyalkanoates (PHAs) ....................................................................... Production of Poly Unsaturated Fatty Acids (PUFA) ............................................................. Production of Compatible Solutes .......................................................................................... FUTURE PROSPECTS ................................................................................................................. CONCLUSION ............................................................................................................................... CONSENT FOR PUBLICATION ................................................................................................ CONFLICT OF INTEREST ......................................................................................................... ACKNOWLEDGEMENT ............................................................................................................. REFERENCES ...............................................................................................................................

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CHAPTER 4 ACIDOPHILIC MICROBES: DIVERSITY AND ADAPTATION TO LOW PH Anirudra Gurung and Cyaria Gurung INTRODUCTION .......................................................................................................................... DIVERSITY OF ACIDOPHILES ................................................................................................. MECHANISMS OF ADAPTATION TO LOW PH .................................................................... Impermeable Cell Membrane ................................................................................................. Decreased Pore Size of Transporters ...................................................................................... Reverse Membrane Potential .................................................................................................. Efflux Proton Transporter .......................................................................................................

105

64 66 70 70 71 73 74 75 76 76 77 77 78 79 81 83 84 84 85 86 86 87 87 87 87

106 107 108 109 110 110 111

Cytoplasmic Buffering ............................................................................................................ Proton Uncoupling .................................................................................................................. Chaperone Proteins ................................................................................................................. Quorum Sensing (QS) System ................................................................................................ CONCLUSION AND FUTURE PROSPECTS ............................................................................ CONSENT FOR PUBLICATION ................................................................................................ CONFLICT OF INTEREST ......................................................................................................... ACKNOWLEDGEMENT ............................................................................................................. REFERENCES ...............................................................................................................................

111 111 112 112 113 113 113 113 113

CHAPTER 5 ALKALIPHILES: DIVERSITY, ADAPTATION AND APPLICATIONS ............. Supriya Mandal and Junaid Jibran Jawed INTRODUCTION .......................................................................................................................... HABITATS AND ISOLATION OF ALKALIPHILES .............................................................. DIVERSITY OF ALKALIPHILES .............................................................................................. MECHANISMS OF ADAPTATION ............................................................................................ Cell Membrane Modifications ................................................................................................ Modifications in the Cytoplasm .............................................................................................. Production of Extracellular Biomolecules .............................................................................. Genomic Properties ................................................................................................................. APPLICATIONS ............................................................................................................................ Biofuels ................................................................................................................................... Enzymes .................................................................................................................................. Bioplastics ............................................................................................................................... Paper Industry ......................................................................................................................... Pharmaceutical Products ......................................................................................................... Bioremediation ........................................................................................................................ FUTURE PROSPECTS ................................................................................................................. CONCLUDING REMARKS ......................................................................................................... LIST OF ABBREVIATIONS ........................................................................................................ CONSENT FOR PUBLICATION ................................................................................................ CONFLICT OF INTEREST ......................................................................................................... ACKNOWLEDGEMENTS ........................................................................................................... REFERENCES ...............................................................................................................................

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CHAPTER 6 HALOPHILIC MICROORGANISMS: DIVERSITY, ADAPTATION AND APPLICATION ....................................................................................................................................... Bomba Dam, Srikanta Pal, Abhijit Sar and Puja Mukherjee INTRODUCTION .......................................................................................................................... SALINE ENVIRONMENTS ......................................................................................................... TAXONOMIC DIVERSITY OF HALOPHILES ....................................................................... Taxonomic Diversity of Halophiles in Sambhar Lake ........................................................... PHYSIOLOGICAL DIVERSITY OF HALOPHILES ............................................................... SALT ADAPTATION MECHANISMS IN HALOPHILES ...................................................... ADDITIONAL BENEFITS OF GENERAL SALT TOLERANCE MACHINERIES ............ Heavy Metal Tolerance ........................................................................................................... Antibiotic Resistance .............................................................................................................. Ionic Liquid Tolerance ............................................................................................................ APPLICATION OF HALOPHILES IN DIFFERENT SETTINGS .......................................... Plant Growth Promotion Under Salt Stress ............................................................................ Halophiles and Fermented Foods ............................................................................................ Industrially Important Enzymes ..............................................................................................

120 123 124 126 127 128 129 130 131 131 132 134 135 136 137 138 139 140 140 140 140 140 146 147 147 149 153 153 155 158 159 160 160 161 161 163 163

Bioremediation of Polluted Environments .............................................................................. Biocontrol Activity ................................................................................................................. Pigments .................................................................................................................................. Biopolymers ............................................................................................................................ Halocins .................................................................................................................................. Compatible Solutes ................................................................................................................. Halophiles and Astrobiology Research ................................................................................... CONCLUDING REMARKS ......................................................................................................... CONSENT FOR PUBLICATION ................................................................................................ CONFLICT OF INTEREST ......................................................................................................... ACKNOWLEDGEMENTS ........................................................................................................... REFERENCES ...............................................................................................................................

163 164 164 164 165 166 166 166 167 167 167 167

CHAPTER 7 PIEZOPHILES: QUIDDITY OF EXTREME PRESSURE DEVOTEES ............... Janki Ruparelia, Aniruddh Rabari, Nishra Joshi, Meenu Saraf and Chaitanya Kumar Jha INTRODUCTION .......................................................................................................................... Origin and Distribution of Piezophiles in Piezosphere ........................................................... Cultivation Methods for Piezophiles ...................................................................................... DIVERSITY OF PIEZOPHILES ................................................................................................. MECHANISMS OF ADAPTATION ............................................................................................ APPLICATIONS ............................................................................................................................ FUTURE PROSPECTS ................................................................................................................. CONCLUDING REMARKS ......................................................................................................... CONSENT FOR PUBLICATION ................................................................................................ CONFLICT OF INTEREST ......................................................................................................... ACKNOWLEDGEMENTS ........................................................................................................... REFERENCES ...............................................................................................................................

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CHAPTER 8 XEROPHILES ............................................................................................................... Aranya Mitra and Avishek Banik INTRODUCTION .......................................................................................................................... DIVERSITY OF XEROPHILIES ................................................................................................. MECHANISMS OF ADAPTATION ............................................................................................ Behavioral Adaptations ........................................................................................................... Physiological Adaptations ...................................................................................................... Metabolic Adaptations ............................................................................................................ Molecular Adaptations ............................................................................................................ ASTROBIOLOGICAL SIGNIFICANCE OF XEROPHILES .................................................. FUTURE PROSPECTS AND CONCLUSION ............................................................................ CONSENT FOR PUBLICATION ................................................................................................ CONFLICT OF INTEREST ......................................................................................................... ACKNOWLEDGEMENTS ........................................................................................................... REFERENCES ...............................................................................................................................

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CHAPTER 9 RADIATION RESISTANT MICROORGANISMS ................................................... Upal Das Ghosh INTRODUCTION .......................................................................................................................... Types of Radiation .................................................................................................................. Ionizing Radiation ......................................................................................................... Non-Ionizing Radiation ................................................................................................. DIVERSITY OF RADIATION RESISTANT BACTERIA AND THEIR EVOLUTION ......

182 184 186 187 189 190 193 193 194 194 194 194

202 203 204 204 207 213 214 215 215 216 216 216 216 223 223 224 224 225 226

MECHANISMS OF RADIATION RESISTANCE ..................................................................... Radiation-Induced Damage .................................................................................................... Ionizing Radiation Induced Damage ...................................................................................... Non-Ionizing Radiation Induced Damage .............................................................................. ADAPTATIONS AGAINST RADIATION .................................................................................. Repair of DNA Damage .......................................................................................................... Repair of Protein Damage ....................................................................................................... Efficient Cellular Damage Control Mechanisms .................................................................... Role of Small Non-Coding RNAs .......................................................................................... APPLICATIONS OF RADIATION RESISTANCE ................................................................... Environmental and Waste Management ................................................................................. Biotechnology and Therapeutics ............................................................................................. FUTURE PROSPECTS ................................................................................................................. CONCLUDING REMARKS ......................................................................................................... CONSENT FOR PUBLICATION ................................................................................................ CONFLICT OF INTEREST ......................................................................................................... ACKNOWLEDGEMENTS ........................................................................................................... REFERENCES ...............................................................................................................................

228 228 230 232 234 235 237 237 238 239 239 239 240 240 241 241 241 241

CHAPTER 10 METALLOPHILES AND HEAVY METAL BIOREMEDIATION ...................... Upashna Chettri and Santa Ram Joshi INTRODUCTION .......................................................................................................................... SOURCES OF HEAVY METAL CONTAMINATION ............................................................. EFFECTS OF METAL ON DIVERSITY OF METALLOPHILIC BACTERIA .................... MECHANISMS AND GENETIC BASIS OF HEAVY METAL RESISTANCE IN BACTERIA ..................................................................................................................................... POTENTIAL ROLE OF BACTERIA IN BIOREMEDIATION .............................................. PHYTOREMEDIATION AND MICROBIAL ASSOCIATIONS ............................................. CONCLUDING REMARKS ......................................................................................................... FUTURE PROSPECTS ................................................................................................................. LIST OF ABBREVIATIONS ........................................................................................................ CONSENT FOR PUBLICATION ................................................................................................ CONFLICT OF INTEREST ......................................................................................................... ACKNOWLEDGEMENTS ........................................................................................................... REFERENCES ...............................................................................................................................

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CHAPTER 11 ANAEROBES ............................................................................................................... Arijit Pal and Sekhar Pal INTRODUCTION .......................................................................................................................... DIVERSITY OF ANAEROBES .................................................................................................... Archaea ................................................................................................................................... Bacteria ................................................................................................................................... MECHANISMS OF ADAPTATION ............................................................................................ Archaeal Mechanisms of Anaerobicity ................................................................................... Bacterial Mechanisms of Anaerobicity ................................................................................... APPLICATIONS OF ANAEROBES ............................................................................................ Production of Biofuel Ethanol and Alcoholic Beverages ....................................................... Waste-Water Treatment .......................................................................................................... Detoxification of Poisonous Gas and Halogenated Aromatic Compounds ............................ Improvement of Soil Fertility ................................................................................................. Production of High Value Organic Acids ............................................................................... Various other Contributions: from Environment to Economy ...............................................

275

247 249 251 253 256 261 262 263 263 263 263 263 263

275 276 281 286 301 301 309 312 312 312 313 313 313 314

FUTURE PROSPECTS ................................................................................................................. CONCLUDING REMARKS ......................................................................................................... CONSENT FOR PUBLICATION ................................................................................................ CONFLICT OF INTEREST ......................................................................................................... ACKNOWLEDGEMENT ............................................................................................................. REFERENCES ...............................................................................................................................

314 315 315 315 315 315

CHAPTER 12 OLIGOTROPHS: MICROBES AT LOW NUTRIENT LEVELS ......................... Bipransh Kumar Tiwary and Nitya Rai INTRODUCTION .......................................................................................................................... OLIGOTROPHS: DEFINITION AND CHARACTERISTICS ................................................ CLASSIFICATION OF OLIGOTROPHS .................................................................................. METHODS OF ISOLATION AND CULTIVATION OF OLIGOTROPHS ........................... Extinction Culturing Method .................................................................................................. High-Throughput Culturing (HTC) Method ........................................................................... Filtration-Acclimatization Method (FAM) ............................................................................. Diffusion Bioreactor Method .................................................................................................. Soil Substrate Membrane System (SSMS) ............................................................................. Chemostat Selection Method .................................................................................................. DIVERSITY OF OLIGOTROPHS ............................................................................................... OLIGOTROPHS VS COPIOTROPHS ........................................................................................ SIGNIFICANCES AND APPLICATIONS OF OLIGOTROPHS ............................................ Biological Monitoring of Heavy Metals ................................................................................. Monitoring of Asepetic Pharmaceutical Production Units ..................................................... Biocontrol ............................................................................................................................... Production of Useful Microbial Metabolites .......................................................................... Plant Growth-Promoting Rhizobacteria (PGPR) .................................................................... Insecticide Bioremediation ..................................................................................................... Sand Fixing Agent .................................................................................................................. CONCLUSION AND FUTURE PROSPECTS ............................................................................ CONSENT FOR PUBLICATION ................................................................................................ CONFLICT OF INTEREST ......................................................................................................... ACKNOWLEDGEMENTS ........................................................................................................... REFERENCES ...............................................................................................................................

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CHAPTER 13 DIVERSITY AND MECHANISMS OF ADAPTATION OF PREDOMINANT BACTERIAL CHEMOLITHOTROPHS IN EXTREME HABITATS ............................................. Kunal Kumar Saha, Subhrangshu Mandal and Masrure Alam INTRODUCTION .......................................................................................................................... DIVERSITY AND MECHANISMS OF EXTREMOPHILIC LITHOTROPHY .................... Iron Lithotrophy ...................................................................................................................... Lithotrophic Attributes by Extremophilic Iron Oxidizing Bacteria (FeOB) ................. Bacterial Diversity and Habitat Specialization Among Extremophilic, Lithotrophic FeOB ............................................................................................................................. Mechanisms of Fe (II) Oxidation by Extremophilic, Lithotrophic FeOB ..................... Sulfur Lithotrophy .................................................................................................................. Sulfur Lithotrophy in Extremophilic Bacterial Candidates .......................................... Bacterial Diversity and Habitat Specialization Among Extremophilic, Lithotrophic Sulphur-Oxidizing Bacteria (SOB) ............................................................................... Mechanisms of Sulfur Oxidation by Extremophilic, Lithotrophic SOB ........................ Hydrogen Lithotrophy ............................................................................................................ Lithotrophy By Extremophilic Hydrogen (H2 ) Oxidizing Bacteria (HOB) ..................

333 334 337 338 339 340 340 340 341 341 342 343 345 345 346 346 346 346 347 347 347 348 348 348 348 356 356 359 359 359 360 362 364 364 364 366 370 370

Bacterial Diversity and Habitat Specialization Among Extremophilic Lithotrophic HOB ............................................................................................................................... Mechanisms of H2 Oxidation by Extremophilic, Lithotrophic HOB ............................ APPLICATIONS OF LITHOTROPHIC EXTREMOPHILIC BACTERIA ........................... CONCLUDING REMARKS ......................................................................................................... CONSENT FOR PUBLICATION ................................................................................................ CONFLICT OF INTEREST ......................................................................................................... ACKNOWLEDGEMENTS ........................................................................................................... REFERENCES ............................................................................................................................... CHAPTER 14 APPLICATIONS OF EXTREMOPHILES .............................................................. Urmimala Sen and Subhra Kanti Mukhopadhyay INTRODUCTION .......................................................................................................................... APPLICATIONS OF OLIGOTROPHS ....................................................................................... APPLICATIONS OF THERMOPHILES .................................................................................... APPLICATIONS OF HALOPHILES .......................................................................................... APPLICATIONS OF PSYCHROPHILES .................................................................................. APPLICATIONS OF ACIDOPHILES ......................................................................................... APPLICATIONS OF ALKALIPHILES ...................................................................................... APPLICATION OF RADIATION-RESISTANT MICROORGANISMS ................................ APPLICATIONS OF PIEZOPHILES ......................................................................................... APPLICATION OF HEAVY METAL RESISTANT MICROORGANISMS ......................... CONCLUSION ............................................................................................................................... CONSENT FOR PUBLICATION ................................................................................................ CONFLICT OF INTEREST ......................................................................................................... ACKNOWLEDGEMENT ............................................................................................................. REFERENCES ...............................................................................................................................

370 379 380 381 383 383 383 383 395 395 397 398 399 402 404 404 405 406 407 407 408 408 408 408

SUBJECT INDEX .................................................................................................................................... 418

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FOREWORD I am extremely happy to know that a book titled “Extremophiles: Diversity, Adaptations and Applications” edited by Dr. Masrure Alam, Assistant Professor and officiating Head, Department of Biological Sciences, Aliah University, Kolkata and Dr. Bipransh Kumar Tiwary, Assistant Professor and Head, Department of Microbiology, North Bengal St. Xavier’ College, Jalpaiguri is ready for academicians. The present book covers the most relevant and promising research on “Extremophiles”. This is evident from the content of the book covering overview on Hyperthermophiles, Acidophilic microbes, Alkaliphiles, Xerophytes and various microorganisms including RadiationResistant Microorganisms. The book also deals with the diversity and the mechanism of adaptation of predominant bacterial chemolithotrophs in extreme habitats. In the past also, the research on extremophiles enabled the scientists to understand the challenges in existing biochemistry and molecular biology and helped to know about the new product in the biotechnology industry. The endeavor in editing the book by both is commendable. I am sure the book will enrich the knowledge of students and faculty of microbiology associated with these fields because this covers all major developments in research on extremophiles. I would also like to thank all the authors for their dedicated effort in taking up such important fields of microbiology and describing the importance of extremophiles for industrial purposes. I wish this effort a grand success.

Ramesh Kumar Pandey Vice-Chancellor Usha Martin University & Former Vice-Chancellor Ranchi University Jharkhand, India

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PREFACE Extremophiles are nature’s ultimate survivors, thriving in environments ranging from the frozen Antarctic to abyssal hot hydrothermal vents. Interestingly, the discovery of several habitats/environments, resembling that of outer space, on the surface of Earth, and the discovery of organisms that thrive in such extreme environments have given many of the clues to find ‘life’ outside the Earth’s environment. Though life is believed to be originated amidst high temperature, highly reducing and acidic conditions of early Earth, many of these sites on the surface of our planet have been explored only recently, which contain environmental extremes that were unimaginable to our forefathers. The organisms that survive and grow under such harsh environmental conditions, which are uninhabitable to other organisms, are called extremophiles. High-temperature environments occur in terrestrial hot springs and marine hydrothermal vents where the temperature could reach 100°C to 350°C. Several thermophilic (optima between 55°C and 65°C) and hyperthermophilic (optima between 80°C and 113°C) bacteria and archaea have been isolated that can grow optimally at temperatures above the boiling point of water. Psychrophiles on the other hand can grow optimally below the freezing point of water. Bacteria, like Deinococcus radiodurans is one of the most radiation-resistant organisms known and is capable of withstanding acute doses of gamma radiation. Environments with extreme atmospheric pressure, for example, deepest sea floor environments (e.g., Mariana trench, 10,898m deep), having a pressure of almost 1200 atm, harbor barophilic/piezophilic microbial community. Xerophiles can tolerate extreme desiccation by entering anhydrobiosis, a state characterized by little intracellular water and no metabolic activity. A number of gram-positive bacteria can form a special resistant, dormant structure called an endospore. These structures are extraordinarily resistant to environmental stresses such as desiccation, heat, ultraviolet radiation, gamma radiation, chemical disinfectants, etc. Environments, like the Dead Sea (a salt lake between Israel and Jordan and the lowest lake in the world) and the Great Salt Lake in Utah, despite having saturated salt (NaCl) concentrations, holds extreme halophiles, like Halobacterium salinarum which can grow at a salt concentration of 6.2 M. Highly acidic environments, like Rio Tinto river in Spain which has a pH of 1 to 2, and Danakil depression in Ethiopia which has a pH of 0, harbor acidophiles (e.g. Sulfolobus acidocaldarius, Ferroplasma acidarmanus and Picrophilus oshimae) which have their growth optimum of pH 0 or closer to it. Bacillus alcalophilus, and Microcystis aeruginosa on the other hand inhabit natural alkaline soda lakes where pH can reach about 12.0. There are a number of anaerobic bacteria and archaea that can live in complete anoxic environments by using terminal electron acceptors other than oxygen. Some microorganisms, called poly-extremophiles, are adapted to multiple environmental extremities. Thus far hundreds of phylogenetically diverse extremophiles have been isolated or identified from diverse environmental extremes. In the last few decades, the research on extremophiles has not only provided ground-breaking discoveries that challenge our understanding of biochemistry and molecular biology but also has boosted the biotech industry to search for new products from them. On the applied side, extremophiles and their enzymes have spawned a multibillion-dollar biotechnology industry, with applications spanning biomedical, pharmaceutical, industrial, environmental, and agricultural sectors. The mechanism of adaptation to such environments by the extremophiles has also been well studied in the last few decades. Thus, the book aims to provide the most comprehensive and reliable current state of knowledge on the diversity of extremophiles along with the descriptions of the environments from which they have been isolated, mechanisms of their adaptation to such harsh environments, their applications in human

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welfare, and future scope. Indeed, the application of extremophiles and their biologically active compounds has opened a new era in biotechnology. However, despite the latest advances, we are just at the beginning of exploring the biotechnological potentials of extremophiles. This book consists of fourteen chapters that explore the fascinating world of microbes in extreme environments. The first chapter deals with the overview of extremophiles and their strategies of adaptations in extreme environments. The rest of the chapters of the book cover the details including recent scientific information and future prospects of all types of extremophiles, including hyperthermophiles, psychrophiles, halophiles, acidophiles, alkaliphiles, xerophiles, chemolithotrophs, oligotrophs and anaerobic and other extremophiles. Each chapter is organized in such a way to cater to the knowledge of extremophiles (underrated fascinating microbes) including diversity, adaptations, and applications to the scientific community. This book provides an overview of the current state of knowledge and all major developments in research of all types of the fascinating group of life-forms i.e., extremophiles. This book is an essential read for microbiologists working with extremophiles and their potential biotechnological applications, as well as for all budding microbiologists. The book is also recommended as a reference text for anyone interested in the field of research encouraging readers to reach out to new worlds and discoveries. Finally, we express our gratitude to Professor Ramesh Kumar Pandey, Vice-Chancellor, Usha Martin University, Ranchi, Jharkhand, India, who has always been an inspirational persona to the young scientific community. With his profound knowledge on the subject, he prudently intuited the importance of the work and kindly wrote the foreword of this edited book. We are also grateful to Prof. Mahammad Ali, Vice Chancellor, Aliah University, Kolkata, India, for providing all necessary facilities and a conducive academic ambience ensuring smooth completion of the book. We are extremely grateful to Fr. Dr. Lalit P Tirkey, Principal, North Bengal St. Xavier’s College, West Bengal, India, for his enthusiastic support and encouragement in the completion of the project. We are also thankful to all authors for their hard work and professionalism in making this book a reality. Their expertise in the contributed chapters is acknowledged and appreciated. Our appreciation and credit go to Mrs. Humaira Hashmi, Editorial Manager Publications, Bentham Books for generous assistance, constant support, and patience in materializing the book. Lastly, we thank everybody who helped us in the successful realization of this book and express our apology that their names could not be mentioned personally.

Masrure Alam Dept. of Biological Sciences Aliah University, IIA/27, New Town Kolkata 700160, West Bengal India Bipransh Kumar Tiwary Department of Microbiology North Bengal St. Xavier’s College Rajganj, Jalpaiguri West Bengal India

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ABOUT THE EDITORS Dr. Masrure Alam Dr. Masrure Alam is an Assistant Professor and former officiating Head of the Department of Biological Sciences, Aliah University, Kolkata, India. He had been associated with the West Bengal Education Services, GoWB, as an Assistant Professor of Microbiology in Bidhannagar College, Salt Lake, Kolkata. He has received his MSc and PhD degrees in Microbiology from The University of Burdwan and The University of Calcutta respectively. Dr. Alam has done his PhD and postdoctoral research in the Department of Microbiology, Bose Institute, Kolkata. His main area of research is microbial ecology and physiology. He has published more than 12 research papers in highly reputed scientific journals such as Molecular Microbiology, Journal of Bacteriology, Applied and Environmental Microbiology, Proteomics, Microbiological Research, FEMS Microbiology Letters, PLoS One, etc. He has also served as reviewer for many reputed journals. Dr. Bipransh Kumar Tiwary Bipransh Kumar Tiwary is an Assistant Professor and Head at Department of Microbiology, North Bengal St. Xavier’s College, Rajganj, Jalpaiguri, West Bengal, India. He received his M.Sc. degree in Microbiology. and Ph.D. degree in Biotechnology from the University of North Bengal, Siliguri, West Bengal. His main areas of research are biochemistry, medical microbiology molecular biology, Computer aided drug design, antimicrobials, quorum sensing in bacteria. He has published research articles in scientific journals such as Plos one, RSC Advance, BMC complementary and alternative medicine and Letters in applied Microbiology and one book. He has experience of teaching biochemistry and molecular biology for more than 10 years. He is reviewer of several reputed journals. He is Lifetime member of Association of Microbiologists of India (AMI), India.

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List of Contributors Abhijit Sar

Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India

Aniruddh Rabari

Microbiology Department, Gujarat Arts and Science College, Ellisbridge, Ahmedabad-380006 Gujarat, India

Anirudra Gurung

Department of Botany, St. Joseph’s College, Darjeeling, 734104, India

Aranya Mitra

School of Biotechnology, Presidency University, Canal Bank Road, DG Block (Newtown), Action Area 1D, Newtown, Kolkata-700156, West Bengal, India

Aranya Mitra

Department of Microbiology and Biotechnology, JIS University, Agarpara, Kolkata- 700109, India

Avishek Banik

School of Biotechnology, Presidency University, Canal Bank Road, DG Block (Newtown), Action Area 1D, Newtown, Kolkata-700156, West Bengal, India

Baishali Pandit

Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata 700160, West Bengal, India, Department of Botany, Surendranath College, 24/2 MG Road, Kolkata-700009, West Bengal, India

Bipransh Kumar Tiwary

Department of Microbiology, North Bengal St. Xavier’s College, Rajganj, Jalpiguri, West Bengal, India

Bomba Dam

Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India

Chaitanya Kumar Jha

Microbiology Department, Gujarat Arts & Science College, Ellisbridge, Ahmedabad-380006 Gujarat, India

Cyaria Gurung

Department of Botany, Siliguri College, Darjeeling, West Bengal 734003, India

Janki Ruparelia

Microbiology Department, Gujarat Arts & Science College, Ellisbridge, Ahmedabad-380006 Gujarat, India

Junaid Jibran Jawed

School of Biotechnology, Presidency University- New Campus, Canal Bank Road, DG Block (Newtown), Action Area 1D, Kolkata- 700156, West Bengal, India

Kunal Kumar Saha

Mycology and plant pathology laboratory, Department of Botany, Visva Bharati University, Santiniketan -731235, West Bengal, India

Masrure Alam

Dept. of Biological Sciences, Aliah University, IIA/27, New Town, Kolkata 700160, West Benga, India

Mazharul Abbasi

Department of Microbiology, Government General Degree College, Narayangarh, Paschim Medinipur, West Bengal, India

Meenu Saraf

Department of Microbiology and Biotechnology, University School of Science Gujarat University, Navrangpura Ahmedabad 380009, Gujarat, India

Nishra Joshi

Microbiology Department, Gujarat Arts & Science College, Ellisbridge, Ahmedabad-380006 Gujarat, India

vi Nitya Rai

Department of Microbiology, North Bengal St. Xavier's College, Rajganj, Jalpiguri, West Bengal-735135, India

Puja Mukherjee

Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India

Santa Ram Joshi

Microbiology Laboratory, Department of Biotechnology & Bioinformatics North-Eastern Hill University Shillong 793022, Meghalaya, India

Sekhar Pal

Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata- 700118, India

Srikanta Pal

Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India

Subhra Kanti Mukhopadhyay

Department of Microbiology, The University of Burdwan, Golapbag, Bardhaman – 713104, West Bengal, India

Subhrangshu Mandal

Mycology and Plant Pathology Laboratory, Department of Botany, Visva Bharati University, Santiniketan-731235, West Bengal, India

Supriya Mandal

School of Biotechnology, Presidency University- New Campus, Canal Bank Road, DG Block (Newtown), Action Area 1D, Kolkata- 700156, West Bengal, West Bengal, India

Upal Das Ghosh

Upal Das Ghosh: Department of Microbiology, Bidhannagar College, Kolkata, India

Upashna Chhetri

Microbiology Laboratory, Department of Biotechnology & Bioinformatics North-Eastern Hill University Shillong 793022, Meghalaya, India

Urmimala Sen

Department of Microbiology, The University of Burdwan, Golapbag, Bardhaman – 713104, West Bengal, India

Extremophiles: Diversity, Adaptation and Applications, 2022, 1-23

1

CHAPTER 1

Extremophiles: An Overview Bipransh Kumar Tiwary1 and Masrure Alam2,* Department of Microbiology, North Bengal St. Xavier’s College, Rajganj, Jalpaiguri, West Bengal, India 2 Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata-700160, West Bengal, India 1

Abstract: Earth contains several environmental extremes which are uninhabitable for most of the living beings. But, astonishingly, in the last few decades, several organisms thriving in such extreme environments have been discovered. “Extremophiles”, meaning “Lovers of Extremities” are the entities that are especially adapted to live in such harsh environmental conditions in which other entities cannot live. The discovery of extremophiles has not only boosted the biotech industry to search for new products from them, but also made researchers to think for the existence of extra-terrestrial life. The most inhospitable environments include physical or chemical extremities, like high or low temperatures, radiation, high pressure, water scarcity, high salinity, pH extremes, and limitation of oxygen. Microorganisms have been found to live in all such environmental conditions, like hyperthermophiles and psychrophiles, acidophiles and alkaliphiles. Bacteria like Deinococcus radiodurans, which is able to withstand extreme gamma radiation, and Moritella sp., able to grow at atmospheric pressure of >1000 atm, have been reported. Environments like the Dead Sea, having saturated NaCl concentrations, hold extreme halophiles like Halobacterium salinarum. Highly acidic environments, like the Rio-Tinto River in Spain or Danakil depression in Ethiopia harbour acidophiles with growth optima of pH zero, or close to it. Bacillus alcalophilus, and Microcystis aeruginosa on the other hand inhabit natural alkaline soda lakes where pH can reach about 12.0. A number of anaerobic prokaryotes can live in complete anoxic environments by using terminal electron acceptors other than oxygen. In this chapter, we shall discuss very briefly the diversity of all extremophiles and their mechanism(s) of adaptation.

Keywords: Acidophiles, Alkaliphiles, Anaerobic microorganisms, Halophiles, Hyperthermophiles, Piezophiles, Psychrophiles, Radiation resistant microorganisms.

Corresponding author Masrure Alam: Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata - 700160, West Bengal, India; E-mail: [email protected]

*

Masrure Alam and Bipransh Kumar Tiwary (Eds.) All rights reserved-© 2022 Bentham Science Publishers

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INTRODUCTION Many scientists across the world are focused on subjects like “origin of life” and “life beyond Earth” and are searching for evidences of past or present life forms on Mars, or on Jupiter’s moon Europa, or Saturn’s moon Enceladus, or anywhere else in our solar system or other parts of the universe. The discovery of several environments on the surface of Earth that may resemble the conditions of outer space, and the discovery of many microorganisms that thrive in such extreme environments, have boosted the confidence of astrobiologists about the existence of life beyond our planet Earth. Several environments, such as high-temperature terrestrial hotsprings, or hydrothermal vents; highly acidic Rio Tinto and Danakil Depression or highly alkaline soda lakes; highly saline Dead Sea and Salt Lake; very high atmospheric/hydrostatic pressure of deep sea, etc. may resemble the extra-terrestrial environmental conditions. Organisms that live in such harsh environmental conditions, which are uninhabitable to other life forms, are called extremophiles (Roman “Extremus” meaning “outermost” plus the Greek “Philos” meaning “lovers”). Several thermophilic and hyperthermophilic bacteria and archaea, some of which even grow above the boiling temperature of water, have been isolated from terrestrial hot springs or marine hydrothermal vents where the temperature could reach 100 °C to 350 °C. On the other hand, psychrophiles can grow optimally below the freezing point of water. Deepest sea floors with extreme hydrostatic pressure (e.g., Mariana trench, 10,898m deep, having pressure of almost 1200 atm.) harbour barophilic/piezophilic microbial community. Deinococcus radiodurans is one of the most radiation-resistant organisms known so far and is able to withstand a severe dose of gamma radiation. Xerophiles can tolerate extreme desiccation by entering anhydrobiosis, a physiological state that allows the organism to survive with little intracellular water and no metabolic activity. Other environments, like the Dead Sea (the lowest lake in the world) and Great Salt Lake in Utah, despite being saturated with salt (NaCl), are inhabited by extreme halophiles, like Halobacterium salinarum which can grow at a salt concentration of 6.2 M. Danakil depression in Ethiopia and Rio-Tinto river in Spain with a pH of almost 0 to 2, are inhabited by extreme acidophiles, like Sulfolobus acidocaldarius, Ferroplasma acidarmanus, Picrophilus oshimae, etc. which have their growth optima of pH 0 or closer to it. Several natural alkaline soda lakes around the world where pH can reach about 12.0 are inhabited by alkaliphiles, such as Bacillus alcalophilus, Microcystis aeruginosa, etc. Some extremophiles, called poly-extremophiles, are adapted to multiple environmental extremities.

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Extremophiles: Diversity, Adaptation and Applications 3

HYPERTHERMOPHILES Diversity Temperature is one of the most important factors that determine the structure, and thus functionality of cellular components of living beings. Change in temperature causes several changes, from the damage of the structure of biomolecules through the formation of ice crystals at low temperature, to the denaturation or degradation of all the biomolecules towards the higher side. Temperature near or above 100 °C denatures structural proteins, enzymes, nucleic acids and other essential biomolecules, as well as affects the interaction or association among those molecules by hindering most of the noncovalent interactions. Fluidity of cell membrane, thereby cellular function, is also affected by high and low temperatures with a decrease in fluidity towards the lower end and an increase in fluidity, ultimately leading to its denaturation, towards higher. Furthermore, due to the low solubility of essential gases, such as O2 or CO2, in water at high temperature, aquatic organisms face problems when the temperature rise. Notwithstanding these damaging effects of high temperature, several organisms have not only been found in the last few decades to endure high temperatures but also to live naturally in environments with temperatures as high as 100 °C or more. Such high-temperature environments are found in terrestrial hot springs and solfataric fields, where the temperature remains high because of the discharge of hot-water heated from underneath magma chambers; and in marine hydrothermal vents where temperature can reach up to about 400 °C because of the discharge of mineral-containing hydrothermal fluids into the surrounding deep sea cold water, building up rock chimneys with temperature gradients [1]. During the 1960s and 1970s Thomas D. Brock isolated numerous thermophilic (organisms which grow optimally at 55 °C to 65 °C with upper limit of up to 80 °C) bacteria and archaea, including Thermus aquaticus and Sulfolobus acidocaldarius which grow optimally at temperatures up to 75 °C, from thermal hot springs of Yellowstone National Park [2 - 4]. These findings changed the previous knowledge of uppertemperature range at which an organism can live. Later, a team led by K. O. Stetter of the University of Regensburg, Germany isolated several bacteria and archaea from boiling springs, mud pools and hydrothermal vents of several areas one after another with higher and higher temperature limit [5]. The first hyperthermophile (organisms that grow optimally above 80 °C) reported was the methanogen Methanothermus fervidus which was found to grow at temperatures as high as 97 °C with optimum being 82 °C [6]. More surprising was the finding of the ability of the archaeon Pyrodictium occultum, isolated from a submarine solfataric field on the hot sea floor at Vulcano Island, Italy, to grow above the boiling point of water (100 °C). P. occultum was reported to grow optimally at 105 °C with an upper limit of 110 °C [7]. Another archaeon Pyrolobus fumarii,

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isolated from the walls of a black smoker hydrothermal vent at the Mid Atlantic Ridge was found to have optimum and maximum growth temperatures even higher (106 °C and 113 °C respectively) [8]. The highest temperature, so far, at which microorganisms have been found to grow is 121 °C, the autoclaving temperature, by Geogemma barossii (known as strain 121) and 122 °C by Methanopyrus kandleri under high hydrostatic pressure [9, 10]. Most of the hyperthermophiles are represented by Archaea except the few bacteria like Thermotoga maritima and Aquifex pyrophilus which have the highest growth temperatures of 90 °C and 95 °C respectively. The hyperthermophiles which can grow close to or above 100 °C are described in more detail in Chapter 2. Mechanisms of Adaptation At extremely high temperatures, proteins (lacking adaptations) are generally aggregated due to irreversible unfolding which exposes the hydrophobic cores causing aggregation. In thermophiles, the molecular adaptations in cellular components such as protein, DNA, membrane lipid, etc. increase their thermal stabilities and provide energy to cope with the high temperatures. The proteins in thermophiles are well adapted to retain structure and function at high temperatures. Thermophilic protein consists of more basic amino acids such as arginine, which helps them to function at high temperatures. The presence of more hydrogen bonds, tight packing of a hydrophobic core, additional Van der Waals interactions, ionic interactions, and increased secondary structures are observed to contribute to the thermostability of the proteins. Further, the presence of more polar and charged residues on the surface contributes to increase the stability of the thermophilic proteins by preventing aggregation at higher temperatures. Increased salt bridge in ionic bonds also enhances the stability of proteins [11]. Moreover, the presence of thermostable residues can protect themselves from denaturation by increasing both the short- and long-range charge interactions [12]. There is also evidence that in thermophilic bacteria, DNA is stabilized by special histone-like proteins that increase the melting temperature of DNA. Further, increased GC base pairs at specific regions and the introduction of positive supertwist by reverse gyrase increase the stability of DNA at high temperatures [13]. The lipid composition of thermophilic membranes is also found favourable for maintaining permeability at high temperatures. Archaeal membranes, consisting of ether-based lipids, are resistant to hydrolysis at high temperatures. Thermophiles also possess thermostable branched-chain fatty acids and polyamines [14].

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PSYCHROPHILES Diversity Low-temperature environments are the most widespread on Earth’s biosphere as more than 80% of it is permanently cold with temperatures of below 5 °C [15 17]. In low-temperature environments, existence of highly diverse and widely distributed extremophiles, mainly bacteria, yeasts and microalgae have been noted despite several other limiting factors (including salinity, osmotic and hydrostatic pressure, oxidative stress, radiation, nutrient availability, etc.) [18, 19]. Lowtemperature inhabiting organisms can be subdivided into two categories. Psychrophiles, organisms that grow optimally at less than 15 °C with the upper limit of 20 °C, and psychrotolerants, which survive at temperatures below 0 °C but grow optimally at 20 °C – 25 °C [20]. Though the lower temperature limit for psychrophiles has not been clearly defined yet, a limit of -12 °C for reproduction and -20 °C for metabolic function have been proposed [21]. Hundreds of prokaryotes of diverse taxa have been reported so far to inhabit different cold environments (details of which are discussed in Chapter 3). Major representatives are the members of the Actinobacteria, Firmicutes, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Chlorobi, Chloroflexi, Cyanobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, and Spirochaetes [22]. Mechanisms of Adaptation To survive at low temperatures, the psychrophiles possess diverse molecular adaptations [23]. They maintain the membrane fluidity by increasing unsaturated fatty acids, branched-chain fatty acids, cyclopropane-containing fatty acids, and short-chain fatty acids in the membranes [23, 24]. The synthesis of RNA and proteins at low temperatures is regulated by the high synthesis of cold shock proteins (CSPs) and chaperones. Further, molecular chaperones help in refolding of proteins and also affect the levels of protein synthesis [25]. Additionally, the synthesis of anti-freeze proteins (AFPs), and their binding to ice crystals inhibit their growth while ice nucleation proteins prevent the supercooling of water by ice crystal formation [26]. Thus, psychrophiles may also use antifreeze- or ice nucleation proteins to reduce the damage caused by ice crystal formation [13, 27, 28]. Another well-studied adaptation is the gathering of compatible solutes as cryo-protectants to resist cell damage. Compatible solutes act as cryo-protectors that decrease the freezing point of the cytoplasm and possibly prevent aggregation or denaturation of proteins, stabilize membranes, and scavenge free radicles in cold conditions [29, 30]. Several adaptations in protein content of psychrophiles have also been studied in detail. The nonpolar

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residues in the protein core are reduced, which causes weaker hydrophobic interactions. The high glycine residues provide higher conformational mobility in proteins. The proline and arginine residues are reduced, which provide conformational rigidity and help in hydrogen bond formation respectively [31, 32]. ACIDOPHILES Diversity Acidophiles are organisms that prefer to grow in acidic environments with growth optima between pH 0 and 5.5. Slightly acidic environments (pH