Physiological and Biotechnological Aspects of Extremophiles

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