Ecophysiology and Biochemistry of Cyanobacteria

Preface
Contents
Editor and Contributors
1: Evolution and Distribution of Cyanobacteria
	1.1 Introduction
	1.2 Evolution of Cyanobacteria
		1.2.1 Structural Evolution
		1.2.2 Genome Evolution
	1.3 Diverse Habitats of Cyanobacteria
		1.3.1 Terrestrial Habitats
		1.3.2 Aquatic Habitats
		1.3.3 Symbiotic Associations
	1.4 Perspective and Conclusion
	References
2: Polyphasic Approach and Cyanobacterial Taxonomy: Some Perspectives and Case Studies
	2.1 Introduction
	2.2 The Development of Cyanobacterial Taxonomy
		2.2.1 The Taxonomy of Nostoc and Nostoc-Like Genera
		2.2.2 The Taxonomy of Calothrix and Related Genera
	2.3 Conclusions
	References
3: Photosynthesis and Energy Flow in Cyanobacteria
	3.1 Introduction
	3.2 Component of Photosynthetic Apparatus
	3.3 Structure of Photosystems (PS I and PS II)
	3.4 Electron Flow in Cyanobacteria
	3.5 Conclusions
	References
4: Impacts of Environmental Stress on Physiology and Biochemistry of Cyanobacteria
	4.1 Introduction
	4.2 Impact of Environmental Stress
		4.2.1 At Morphological Level (Membrane Structure)
	4.3 Physiological and Biochemical Alteration in Cyanobacteria Under Stress Condition
		4.3.1 Alteration in Growth and Photosynthetic Pigment Contents
		4.3.2 Alteration in Photosynthetic Activity and Damage to PS II Photochemistry
		4.3.3 Inflection on Nitrogen Metabolism (Inorganic Nitrogen Uptake Nitrate and Nitrite Uptake and Ammonia Assimilation)
	4.4 Modulation of Oxidative Stress and Damage to Macromolecule
		4.4.1 Influence on Macromolecules
	4.5 Tolerance Mechanism in Cyanobacterial System
		4.5.1 Tolerance Mechanism at Morphological and Biochemical Level
		4.5.2 Tolerance Mechanism at Molecular Level
			4.5.2.1 Molecular Chaperone
			4.5.2.2 Transcriptional and Post-translational Regulation
	4.6 Conclusions
	References
5: Photosynthesis Under Abiotic Stress
	5.1 Introduction
	5.2 Light
		5.2.1 High Light Intensity
		5.2.2 Low Light Intensity
	5.3 Temperature
		5.3.1 Cold
		5.3.2 Heat
	5.4 Nutrient Starvation
		5.4.1 Carbon and Nitrogen
			5.4.1.1 Inorganic Carbon
			5.4.1.2 Nitrogen
		5.4.2 Iron
		5.4.3 Phosphorus
	5.5 Conclusions
	References
6: UV Stress Responses in Cyanobacteria
	6.1 Introduction
	6.2 Exposure to Solar UV Radiation
	6.3 UV Effects on Cyanobacteria
		6.3.1 Damage and Repair of DNA
		6.3.2 Reactive Oxygen Species
	6.4 UV Damage of the Photosynthetic Apparatus and Repair
	6.5 Motility and Orientation
	6.6 UV-Screening Pigments
	6.7 Conclusions
	References
7: Molecular Mechanisms of Stress Tolerance in Cyanobacteria
	7.1 Introduction
	7.2 Biotechnology and the Importance of Cyanobacteria
	7.3 The Diversity and Abundance of Cyanobacteria
		7.3.1 Growth of Cyanobacteria
		7.3.2 Hot vs. Cold Environments
		7.3.3 Freshwater vs. Saltwater Environments
		7.3.4 Solitary vs. Symbiotic Life
	7.4 Stressful Environments Occupied by Cyanobacteria
		7.4.1 Cyanobacterial Coping Mechanisms During Stress
		7.4.2 Temperature Variations and Adaptive Mechanisms
		7.4.3 UV Stress and the Mechanisms of Protection
		7.4.4 Adapting to Hypersalinity Stress and Other Coping Mechanisms
		7.4.5 Redox Controlling Mechanisms
	7.5 Perspective and Conclusion
	References
8: Stress Proteins and Signal Transduction in Cyanobacteria
	8.1 Introduction
	8.2 Stress-responsive Proteins Under Various Abiotic Stresses
	8.3 Two-component Signal Transduction Pathways: Histidine Kinases (Hiks) and Response Regulators (Rre)
		8.3.1 Histidine Kinases
		8.3.2 Response Regulators
		8.3.3 Hybrid Kinases
	8.4 Serine/Threonine Kinases (STKs): Phosphorylation on Ser, Thr, and Tyr Residues in Cyanobacteria
	8.5 Other Potential Sensors and Transducers in Cyanobacteria
		8.5.1 RNA Polymerase Sigma Factors and Transcription Factors
		8.5.2 DNA Supercoiling: Role in Perception of Stress Signals and The Regulation of Gene Expression
	8.6 Conclusions
	References
9: Evolution and Diversification of the GroEL/Chaperonin Paralogs in Cyanobacteria
	9.1 Introduction
	9.2 The Hsp60/Chaperonin 60/GroEL Family
		9.2.1 Structure of GroEL and the GroEL-GroES Complex
		9.2.2 Mechanism of Protein Folding Assisted by E. coli GroEL
	9.3 Multiple GroELs in Cyanobacteria
		9.3.1 Paralogs of Cyanobacterial Molecular Chaperones and Three Alternative Outcomes in the Evolution of Duplicate Genes
		9.3.2 Gene Organization of groEL1 and groEL2 in Cyanobacterial Genomes
		9.3.3 Regulation of Transcription of groESL1 and groEL2 in Cyanobacteria
			9.3.3.1 Positive Regulation of groESL Transcription by the Alternative Sigma Factor σ32 in E. coli. For Details, See Guisbert ...
			9.3.3.2 Negative Regulation of groESL Transcription by the CIRCE/HrcA System in B. subtilis. For Details, See Schumann (2016)
			9.3.3.3 Regulation of Transcription of groESL1 and groEL2 in Cyanobacteria
				A Negative Regulation by the CIRCE/HrcA System
				A Novel Positive Regulation by K-Box
			9.3.3.4 The Evolution of Regulatory Mechanisms in Cyanobacterial groEL Paralogs
	9.4 Structure and Function of GroEL Paralogs in Cyanobacteria
		9.4.1 Function of GroEL1 and GroEL2
			9.4.1.1 Complementation Analysis with E. coli groEL Mutants
			9.4.1.2 Function of GroEL1 and GroEL2 in Cyanobacteria
		9.4.2 Oligomers of GroEL
		9.4.3 Interaction of GroEL1 and GroEL2 with GroES
		9.4.4 In Vitro Chaperone Function of GroEL1 and GroEL2
			9.4.4.1 Anti-Aggregation Activity of GroEL1 and GroEL2
			9.4.4.2 ATPase Activity of GroEL1 and GroEL2
			9.4.4.3 Refolding of Non-native Protein with the Assistance of GroEL1 and GroEL2
	9.5 Concluding Remarks
	References
10: Chromatic Acclimation in Cyanobacteria: Photomorphogenesis in Response to Light Quality
	10.1 Introduction
	10.2 History and Concept of Complementary Chromatic Adaptation Vs. Acclimation
	10.3 Structural Components of PBS and CA
		10.3.1 Green/Red Responsive CA
			10.3.1.1 Type 1
			10.3.1.2 Type 2
			10.3.1.3 Type 3
		10.3.2 Blue/Green Responsive CA
			10.3.2.1 Type 4
		10.3.3 Red/Far-Red Responsive CA
			10.3.3.1 Type 5
			10.3.3.2 Type 6
	10.4 Molecular Mechanism of CA
	10.5 Cellular Processes Controlled by RcaE Other than Type 3 CA
	10.6 Significance of CA
	References
11: Phenomenon of Allelopathy in Cyanobacteria
	11.1 Introduction
	11.2 Methods of Cyanobacterial Allelopathy Examination
	11.3 Taxonomic Position of the Allelopathic Cyanobacteria and Their Effect on Coexisting Phytoplankton Species
		11.3.1 The Allelopathic Interaction Between Cyanobacteria
		11.3.2 The Allelopathic Effect Between Cyanobacteria and Green Algae
		11.3.3 The Allelopathic Effect Between Cyanobacteria and Diatoms
		11.3.4 The Allelopathic Effect Between Cyanobacteria and Other Microalgae
	11.4 Factors Affecting Cyanobacterial Allelopathy and Modes of Action of Cyanobacterial Allelochemicals
	11.5 Conclusions
	References
12: Nitrogen Metabolism in Cyanobacteria
	12.1 Introduction
	12.2 Heterocyst Differentiation
	12.3 Nitrogenase and Alternate Nitrogenase
	12.4 Uptake of Nitrogen Sources
	12.5 Ammonium Incorporation into Carbon Skeletons
	12.6 Cyanobacteria as Biofertilizer
	12.7 Conclusions
	References
13: Phycoremediation of Wastewater
	13.1 Introduction
	13.2 Cyanobacterial Diversity in Wastewater
	13.3 Use of Cyanobacterial Monocultures in Nutrient Sequestration and Biomass Production
	13.4 Significance and Promise of Cyanobacterial Consortial Approach in the Remediation of Wastewater
	13.5 Wastewater Treatment Using Cyanobacterial Consortia
		13.5.1 Municipal Wastewater
		13.5.2 Industrial Wastewaters
		13.5.3 Heavy Metal Removal by Cyanobacteria
			13.5.3.1 Mechanism of Heavy Metal Removal by Cyanobacteria
		13.5.4 Water Quality Improvement by Cyanobacteria
		13.5.5 CO2 Sequestration
	13.6 Conclusion
	13.7 Future Perspectives
	References
14: Environmental Resilience and Circular Agronomy Using Cyanobacteria Grown in Wastewater and Supplemented with Industrial Fl...
	14.1 Introduction
	14.2 Global Challenge of Wastewater Disposal and Flue Gas Mitigation
	14.3 Cyanobacterial Wastewater Treatment
		14.3.1 Types of Cyanobacterial WWT Systems
			14.3.1.1 High Rate Algal Pond (HRAP)
			14.3.1.2 Closed Photobioreactors (PBRs)
			14.3.1.3 Biofilm Reactors
		14.3.2 Nutrients Removal
		14.3.3 Removal of Heavy Metals and PPCPs
			14.3.3.1 Biosorption
			14.3.3.2 Bioaccumulation
			14.3.3.3 Photolysis
			14.3.3.4 Biodegradation
	14.4 Cyanobacterial Flue Gas Mitigation
		14.4.1 CO2 Sequestration by Cyanobacteria
		14.4.2 Potential of Cyanobacterial Genetic Engineering
	14.5 On-field Challenges and Opportunities in Cyanobacteria-Based Remediation
	14.6 Cyanobacterial Biomass Application as Biofertilizer/Soil Conditioner
		14.6.1 Nitrogen and Phosphorus Contribution
		14.6.2 Reclamation of Salt-affected Soils and Improvement in Soil Fertility
		14.6.3 Plant Growth Promoters/Chemicals by Cyanobacteria
		14.6.4 Biocontrol Agent
	14.7 Challenges and Opportunities of Cyanobacterial Biofertilizers
	14.8 Conclusion
	References
15: Antioxidant, Anti-aging and Anti-neurodegenerative Biomolecules from Cyanobacteria
	15.1 Introduction
	15.2 Cyanobacteria: A Natural Source of Antioxidants
	15.3 Cyanobacterial Biomolecules
		15.3.1 Mycosporine Like Amino Acids (MAA)
		15.3.2 Scytonemin
		15.3.3 Phycobiliproteins (PBPs)
	15.4 Concluding Remarks
	References
16: Engineering Challenges of Carbon Dioxide Capture and Sequestration by Cyanobacteria
	16.1 Introduction
	16.2 Options for Capture and Sequestration
	16.3 Economic Considerations
	16.4 Cost of CO2 Sequestration
	16.5 An Integrated Concept of CO2 Sequestration
	16.6 The PBR as a System
	16.7 Sf/V ratio Milestone for Evaluation of Natural Light Illumination
	16.8 Light Criterion
	16.9 Sf/V Ratio Linked with Algal Physiology
	16.10 Flashing Light Effect (FLE) as Another Key Parameter for Optimal Biomass Production
	16.11 CO2 Fixation by Cyanobacteria/Microalgae
	16.12 Studies on CO2 Utilization in PBRs by Using Microalgae
	16.13 Cultivation of Cyanobacteria and Influence of Working Parameters on the Process
	16.14 Internal Illumination of PBRs as a Key for Optimization of Biomass Production
	16.15 Construction Types of PBRs and Large-Scale Application of the Photosynthetic Carbon Fixing Method
	16.16 Conclusion
	16.17 Future Prospects
	References
17: Engineering Cyanobacteria Cell Factories for Photosynthetic Production of Sucrose
	17.1 Introduction
	17.2 Physiological and Metabolic Background of Cyanobacterial Sucrose Synthesis
		17.2.1 Physiological Significance of Cyanobacterial Sucrose Synthesis
		17.2.2 Metabolic Mechanisms of Cyanobacterial Sucrose Synthesis
		17.2.3 Regulatory Mechanism of Sucrose Synthesis in Cyanobacteria Under Salt Stress
		17.2.4 Sucrose Synthesis in Cyanobacteria Under Salt-Free Conditions
		17.2.5 Metabolic Mechanisms of Cyanobacterial Sucrose Degradation
		17.2.6 Strategies for Cyanobacteria in Response to Decreased Salinity in the Environment
	17.3 Metabolic Engineering Strategies for Cyanobacteria Based Photosynthetic Production of Sucrose
		17.3.1 Introduction of Sucrose Transporter
		17.3.2 Enhancing Sucrose Synthesis Pathway and Weakening the Degradation Pathways
		17.3.3 Disturbance of Glycogen Metabolism
		17.3.4 Biomass Accumulation Arresting Strategy
		17.3.5 Reform Photosynthetic Electron Flux of Cyanobacteria
		17.3.6 Prospect of Metabolic Engineering Strategies for Sugar Production by Cyanobacteria
	17.4 Synthetic Light-Driven Consortia Based on Cyanobacterial Photosynthetic Sucrose Production
		17.4.1 The Proof of Concept of Synthetic Light-Driven Consortia System
		17.4.2 Development and Application of Synthetic Light-Driven Consortia Synthesis System
		17.4.3 Engineering and Understanding the Mutual Interaction Mechanisms in the Synthetic Light-Driven Consortia
	17.5 Summary and Prospect
	References
18: Optimal Biomass Production by Cyanobacteria, Mathematical Evaluation, and Improvements in the Light of Biorefinery Concept
	18.1 Introduction
	18.2 Principles of System Analysis Theory
	18.3 Overview of UHDC Cultivation Techniques
	18.4 Applications of the Principles of System Analysis Theory to PBR Design and Scale-Up
	18.5 Modeling, Optimization, and Scale-Up of PBRs
	18.6 Algal Biomass Biorefinery Concept
	18.7 Downstream Bioprocessing of Microalgae Biomass
		18.7.1 Carbohydrate Fraction
		18.7.2 Protein Fraction
		18.7.3 Pigments
	18.8 Utilization of Biomass to Biofuels
		18.8.1 Biochemical Process
			18.8.1.1 First Hierarchic Level
			18.8.1.2 Second Hierarchic Level
		18.8.2 Thermochemical Conversion
		18.8.3 Transesterification
		18.8.4 Microalgal Cultivation and Microbial Fuel Cell (MFC) Systems
	18.9 Techno-Economic Analysis and Life Cycle Analysis (LCA)
	18.10 Challenges and Future Prospects
	18.11 Conclusions
	References
19: Cyanobacteria as Renewable Sources of Bioenergy (Biohydrogen, Bioethanol, and Bio-Oil Production)
	19.1 Introduction
	19.2 Stages of Biofuel Development
	19.3 Cyanobacterial Biohydrogen Production
		19.3.1 Utilization of Light for the Biohydrogen Production
			19.3.1.1 Photolysis
			19.3.1.2 Catabolic Hydrogen Production
		19.3.2 Dark Fermentative Biohydrogen Production
	19.4 Cyanobacterial Bioethanol Production
		19.4.1 Cyanobacterial Carbohydrate Accumulation
		19.4.2 Bioethanol by Hydrolysis and Fermentation
		19.4.3 Bioethanol by Dark Fermentation
		19.4.4 Bioethanol by Photofermentation
	19.5 Cyanobacteria for Bio-Oil Production
		19.5.1 Pyrolysis
		19.5.2 Pyrolyzed Bio-Oil Characteristics
		19.5.3 Catalysts for Bio-Oil
			19.5.3.1 Zeolite Catalysts
			19.5.3.2 Metal-Loaded Catalysts
		19.5.4 Catalytic Processing Methods
		19.5.5 Deoxygenation and Denitrogenation of Bio-Oils
	19.6 Conclusion
	References
20: Cyanobacteria as a Competing Source of Bioenergy: Metabolic Engineering and Modeling Approach for Medium Optimization
	20.1 Introduction
	20.2 Role of Metabolic Engineering to Achieve Effective Technology from Cyanobacteria
	20.3 Biofuel Production Perspectives
	20.4 Nutrient Medium Effects over Cyanobacteria Performance at the Cellular Level
		20.4.1 Siderophores as Key Factors in Metal Transport
		20.4.2 Cynobacteria and their Siderophores
		20.4.3 Current Studies on Iron Uptake by Cyanobacteria
		20.4.4 Siderophores and Future Perspectives in the Area
	20.5 Process Development at Macro Population Level
		20.5.1 A Complex Theoretical Approach for Cyanobacteria/Microalgae Nutrient Medium Optimization
		20.5.2 Description of the Algorithm
		20.5.3 Theoretical Basis for Algorithm Development
		20.5.4 Subsystem I-Cyanobacteria/Microalgae Physiology
			20.5.4.1 Cyanobacteria/Microalgae Biomass Elemental Composition
			20.5.4.2 Linear Programming Procedure
			20.5.4.3 Requirements for Nutrients in Algology
			20.5.4.4 Future Perspective: Medium Optimization for Cyanobacteria/Microalgae
		20.5.5 Subsystem II-Flue Gas
		20.5.6 Subsystem III-Water Chemistry
		20.5.7 Procedure of Decision-Making
		20.5.8 Choice of Criterion for Medium Design
	20.6 Modeling Procedure and Photobioreactors (PBRs) Design
	20.7 Complex Biorefinery Concept for Cyanobacteria Biomass Use
	20.8 Conclusions
	20.9 Future Perspectives
	References