Physiological and Biotechnological Aspects of Extremophiles

Description

Physiological and Biotechnological Aspects of Extremophiles highlights the current and topical areas of research in this rapidly growing field. Expert authors from around the world provide the latest insights into the mechanisms of these fascinating organisms use to survive. The vast majority of extremophiles are microbes which include archaea, bacteria and some eukaryotes. These microbes live under chemical and physical extremes that are usually lethal to cellular molecules, yet they manage to survive and even thrive. Extremophiles have important practical uses. They are a valuable source of industrially important enzymes and recent research has revealed novel mechanisms and biomolecular structures with a broad range of potential applications in biotechnology, biomining, and bioremediation. Aimed at research scientists, students, microbiologists, and biotechnologists, this book is an essential reading for scientists working with extremophiles and a recommended reference text for anyone interested in the microbiology, bioprospecting, biomining, biofuels, and extremozymes of these organisms. Physiological and Biotechnological Aspects of Extremophiles Copyright Contents List of contributors About the editors Preface Acknowledgments 1 Overview of extremophiles 1.1 Introduction 1.2 Eukaryotic extremophiles 1.3 Prokaryotic extremophiles in diverse habitats 1.4 Biotechnological potential of extremophiles 1.5 Molecular approaches like metagenomics and whole genome sequencing (WGS) of extremophiles 1.6 Conclusion Acknowledgments References Further reading 2 Physiology of extremophiles 2.1 Introduction 2.2 Taxonomy of extremophiles 2.3 Diversity of extremophiles 2.4 Physiological adaptations of extremophiles 2.4.1 Psychrophiles 2.4.2 Thermophiles 2.4.3 Alkaliphiles 2.4.4 Acidophiles 2.4.5 Halophiles 2.4.6 Peizophiles 2.5 Genomics and evolution 2.6 Chemotaxis in extremophiles 2.7 Conclusions and future directions Acknowledgments References Further reading 3 Mechanism of resistance focusing on copper, mercury and arsenic in extremophilic organisms, how acidophiles and thermophi... 3.1 Introduction 3.2 Mechanism 1—cellular sequestration by thiol systems 3.2.1 Low molecular weight (LMW) thiols 3.2.2 Protein thiols 3.3 Mechanism 2—none thiol, extracellular and intracellular complexation 3.3.1 Nanoparticles 3.3.2 Inorganic polyphosphates 3.4 Mechanism 3—enzymatic detoxification 3.4.1 Copper (Cu) 3.4.2 Mercury 3.4.3 Arsenic 3.5 Mechanism 4—efflux pumps and transporter 3.5.1 Copper 3.5.2 Mercury 3.5.3 Arsenic 3.6 Conclusions and future perspectives References 4 Halotolerant microbes and their applications in sustainable agriculture 4.1 Introduction 4.2 Halotolerant biota 4.3 Rhizospheric bacteria and plant growth promotion 4.4 Stress alleviation through halotolerant rhizospheric bacteria 4.5 Beneficial attributes of halotolerant PGPR 4.6 Conclusions and future perspective Acknowledgments References 5 Halophilic microorganisms: Interesting group of extremophiles with important applications in biotechnology and environment 5.1 Introduction 5.2 Habitats of halophilic microorganisms 5.3 Classification 5.4 Mechanisms of salt adaptation 5.5 Structural characteristics of halophilic proteins 5.6 Current and potential applications of halophiles 5.6.1 Food fermentation 5.6.2 Production of stable enzyme 5.6.3 Production of organic osmotic solutes 5.6.4 Production of biosurfactants and exopolysaccharides 5.6.5 Liposomes production 5.6.6 Processing of halogenated products 5.6.7 Production of alternative energy 5.6.8 Production of polyhydroxyalkanoates (PHA) 5.6.9 Transfer of the halo-tolerance 5.6.10 Production of bacteriorhodopsin with original roles 5.6.11 Important role in the bioremediation 5.7 New molecular and genomic approaches 5.7.1 Development of new genetic tools for halophiles 5.7.2 Genomic and metagenomic sequencing 5.8 Conclusion References 6 Overview of extremophiles and their food and medical applications 6.1 Introduction: what are extremophiles? 6.2 Adaptations of extremophiles at a molecular level 6.3 Thermophiles: life at high temperature 6.3.1 Habitats and diversity 6.3.2 Physiology and adaptation to high temperature 6.3.3 Thermophiles in medicine and food 6.3.4 Thermophilic enzymes and their applications 6.4 Psychrophiles: life at low temperature 6.4.1 Habitats and diversity 6.4.2 Physiological adaptation to low temperature 6.4.3 Applications of enzymes and metabolites from psychrophiles 6.5 Halophiles 6.5.1 Habitats and diversity 6.5.2 Physiological adaptations to high salt concentration 6.5.3 Medical applications of molecules from halophiles 6.5.4 Halophiles and food products 6.6 Acidophiles 6.6.1 Habitats and diversity 6.6.2 Physiological adaptation to low pH 6.6.3 Food and medicinal relevance of acidophiles 6.7 Alkaliphiles 6.7.1 Habitats and diversity 6.7.2 Physiological adaptation to high pH 6.7.3 Applications of alkaliphile enzymes 6.8 Piezophiles 6.8.1 Habitats and diversity 6.8.2 Physiological adaptation to high pressure 6.9 Radioresistant microorganisms 6.9.1 Diversity and survival strategy 6.9.2 Defense against ultraviolet radiation: sunscreen molecules and their applications 6.10 Xerophiles: life with little or no water 6.11 Metallophiles 6.12 Conclusions References 7 Applications of extremophiles in astrobiology 7.1 Introduction and historical background 7.2 Study of extremophiles in astrobiology 7.3 Planetary field analogue sites in India and its extremophilic microbial diversity 7.3.1 Lonar lake 7.3.2 Extremophiles from rocks, seawater and intertidal sea zones in arabian sea 7.3.3 Salt deposits and saline systems in Rajasthan, Gujarat and Maharashtra 7.3.4 Mud volcanoes of Andaman 7.3.5 Geothermal hotsprings, cold deserts and glaciers in Leh Ladakh, Himalayas 7.4 Extremophiles from planetary field analogue sites in Europe: astrobiological implications 7.4.1 Rio Tinto, Spain 7.4.2 Ny-Ålesund in Svalbard archipelago of Norway 7.4.3 The Ibn battuta center near Marrakech, Morocco 7.4.4 The Kamchatka Peninsula, Russia 7.4.5 Tirez Lake, Spain 7.5 Micro-organisms in earth’s upper atmosphere and outer space: applications in astrobiology missions 7.6 Extremophiles from space craft assembly room: applications in planetary protection 7.7 Conclusion and future outlook Acknowledgments References Further reading 8 High-pressure adaptation of extremophiles and biotechnological applications 8.1 Introduction 8.2 Effects of pressure on macromolecules and cells 8.2.1 Nucleic acids 8.2.2 Proteins 8.2.3 Phospholipids 8.2.4 Cells 8.3 Pressure adaptation in piezophiles 8.3.1 Genomes 8.3.2 Proteins 8.3.3 Membrane lipids 8.4 Pressure biotechnological applications 8.4.1 Food industry 8.4.1.1 Food preservation 8.4.1.2 Pre-treatment 8.4.2 Allergenicity and digestibility 8.4.3 Medical applications 8.4.3.1 Antiviral vaccines 8.4.3.2 Bacterial ghosts 8.4.3.3 Vaccine preservation 8.4.3.4 Cryopreservation 8.4.4 Biotechnological applications 8.4.4.1 Bio-purification 8.4.4.2 Modulation of cell activity 8.5 Biotechnological applications of piezophiles 8.6 Conclusion and future perspectives References 9 Fructanogenic halophiles: a new perspective on extremophiles 9.1 Introduction 9.2 Fructans 9.3 Microbial fructan synthesis mechanism 9.4 Fructanogenic halophiles 9.5 Putative GH68 family enzymes of haloarchaea 9.6 Levan and levansucrase from Halomonas smyrnensis AAD6 9.7 Conclusions and future directions References 10 Applications of sulfur oxidizing bacteria 10.1 Introduction 10.2 Oxidation behavior of sulfur oxidizing bacteria 10.3 Photoautotrophic oxidation 10.4 Chemolithotrophic sulfide oxidation 10.5 Enzyme responsible for sulfur oxidation 10.6 Applications 10.6.1 Sulfur oxidizing bacteria in biogeochemical cycling 10.6.2 Bioleaching 10.6.3 Bioremediation 10.6.4 Biofilteration 10.6.5 Biofertilizers 10.6.6 Bio controlling agent 10.6.7 Deodorization 10.6.8 Rubber recycling 10.6.9 Biosensor 10.7 Conclusions References Further reading 11 Physiological and genomic perspective of halophiles among different salt concentrations 11.1 Introduction 11.2 Classification and evolutionary relationships among halophiles 11.3 Mechanism of salt adaptation in halophiles 11.3.1 ‘‘High-salt-in’’ strategy 11.3.2 ‘‘low-salt-in’’ strategy 11.4 Extracellular hydrolytic enzymes from haloarchaea 11.5 Genomic insights into halophilic prokaryotes 11.5.1 Case study of square archaeon Haloquadratumwalsbyi 11.5.2 Case study of Halobacterium sp. NRC-1 11.6 Concluding remarks References Further reading 12 CRISPR/Cas system of prokaryotic extremophiles and its applications 12.1 Introduction 12.2 Organization of CRISPR/Cas in bacteria 12.3 Classification of CRISPR cas system 12.3.1 Type I CRISPR system 12.3.2 Type II CRISPR or gRNA-Cas9 complex system 12.3.3 Type III CRISPR system 12.4 CRISPR-Cas system in extremophiles 12.5 CRISPR/Cas system of halophilic archaea 12.6 Delivery methods 12.7 Applications 12.8 Conclusion and future directions Acknowledgments References Further reading 13 Lipases/esterases from extremophiles: main features and potential biotechnological applications 13.1 Introduction 13.2 Structural features and classification of esterases/lipases 13.3 Thermophilic esterases/lipases 13.4 Psychrophilic esterases/lipases 13.5 Other extremophilic esterases/lipases 13.5.1 Halophiles 13.5.2 Alkalophiles/acidophiles 13.6 Running and potential applications for extremophilic esterases/lipases 13.6.1 Detergent 13.6.2 Food 13.6.3 Biodiesel 13.6.4 Drug 13.6.5 Oleochemical 13.6.6 Dairy 13.7 Conclusion and future References 14 Thermostable Thermoanaerobacter alcohol dehydrogenases and their use in organic synthesis 14.1 Introduction 14.2 Thermoanaerobacter ADHs and their role in physiology 14.3 Structure and thermostability 14.3.1 Structure and binding pocket specificity 14.3.2 Thermal stability of TADHs 14.4 Biocatalysis using thermostable TADHs 14.5 Enzyme improvement 14.5.1 Altering cofactor preference 14.5.2 Altering stereoselectivity 14.5.3 Altering substrate specificity 14.6 Conclusions and future directions References 15 Biotechnological platforms of the moderate thermophiles, Geobacillus species: notable properties and genetic tools 15.1 Introduction 15.2 Overview of the genus Geobacillus 15.2.1 History 15.2.2 Species placed under the genus Geobacillus 15.2.3 Diverse habitats and their implications 15.2.4 Cellular characterization 15.2.5 Genomic features 15.3 Genetic tools for Geobacillus spp. 15.3.1 Plasmid replicons 15.3.2 Antibiotic resistance markers 15.3.3 Counterselection markers 15.3.4 Recombinant plasmids 15.3.5 Protoplast transformation 15.3.6 Electroporation 15.3.7 Conjugative plasmid transfer 15.3.8 Strategic circumvention of restriction-modification (RM) systems 15.3.9 Genetic elements to control gene expression 15.3.10 Reporter proteins 15.3.11 Protein secretion 15.4 Geobacillus spp. that have potential in whole-cell applications 15.4.1 G. caldoxylosilyticus T20 15.4.2 G. kaustophilus HTA426 15.4.3 G. stearothermophilus ATCC 12978 15.4.4 G. stearothermophilus NUB3621 15.4.5 G. thermocatenulatus 11 15.4.6 G. thermodenitrificans OS27 15.4.7 G. thermodenitrificans T12 15.4.8 G. thermoglucosidasius DSM 2542 15.4.9 G. thermoglucosidasius M10EXG 15.4.10 G. thermoglucosidasius NCIMB 11955 15.4.11 G. thermoglucosidasius NY05 15.4.12 G. thermoglucosidasius PB94A 15.4.13 Geobacillus sp. LC300 15.4.14 Geobacillus sp. XT15 15.5 Conclusion and perspective Acknowledgments References 16 Thermophiles and thermophilic hydrolases 16.1 Introduction 16.2 Discovery and diversity of thermophiles 16.3 Thermophilic adaptations 16.3.1 Membrane level adaptations 16.3.2 Genome level adaptations 16.3.3 Proteome level adaptations 16.3.3.1 Amino acid composition 16.3.3.2 Surface and core distribution of amino acids 16.3.3.3 Ion pair networks, hydrogen bonds and aromatic interactions 16.3.3.4 Hydrophobic interactions and disulfide bonds 16.3.3.5 Secondary structures 16.3.3.6 Protein packing and folding 16.4 Thermophilic enzymes 16.4.1 Amylases 16.4.2 Proteases 16.4.3 Cellulases 16.4.4 Xylanases 16.4.5 Lipases 16.5 Conclusion References 17 Effects of single nucleotide mutations in the genome of multi-drug resistant biofilm producing Pseudomonas aeruginosa 17.1 Introduction 17.2 β-Lactam resistance 17.3 Fluoroquinolone resistance 17.4 Aminoglycoside resistance 17.5 Target efflux pumps (before jumping to each system give 2-3 lines details about this) 17.5.1 MexAB-OprM 17.5.2 MexXY-OprM 17.5.3 MexCD-OprJ 17.5.4 MexEF-OprN 17.6 Antibiotic resistance and bacterial phenotype in biofilm formation 17.7 Conclusion References 18 Understanding the structural basis of adaptation in enzymes from psychrophiles 18.1 Introduction 18.2 Cold adapted enzymes 18.3 Structure-function relationship of cold adapted enzymes 18.4 Conclusion and future directions References 19 Molecular and functional characterization of major compatible solute in Deep Sea halophilic actinobacteria of active vol... 19.1 Introduction 19.2 Ectoine – a major compatible solute in halophilic eubacteria 19.3 Physicochemical properties of ectoine 19.4 Osmolytic properties of ectoine 19.5 Biosynthesis of ectoine 19.6 Transport of ectoine 19.7 Industrial production of ectoine 19.8 Biotechnological applications of ectoine 19.8.1 Chemical chaperones for protein folding 19.8.2 Enhancing PCR 19.8.3 Cryo-protection of microorganisms 19.8.4 Use in cosmeceuticals and pharmaceuticals 19.8.5 Generation of stress-resistant transgenic organisms 19.8.6 Ectoine based products in market 19.9 Molecular and functional characterization of ectoine in deep sea halophilic actinobacteria, nocardiopsis alba 19.10 PCR amplification, cloning and sequencing of ectoine biosynthesis genes 19.11 Molecular characterization of ectoine biosynthesis genes 19.12 Sequence analysis of ectA, B and C genes 19.13 Phylogenetic tree construction and analysis of ectoine biosynthesis genes 19.14 Concluding remarks Acknowledgments References 20 Antarctic microorganisms as sources of biotechnological products 20.1 Introduction 20.2 Bioprospection of microbial derived bioactive compounds in Antarctica 20.2.1 Enzymes 20.2.1.1 Discovery and purification 20.2.1.2 Activity retention 20.2.1.3 Enzymes for biorefinery and biodiesel production 20.2.1.4 Enzymes for pharmaceuticals and cosmetics production 20.2.1.5 Enzymes for agriculture and brewing 20.2.1.6 Immobilization of Antarctic-derived enzymes 20.2.2 Drug discovery 20.2.2.1 Antimicrobial drug discovery 20.2.2.2 Anticancer drug discovery 20.2.3 Ice-binding proteins 20.3 Nanoparticles 20.3.1 Cadmium nanoparticles 20.3.2 Iron-oxide nanoparticles 20.4 Conclusion and future directions References 21 The secretomes of extremophiles 21.1 Introduction 21.2 The Sec pathway 21.3 The Tat pathway 21.4 The signal sequence 21.5 Secretomes of archaea 21.6 Conclusion and future directions References 22 Carbonic anhydrase from extremophiles and their potential use in biotechnological applications 22.1 Extremophiles 22.2 Bacterial carbonic anhydrases 22.3 Carbonic anhydrases in extremophilic bacteria 22.4 Potential use of extreme carbonic anhydrases in biotechnological applications 22.4.1 Biosensors 22.4.2 Artificial lungs 22.4.3 Post-combustion carbon dioxide capture 22.5 SspCA immobilization 22.5.1 Polyurethane foam 22.5.2 Ionic liquid membranes (supported ionic liquid membranes) 22.5.3 Magnetic particles 22.5.4 In vivo immobilization 22.6 Conclusion References 23 Understanding the protein sequence and structural adaptation in extremophilic organisms through machine learning techniques 23.1 Introduction 23.2 Databases 23.3 Machine learning 23.3.1 Machine learning platforms 23.3.2 Feature extraction and representation 23.3.3 Feature selection 23.3.4 Model performance validation 23.3.4.1 Types of validation method for testing the performance of trained machine learning models 23.3.5 Model performance evaluation metrics 23.4 Statistical analysis for inferring the molecular basis of extremophilic adaptation 23.5 Inferences from preceding methods 23.6 Conclusion References 24 Exploration of extremophiles genomes through gene study for hidden biotechnological and future potential 24.1 Introduction 24.2 Types and characteristics of extremophiles 24.2.1 Temperature adaptation 24.2.2 pH adaptation 24.2.3 Salt adaptation 24.2.4 Pressure adaptation 24.3 Survival strategy to combat cold stress 24.3.1 Membrane fluidity 24.3.2 Protein synthesis and cold-accustomed protein 24.3.3 Structural adaptation of cold-active enzyme 24.3.4 Mutational study 24.4 Bioactive natural products by extremophiles 24.4.1 Gene study 24.4.2 Bioactive natural products 24.5 Biotechnological use of extremophiles 24.5.1 Polymerase chain reaction 24.5.2 Biomining 24.5.3 Biofuel production 24.5.4 Industrial use 24.5.5 Medicinal aspects 24.6 Conclusion References 25 The ecophysiology, genetics, adaptive significance, and biotechnology of nickel hyperaccumulation in plants 25.1 Introduction 25.2 Physiology: mechanisms of Ni uptake, translocation, chelation, and storage 25.2.1 Uptake 25.2.2 Chelation 25.2.3 Transport 25.2.4 Localization and storage 25.3 Why hyperaccumulate nickel? 25.3.1 Elemental defense 25.3.2 Nutritional demand 25.3.3 Elemental allelopathy 25.3.4 Drought tolerance 25.4 Genetics of nickel accumulation 25.4.1 Identification of target genes involved in Ni hyperaccumulation by transporters 25.4.2 Identification of target genes involved in Ni hyperaccumulation by chelators 25.5 Phytoremediation and agromining 25.6 Conclusion Acknowledgments References Further Reading Index