Survival Strategies in Cold-adapted Microorganisms

Preface
Contents
About the Editors
1: Cyanobacteria in Cold Ecosystem: Tolerance and Adaptation
1.1 Introduction
1.2 Significance of Cold Ecosystem
1.3 Ecology and Biogeochemistry of Cyanobacteria
1.3.1 Cryptic Niches
1.3.2 Hypoliths
1.3.3 Endoliths
1.3.4 Cryoconites
1.3.5 Aquatic Habitats
1.4 Ecophysiology of Polar Cyanobacteria and Functional Role of Arctic and Antarctic Cyanobacteria
1.5 Polar Region: Extreme Environmental Parameters and Stress Factors
1.6 Polar Cyanobacteria: Response to Various Stress Factors
1.6.1 General Mechanism of Adaptation
1.6.2 Stress Avoidance
1.6.3 Stress Tolerance
1.6.4 Dormant Cell Formation
1.6.5 Morphological Structures
1.6.6 Consortia
1.6.7 Low Temperature
1.6.8 Temperature Perception
1.6.9 Lipids
1.6.10 Proteins/Enzymes
1.6.11 Freeze/Melting Cycles
1.6.12 Antifreeze Proteins
1.6.13 Compatible Solutes and Cryoprotectants
1.6.14 Ice Nucleation Proteins
1.6.15 Dessication
1.6.16 Extracellular Envelopes
1.6.17 Water Stress Proteins
1.6.18 Salinity
1.6.19 Ionic Regulation
1.6.20 Osmotic Regulation
1.6.21 Irradiance (PAR) and Ultraviolet Radiation (UVR)
1.6.22 Photosynthesis and Photoinhibition at Low Temperature
1.6.23 Screening Compounds
1.6.24 Antioxidants
1.6.25 Survival Strategies: Insight from Metagenomics
1.6.26 Subzero Temperature Effect
1.7 Impact of Rise in Global Temperature on Polar Cyanobacteria
1.7.1 Nitrogen Cycling
1.7.2 Carbon Cycling
1.8 Conclusion
References
2: Cold-Adapted Fungi: Evaluation and Comparison of Their Habitats, Molecular Adaptations and Industrial Applications
2.1 Introduction
2.2 Natural Habitats and Their Occurrence
2.3 Temperature Range
2.4 Cold Adaptations in Fungi: Definition
2.5 Cold-Adapted Fungi: A Background
2.6 Molecular Adaptations
2.7 The Arctic
2.8 The Antarctic
2.9 Nonpolar Regions
2.10 Arctic Fungi
2.10.1 Plant-Associated and Free-Living Fungi of Arctic Soils
2.10.2 Glacial Ice
2.10.3 Marine Fungi from the Arctic
2.11 Antarctic Fungi
2.11.1 Soils
2.11.2 Antarctic Permafrost
2.11.3 Endolithic Communities
2.12 Harmful Effects in Plants, Animals and Humans
2.13 Applications of Fungi in Industry
2.13.1 Cold-Active Enzymes
2.13.1.1 Proteases
2.13.1.2 Chitinases
2.13.1.3 Cellulases and Pectinases
2.13.1.4 Amylases
2.13.1.5 Xylanases
2.13.1.6 Lipolytic Enzymes
2.13.2 Pharmaceutical Products
2.13.3 Bioremediation
2.13.4 Pigment Production
2.14 Agriculture
2.15 Conclusion
References
3: Microbial Life in Cold Regions of the Deep Sea
3.1 Introduction
3.2 Deep Sea as a Microbial Habitat
3.2.1 With Low Temperature
3.2.2 With High Pressure
3.3 Microbial Diversity in Deep Sea
3.4 Microbial Adaptations at Deep Sea
3.4.1 Low-Temperature Adaptations
3.4.1.1 Maintenance of Membrane Structure by the Generation of Unsaturated Fatty Acids
3.4.1.2 Cold-Shock Proteins (CSP)
Functions of Cold-Shock Proteins
3.4.1.3 Viable but Non-Culturable Cell (VBNC)
Mechanism of VBNC Formation
3.4.1.4 Antifreeze Proteins
Mechanism of AFP
3.4.1.5 Adaptation Mechanism of Psychrophilic Enzymes
3.4.1.6 Piezophiles/Barophiles
3.4.2 Adaptation Mechanism of Piezophiles (High-Pressure Adaptations)
3.4.2.1 Membrane Lipid Adaptation
3.4.2.2 Outer Membrane Porins
3.4.2.3 Membrane Transport
3.4.2.4 Respiratory Chain
3.4.2.5 Motility Under High Pressure
3.4.2.6 Enzymes Adaptations Under High Pressure
Low Stability
High Compressibility
High Absolute Activity
High Relative Activity at High Pressures
3.5 Microbial Nutrition and Metabolism in Deep Sea
3.5.1 Chemistry of Deep Sea
3.5.2 Microbial Metabolism in Deep Sea
3.6 Conclusion
References
4: Adaptation to Cold Environment: The Survival Strategy of Psychrophiles
4.1 Introduction
4.2 Ecological Adaptability of Psychrophiles
4.3 Environmental Adaptability of Psychrophiles
4.3.1 Membrane Fluidity
4.3.2 Cold-Shock and Heat-Shock Responses
4.3.3 Antifreeze Proteins (AFPs)
4.3.4 Cryoprotectants
4.3.5 Cold-Adapted Enzymes
4.3.6 Carotenoid Pigments
4.3.7 Protein Folding in Psychrophiles
4.3.7.1 Marine Environment
4.3.7.2 Non-marine Environment
4.3.7.3 Glacier Environment
4.4 Adaptation to Cold Habitat
4.4.1 Morphological Features
4.4.2 Molecular Aspects
4.4.3 Other Special Features
4.5 RandD Effort Innovation Technologies to Find Specific Adaptations
4.6 Conclusion
References
5: Enzymatic Behaviour of Cold Adapted Microbes
5.1 Introduction
5.2 Psychrophillic Enzymes
5.2.1 Cold Adapted Activity
5.2.1.1 Inactivation and Unfolding
5.2.1.2 Active Site Architecture
5.2.1.3 Active Site Dynamics
5.2.1.4 Adaptive Drift and Adaptive Optimization of Substrate Affinity
5.2.1.5 Comparative Structural Analysis of Extremophiles
5.2.1.6 Composition of Amino Acids
5.2.1.7 Secondary Structural Elements
5.2.1.8 Comparative Proteome Analysis
5.2.1.9 Amino Acid Substitution Pattern
5.3 Kinetics and Energetics of Cold Activity
5.4 Conformational Stability
5.4.1 Structural Origin of Low Stability
5.5 Folding Funnel Model of Cold Active Enzymes
5.6 Psychrophillic Enzymes in Biotechnology
5.6.1 Heat Lability in Molecular Biology
5.6.2 Application of Cold Active Enzymes for Manufacturing Chemicals and Wastewater Treatment
5.6.3 Cold Active Enzymes Used in the Food Industry
5.7 Future Prospects
5.8 Conclusion
References
6: An Overview of Survival Strategies of Psychrophiles and Their Applications
6.1 Introduction
6.2 Types of Extremophiles
6.2.1 Thermophiles
6.2.2 Psychrophiles
6.2.3 Acidophiles
6.2.4 Alkaliphiles
6.2.5 Halophiles
6.2.6 Piezophiles
6.3 Survival Strategies Adapted by Psychrophiles
6.3.1 Cell Membrane Fluidity
6.3.2 Antifreeze Proteins (AFPs)
6.3.3 Cold Shock Proteins
6.4 Applications of Cold Adapted Microbes
6.4.1 Psychrophilic Enzymes in Different Industries
6.4.2 Use of Psychrophilic Microorganisms in Bioremediation
6.4.3 Role of Psychrophiles in Medicine and Pharmaceuticals
6.4.4 Role of Psychrophiles in Domestic Purposes
6.4.5 Application of Psychrophiles in Textile-Based Industries
6.5 Psychrophiles Used in Fine Chemical Synthesis
6.6 Role of Psychrophiles in Agriculture
6.7 Conclusion and Future Prospectives
References
7: Microbial Genes Responsible for Cold Adaptation
7.1 Introduction
7.2 Cold-Adapted Microorganisms
7.2.1 Diversity of Cold-Adapted Microorganisms
7.2.2 Strategies for Cold Adaptation
7.3 Cold Adaptation Genes
7.3.1 Cold Shock Response
7.3.1.1 Cold Shock Response in E. coli
7.3.1.2 Cold Shock Response in B. subtilis
7.3.1.3 Cold Shock Response in Psychrotrophs and Psychrophiles
7.3.2 Cold Acclimation Proteins
7.4 Genomic Studies
7.4.1 Psychrotrophic Microorganisms
7.4.2 Microbial Physiological Adaptations
7.4.3 Cell Membrane Modulation
7.4.4 Osmoprotection and Cryoprotection: Compatible Solutes
7.4.5 Freeze Protection
7.4.6 Extracellular Compounds
7.4.7 Transport and Diffusion
7.4.8 RNA/DNA Secondary Structure
7.4.9 Substrate Oxidation
7.5 Conclusion
References
8: Survival Strategies in Cold-Adapted Microorganisms
8.1 Introductions
8.2 Survival Strategies of Cold-Adapted Microorganisms: Initial Studies
8.2.1 Physiological Adaptations Exhibited by Cold-Adapted Microorganisms
8.2.2 Structural Alterations of Proteins/Enzymes in Cold-Adapted Microorganisms
8.2.3 Alterations Ensuring Biomembrane Fluidity in Cold-Adapted Microorganism
8.2.4 Other Subtle Adaptations Exhibited by Cold-Adapted Microorganisms
8.2.5 Metagenomics- and Genomics-Based Studies of Cold-Adapted Microorganisms
8.3 Systems Biology Studies of Cold-Adapted Microorganisms
8.3.1 Comparative Genomic Studies of Cold-Adapted Microorganisms
8.3.2 Transcriptomics Studies of Cold-Adapted Microorganisms
8.3.3 Proteomics Studies of Cold-Adapted Microorganisms
8.4 Conclusion and Future Prospects
References
9: Microbial Adaptations Under Low Temperature
9.1 Introduction
9.2 Microbial Adaptations Under Low Temperature
9.2.1 Sensing the Temperature
9.2.2 Structural Adaptation of Enzymes
9.2.3 Membrane Fluidity
9.2.4 Metabolism at Low Temperatures
9.2.5 Heat-Shock Proteins
9.2.6 Cold-Shock Proteins
9.2.7 Cryoprotectants
9.2.8 Antifreeze Proteins
9.3 Future Prospects
References
10: Molecular Mechanisms of Cold-Adapted Microorganisms
10.1 Introduction
10.2 Cold-Adapted Enzymes
10.3 Modifications in Transcription and Translation
10.4 Role of Polyhydroxyalkanoates (PHA)
10.5 Cryoprotectant and Cold-Shock Proteins
10.6 Role of RNA Degradosome
10.7 Changes in Membrane Fluidity
10.8 Fatty Acid Desaturation
10.9 Branching of Fatty Acids
10.10 Cis- and Trans-Fatty Acids
10.11 Amino Acid: Composition and Length Variation
10.12 Modifications at Protein-Folding Stage
10.12.1 Translation
10.12.2 Folding Assistance
10.13 Conclusion
References
11: Microbe-Mediated Plant Functional Traits and Stress Tolerance: The Multi-Omics Approaches
11.1 Introduction
11.1.1 Rhizosphere Microbiome
11.1.2 Phyllosphere Microbiome
11.1.2.1 Endophytic Microbes
11.2 Plant-Associated Microbial Communities and their Functional Roles
11.2.1 Seed Germination and Nutrient Acquisition
11.2.2 Phytoharmones/Bioactive Compound Production
11.2.3 Tolerance to Biotic and Abiotic Stresses
11.2.3.1 Resistance Against Biotic Stress
11.2.3.2 Resistance Against Abiotic Stresses
11.2.3.3 Cold Stress Tolerance
11.3 Multi-Omics Approaches for Characterization of Plant Microbiome
11.4 Bacterial Genome Sequencing
11.5 Genome-Wide Association Studies (GWAS)
11.6 Conclusion
References
12: Omic Technologies and Cold Adaptations
12.1 Introduction
12.2 Need for Identifying Psychrophiles and their Biosynthetic Potential
12.2.1 Ecological Impacts
12.2.2 Economic Importance
12.3 Challenges in Studying Psychrophiles by Conventional Approaches
12.3.1 Viable but Nonculturable (VBNC) State
12.3.2 Missing in Vivo Signaling Factor or Component in Media
12.3.3 Use of Growth Inducers
12.4 Culture-Independent Microbial Identification: Molecular Analytical Methods
12.4.1 Phylogenetic Marker Gene Sequencing
12.4.2 Molecular Fingerprinting Techniques
12.4.3 DNA Hybridization-Based Methods
12.5 ``-Omics´´-Based Platforms for Microbial Identification
12.5.1 Metagenomics: Evaluating DNA Sequences
12.5.1.1 Second-Generation Sequencers (Sequencing by Synthesis)
12.5.1.2 Third-Generation Sequencers (Real-Time Single-Molecule Sequencing)
12.5.1.3 Historical Perspective of Metagenomic Studies
12.5.1.4 Shotgun Metagenomic Workflow
12.5.2 Metatranscriptomics
12.5.3 Metaproteomics
12.5.4 Metabolomics
12.5.5 Other Developing ``-Omic´´ Methods
12.6 The Holistic Picture of ``-Omic´´ Methods
12.7 Conclusion
References
13: Use of Proteomics and Transcriptomics to Identify Proteins for Cold Adaptation in Microbes
13.1 Introduction
13.2 Physiological Adaptations of Psychrophiles
13.3 Omics to Explore Structural and Physiological Features in Psychrophiles
13.3.1 Brief about Genomics and Metagenomics
13.3.1.1 Comparative Genomics
13.3.1.2 Functional Genomics
Microarrays
Quantitative PCR (qPCR)
RNA-Seq
13.3.1.3 Metagenomics
13.3.2 Application of Genomic Tools on Psychrophiles
13.3.2.1 Comparative Genomics of Psychrophiles
13.3.2.2 Functional Genomics of Psychrophiles
13.3.2.3 Metagenomics of Psychrophiles
13.3.3 Brief About Proteomic Techniques
13.3.3.1 Protein Sample Preparation of Extremophiles
13.3.3.2 Qualitative or Conventional Proteomics
Electrophoresis for Resolving Proteins in a Sample
Identification of Proteins
13.3.3.3 Quantitative Proteomics
13.3.3.4 Application of Proteomic Tools on Psychrophiles
13.4 Conclusion
References
14: Cold-Adapted Microorganisms and their Potential Role in Plant Growth
14.1 Introduction
14.2 Possible Mechanisms Involved in Cold Tolerance in Microorganisms
14.2.1 Maintaining Fluidity of the Membranes
14.2.2 Adaptions Related to Protein Synthesis
14.2.3 Responses to Cold Shock
14.2.4 Cryoprotectants
14.2.5 Cold-Tolerant Enzymes
14.3 Role of Cold-Adapted Microorganisms in Plant Growth Promotion and Plant Defenses
14.3.1 Cold-Adapted Fungi
14.3.2 Cold-Adapted Bacteria and Plant Growth Promotion
14.4 Other Possible Applications of Cold-Adapted Microorganisms
14.4.1 Enzyme Production
14.4.2 Bioremediation Using Cold-Adapted Microorganisms
14.4.3 Pigment Production
14.5 Future Scope and Potential
14.6 Conclusion
References
15: Structure and Functions of Rice and Wheat Microbiome
15.1 Introduction
15.2 Rice Microbiome
15.2.1 Structure and Function of Rice Rhizosphere Microbiome
15.2.2 Structure and Function of Rice Phyllosphere Microbiome
15.3 Wheat Microbiome
15.3.1 Structure and Functions of the Wheat Rhizosphere Microbiome.
15.3.2 Structure and Functions of the Wheat Phyllosphere Microbiome
15.4 Conclusion and Future Prospects
References
16: Cold-Adapted Microorganisms: Survival Strategies and Biotechnological Significance
16.1 Introduction
16.2 How Does Psychrophiles and Psychrotrophs Grow at Lower Temperature?
16.3 Role of Metabolic Pathway in Cold Adaptation
16.4 Polyhydroxyalkonoate Metabolisms
16.5 Temperature-Induced Modifications in Cell Membrane
16.6 Enzyme Adaptations in Cold Stress
16.7 Compounds Involved in Cold Adaptation
16.8 Carotenoids´ Role in Cold Adaptations
16.9 Potential Role of Cold Microorganisms in Biotechnology
16.9.1 Saving Energy
16.9.2 Promoting Plant Growth in Cold Regions
16.9.3 Enzyme Production
16.9.4 Biodegradation and Bioremediation
16.9.5 Recombinant Protein System
16.9.6 Psychrophiles and Enzymes at Industry Level
16.10 Molecular Adaptation in Response to Cold Stress
16.11 Bacterial Adaptations to Cold Stress
16.11.1 Heat Shock Protein Role in Cold Stress
16.11.2 Antifreeze Protein Role in Cold Stress
16.11.3 Ribonuclease Role in Cold Stress
16.12 Conclusion
References
17: An Insight to Cold-Adapted Microorganisms and their Importance in Agriculture
17.1 Introduction
17.2 Ecological Diversity of Cold-Adapted Microorganisms
17.3 Effect of Cold Stress on Plants and Microorganisms
17.4 Cold-Adapted PGPR as Bioinoculants for Stress Management
17.4.1 Cold-Adapted Plant Growth-Promoting Rhizobacteria
17.4.2 Indoleacetic Acid Producers
17.4.3 ACC-Deaminase Producers
17.4.4 Siderophore Producers
17.4.5 Role of Microbes in Nitrogen Fixation
17.4.6 Role of Phosphate Solubilizers
17.5 Mechanisms to Combat Cold Stress
17.5.1 Alterations in Cellular Envelope and Movement
17.5.2 Membrane Fluidity
17.5.3 Protection Against Reactive Oxygen Species (ROS)
17.5.4 Changes in Energy Metabolism and Growth
17.5.5 Synthesis of Cryoprotectants, Compatible Solutes, and Exopolysaccharides (EPS)
17.5.6 Cold Shock Proteins and Enzymes
17.6 Cold-Adapted Microbes as Biocontrol Agents
17.7 Ice Bacteria for Frost Management
17.8 Tolerance or Management of Chilling Resistance by Cold-Tolerant PGPRs
17.9 Conclusion
References
18: Nanotechnology for Agricultural and Environmental Sustainability
18.1 Introduction
18.2 Nanotechnology in Agriculture
18.2.1 Soil Fertility
18.2.2 Plant Growth
18.2.3 Plant Growth and Development
18.2.4 Fertilizer Release
18.2.5 Pesticide, Herbicide, and Insecticide Release
18.3 Antimicrobial Activity of Nanoparticles
18.4 Psychrophiles´ Role in Agriculture
18.5 In Food Sector
18.6 Conclusion and Future Prospects
References
19: Recent Trends and Advancements for Agro-Environmental Sustainability at Higher Altitudes
19.1 Introduction
19.2 Rhizosphere Engineering
19.2.1 Rhizosphere Engineering Using Microbes
19.2.2 Plant-Based Methods of Rhizosphere Engineering
19.2.3 Plant-Microbe-Mediated Rhizosphere Engineering
19.3 Culture-Dependent and Culture-Independent Techniques to Study Microbial Diversity in Hilly Agro-Ecosystem
19.4 Role of Nanotechnology for Plant Growth, Development, and Soil Health
19.5 Conclusion and Future Prospects
References