Grand Challenges in Algae Biotechnology (Grand Challenges in Biology and Biotechnology)

Preface
Contents
Editors and Contributors
Part I: Cultivation Systems
	Chapter 1: Commercial Microalgal Cultivation Systems
		1.1 Introduction
			1.1.1 Microalgae and Their Potential
			1.1.2 Industrial Production of Microalgae
			1.1.3 Function of a Photobioreactor
		1.2 Photobioreactor Design
			1.2.1 Growth Conditions
				1.2.1.1 Nutrients
				1.2.1.2 Gas Exchange
				1.2.1.3 Temperature
				1.2.1.4 Sunlight
				1.2.1.5 Improving Commercial Microalgal Production
			1.2.2 Materials
			1.2.3 Cleaning and Sanitizing
		1.3 Photobioreactor Management
			1.3.1 A Simple Production Model
			1.3.2 Harvest Strategies
			1.3.3 Intrinsic Growth Rate, Initial Biomass and Respiration
				1.3.3.1 Intrinsic Growth Rate
				1.3.3.2 Initial Biomass
				1.3.3.3 Respiration
		1.4 New Developments in PBRs
		1.5 Conclusions
		References
	Chapter 2: Operational, Prophylactic, and Interdictive Technologies for Algal Crop Protection
		2.1 Introduction
		2.2 Chemical and Biochemical Interventions
			2.2.1 Copper
			2.2.2 Bleach
			2.2.3 Other Oxidants
			2.2.4 Natural Compounds
			2.2.5 Biocides
		2.3 Physical Disruption or Removal
			2.3.1 Hydrodynamic Shear
			2.3.2 Hydrodynamic Cavitation
			2.3.3 Ultrasonication
			2.3.4 Pulsed Electric Fields
			2.3.5 Foam Flotation
			2.3.6 Hydrocyclone
			2.3.7 Filtration
		2.4 Nutritional Control
			2.4.1 Phosphate
			2.4.2 Nitrogen Source: Urea and Ammonia Versus Nitrate
			2.4.3 Other Inorganic Salts
		2.5 Cultivation System Operation Strategies
			2.5.1 Cultivation Under Alkaline pH
			2.5.2 Transient pH Shifts
			2.5.3 CO2 Asphyxiation and Anoxia
		2.6 Biological Control
			2.6.1 Polyculture, Natural Assemblages, and Crop Rotation
			2.6.2 Trophic Control
			2.6.3 Allelopathy and Natural Defenses of Microalgae
		2.7 Advanced Methods
			2.7.1 Genetic Engineering Strategies
			2.7.2 Industrial Microbial Ecology
		2.8 Detection Methodologies
		2.9 Conclusion
		References
	Chapter 3: Heterotrophic Growth of Microalgae
		3.1 Eukaryotic Microalgae as Cell Factories for the Production of Valuable Biomolecules
			3.1.1 Heterotrophic Production of Fatty Acids and Lipids
				3.1.1.1 Examples of Total Lipid Production in Heterotrophy
				3.1.1.2 Examples of ω-3 Polyunsaturated Fatty Acid Production in Heterotrophy
			3.1.2 Pigments
				3.1.2.1 Lutein
				3.1.2.2 Astaxanthin
				3.1.2.3 Phycocyanin
			3.1.3 Antibacterial and Antifungal Activities in Heterotrophy
			3.1.4 Bioactive Products of Cyanobacteria
		3.2 Basal Carbon Metabolism of Microalgae Under Heterotrophy
			3.2.1 Molecular Analysis of Heterotrophic Metabolism in Model Microalgal Species
				3.2.1.1 Chlamydomonas reinhardtii
				3.2.1.2 Euglena gracilis
				3.2.1.3 Galdieria sulphuraria
				3.2.1.4 Heterotrophic Metabolism of Microalgae Belonging to Other Phyla
		3.3 Productivities of Heterotrophic Microalgal Cultures
		3.4 Conclusions
		References
	Chapter 4: Agronomic Practices for Photoautotrophic Production of Algae Biomass
		4.1 Introduction
			4.1.1 Photoautotrophic Growth Systems
				4.1.1.1 Photobioreactors
				4.1.1.2 Open Ponds
				4.1.1.3 Covered Ponds
		4.2 Agronomic Practices for Algae Production
			4.2.1 Balance of Manual Monitoring Versus Automation
			4.2.2 Cultivation Management
				4.2.2.1 Year-Round Cultivation Versus Seasonal Crop Rotation
			4.2.3 Water Chemistry
				4.2.3.1 Fertilizer Selection
				4.2.3.2 Trace Elements
				4.2.3.3 Other Components
				4.2.3.4 Carbon Dioxide
			4.2.4 Fertilizer Use Efficiency and Feeding Management
			4.2.5 Harvest Management and Impacts
			4.2.6 Crop Protection
				4.2.6.1 Monitoring
				4.2.6.2 Proactive Versus Reactive Treatments
				4.2.6.3 Cultural Practices for Pest Prevention
				4.2.6.4 Maintaining an Environment Versus Temporary Changes
				4.2.6.5 Management over Changing Seasons
				4.2.6.6 Identifying New Pests
				4.2.6.7 Identifying and Responding to Potential Crop Failure
			4.2.7 The Role of the Agronomist on an Algae Farm
		4.3 Remaining Challenges
			4.3.1 Infrastructure
			4.3.2 Crop Protection Options
			4.3.3 Other
		4.4 Conclusions
		References
Part II: Genetic and Metabolic Engineering
	Chapter 5: Advances in Genetic Engineering of Microalgae
		5.1 Introduction
		5.2 The Omics Groundwork for Genetic Engineering
			5.2.1 Genomics
			5.2.2 Epigenomics
			5.2.3 Metagenomics
			5.2.4 Transcriptomics
			5.2.5 Proteomics
			5.2.6 Lipidomics
			5.2.7 Glycomics
			5.2.8 Metabolomics
		5.3 Key Elements of Genetic Engineering
			5.3.1 Selectable Marker Genes
			5.3.2 Reporter Genes
			5.3.3 Regulatory Sequences
			5.3.4 UTRs
			5.3.5 Introns
			5.3.6 Codon Usage
			5.3.7 De Novo DNA Synthesis
			5.3.8 Vector Construction
			5.3.9 Transformation Methods
			5.3.10 Selection
			5.3.11 Genetically Transformable Microalgae Species
			5.3.12 Gene Silencing, Gene Knockout, and Genome Editing
			5.3.13 Unwanted Silencing of Transgenes
		5.4 The Application of Genetic Engineering
			5.4.1 Enzymes
			5.4.2 Antibodies and Immunotoxins
			5.4.3 Bioactive Peptides and Hormones
			5.4.4 Insecticides
			5.4.5 Vaccines
			5.4.6 Food Additives and Cosmetic Ingredients
			5.4.7 Optogenetic Tools for Neuroscience
			5.4.8 Wastewater Treatment and Bioremediation
			5.4.9 Liquid Biofuels and Hydrogen
		5.5 Conclusions
		References
	Chapter 6: Optimization of Microalgae Photosynthetic Metabolism to Close the Gap with Potential Productivity
		6.1 Introduction
		6.2 The Untapped Potential of Microalgae
			6.2.1 Microalgae as Feedstock for a Sustainable Global Economy
			6.2.2 Microalgae Photosynthetic Metabolism
				6.2.2.1 Light Reactions
				6.2.2.2 Carbon Fixation
			6.2.3 How Microalgae Photosynthetic Metabolism Responds to Intensive Cultivation
		6.3 Genetic Engineering of Photosynthetic Metabolism
			6.3.1 Improvement of Light Reactions
				6.3.1.1 Engineering Light-Harvesting to Increase Light Homogeneity
				6.3.1.2 Engineering Light-Harvesting to Increase Exploitable Radiation
				6.3.1.3 Reprogramming Photo-Protection Mechanisms
			6.3.2 Improvement of Carbon Fixation Rate
				6.3.2.1 Engineering Rubisco and Substrates Availability
				6.3.2.2 Engineering Photorespiration
				6.3.2.3 Synthetic Pathways for Carbon Fixation
		6.4 In Silico Approaches to Drive Genetic Engineering of Photosynthetic Metabolism
			6.4.1 Photosynthesis Metabolic Engineering and Industrial Cultivation
			6.4.2 Mathematical Models to Direct Metabolic Engineering of Photosynthesis
		6.5 Conclusions
		References
	Chapter 7: Metabolic Engineering and Synthetic Biology Approaches to Enhancing Production of Long-Chain Polyunsaturated Fatty ...
		7.1 Introduction
		7.2 LC-PUFA in Nutrition and Health
		7.3 Omega-3 Fatty Acid Production by Microalgae
			7.3.1 LC-PUFA-Producing Microalgae in Aquaculture
			7.3.2 LC-PUFA Biosynthesis
				7.3.2.1 Aerobic Pathway
				7.3.2.2 Anaerobic Pathway (PKS)
			7.3.3 Intracellular Compartmentation and Partitioning of LC-PUFA in Microalgae
		7.4 Recent Advances in the Metabolic Engineering of Microalgae to Enhance Production of LC-PUFA
			7.4.1 Diatoms
				7.4.1.1 Overexpressing Enzymes of Fatty Acid and TAG Biosynthetic Pathways
				7.4.1.2 Blocking Competing Pathways
			7.4.2 Nannochloropsis
			7.4.3 Systems Biology Approaches in Studying Algal Lipid LC-PUFA Production
			7.4.4 Alternative Approaches: Adaptive Laboratory Evolution and Chemical Genetics for LC-PUFA-Producing Strains Improvement
			7.4.5 The Initial Risk Assessment of Genetically Modified Microalgae Cultivation for Large-Scale LC-PUFA Production
		7.5 Perspectives and Conclusions
		References
Part III: Integrated Approaches
	Chapter 8: Integrated Biorefineries for Algal Biomolecules
		8.1 Introduction
		8.2 The Challenge of Biomolecule Extraction from Algae
			8.2.1 Unit Operations Dimension
			8.2.2 Cell-Structure Dimension
		8.3 Towards a Mechanistic Approach in Algae Biorefinery
			8.3.1 Design the Right Cell Architecture
			8.3.2 Cell Disintegration by Lytic Organisms, Enzymes and Selective Chemicals
			8.3.3 Demulsification
			8.3.4 Membraneless Osmosis
			8.3.5 Ionic Liquid Recovery
			8.3.6 Multi-product Biorefinery and Functionality
			8.3.7 Process Integration
		8.4 Future Directions: Biorefinery Intensification
			8.4.1 Self-Disintegration
			8.4.2 Simultaneous Disruption and Disentanglement
			8.4.3 Self-Separating Systems
		8.5 Techno-economic Analysis
		8.6 Concluding Remarks
		References
	Chapter 9: Combining Microalgae-Based Wastewater Treatment with Biofuel and Bio-Based Production in the Frame of a Biorefinery
		9.1 Introduction
			9.1.1 Wastewater: Industries/Economic Sectors
			9.1.2 Wastewater Treatment
			9.1.3 Microalgae-Based Wastewater Treatment
			9.1.4 Algal-Bacterial Consortia in Wastewater Treatment
			9.1.5 Subcritical Water Extraction of Bioactive Compounds
			9.1.6 Microalgae-Based Bioenergy
			9.1.7 Microalgae-Based Biofertilizers
		9.2 Wastewater Conversions Toward Biofuels and Bio-Based Products
			9.2.1 Urban
			9.2.2 Food
				9.2.2.1 Dairy
				9.2.2.2 Brewery
				9.2.2.3 Potato
				9.2.2.4 Coffee
				9.2.2.5 Yeast
			9.2.3 Livestock Production
				9.2.3.1 Swine
				9.2.3.2 Poultry
				9.2.3.3 Cattle
			9.2.4 Agriculture
			9.2.5 Aquaculture
		9.3 Environmental Benefits of Coupling Algae-Based Wastewater Treatment with Production of Biofuels and/or Bio-Products Throug...
		9.4 Conclusions
		References
	Chapter 10: Microalgal Consortia: From Wastewater Treatment to Bioenergy Production
		10.1 Introduction
		10.2 Applications of Microalgae
			10.2.1 CO2 Capture
			10.2.2 Nutrients Removal from Wastewaters
			10.2.3 Bioenergy Production
		10.3 Interactions and Benefits of Using Microalgal Consortia
			10.3.1 Microalgal Consortia
			10.3.2 Microalgal-Bacterial Consortia
		10.4 Applications of Microalgal Consortia
			10.4.1 CO2 Capture
			10.4.2 Nutrients Removal (Wastewater Polishing)
			10.4.3 Bioenergy Production
		10.5 Research Needs
		10.6 Conclusions
		References
	Chapter 11: Downstream Green Processes for Recovery of Bioactives from Algae
		11.1 Introduction
			11.1.1 Marine Resources
		11.2 Algae as Source of Bioactive or Valuable Compounds
			11.2.1 Lipids
			11.2.2 Proteins and Peptides
			11.2.3 Polysaccharides
			11.2.4 Phenolic Compounds
			11.2.5 Alkaloids
			11.2.6 Carotenoids
		11.3 How to Improve the Production of Bioactive Metabolites
			11.3.1 Marine Biotechnology
			11.3.2 Optimization of Upstream and Downstream Processes
				11.3.2.1 Upstream Processes
				11.3.2.2 Downstream Processes
					11.3.2.2.1 Assisted Extraction Techniques
					11.3.2.2.2 Compressed Fluids´ Extraction Techniques
						11.3.2.2.2.1 Supercritical Fluid Extraction
						11.3.2.2.2.2 Gas-Expanded Liquid Extraction
						11.3.2.2.2.3 Pressurized Liquid Extraction
			11.3.3 Integrated Processes
			11.3.4 Biorefinery
		11.4 Conclusions
		References
Part IV: Framework and Progress of Practical Applications
	Chapter 12: Bioactive Compounds from Microalgae and Their Potential Applications as Pharmaceuticals and Nutraceuticals
		12.1 Introduction
		12.2 Bioactivities of Microalgal Compounds and Their Potential Applications as Pharmaceuticals and Nutraceuticals
			12.2.1 Antibacterial Activity
			12.2.2 Antiviral Activity
			12.2.3 Immunomodulatory Activity
			12.2.4 Anticancer Activity
			12.2.5 Beneficial Effects Against Metabolic Disorders and Other Diseases
			12.2.6 Other Bioactivities
		12.3 Mass Culture of Microalgae for the Production of Pharmaceuticals and Nutraceuticals
		12.4 Future Directions of Research
		12.5 Concluding Remarks
		References
	Chapter 13: Metal Pollution in Water: Toxicity, Tolerance and Use of Algae as a Potential Remediation Solution
		13.1 Introduction
			13.1.1 Metal Pollution in Aquatic Environments
			13.1.2 Mechanisms of Metal Toxicity to Algae
			13.1.3 Strategies Used by Algae to Cope with Metals in Their Environment
				13.1.3.1 Cellular Defence Through Metal Uptake and Sequestration Mechanisms
				13.1.3.2 Maintenance of Cellular Redox Balance Under Metal Stress
				13.1.3.3 Heat Shock Protein Response to Metal Stress
				13.1.3.4 Tolerance Acquired Through Physiological Acclimation and Genetic Adaptation to Metal Stress
		13.2 Can Algae Be Used for Bioremediation of Metal Pollution?
			13.2.1 Macroalgae
			13.2.2 Microalgae
			13.2.3 Bacterial-Periphyton Interactions in Biofilms
		13.3 Conclusions and Suggestions for Further Work
		References
	Chapter 14: Benefits of Algal Extracts in Sustainable Agriculture
		14.1 Introduction
		14.2 Major Algal Metabolites
			14.2.1 Phenols
			14.2.2 Terpenoids
			14.2.3 Free Fatty Acids
			14.2.4 Polysaccharides
			14.2.5 Carotenoids
		14.3 Algal Metabolites as Biostimulants or Biofertilizers
			14.3.1 Impact on Soil Aggregation and Porosity
			14.3.2 Impact on Soil Macro- and Micro-environment
			14.3.3 Genetically Modified Algae in Sustainable Agriculture
		14.4 Algal Metabolites in Plant Protection and Development
			14.4.1 Antimicrobial Activity
			14.4.2 Antinematodal Activity
			14.4.3 Bioinsecticidal Activity
		14.5 Influence of Algal Metabolites in Animal Host Physiology
			14.5.1 Macroalgal Impacts
			14.5.2 Symbiosis Through Metabolite Transfer
			14.5.3 Microalgal Impacts
		14.6 Algal Phytohormones in Sustainable Agriculture
			14.6.1 Auxins
			14.6.2 Gibberellins
			14.6.3 Cytokinins
			14.6.4 Abscisic Acid
			14.6.5 Ethylene
		14.7 Summary and Future Perspectives
		References
	Chapter 15: Deriving Economic Value from Metabolites in Cyanobacteria
		15.1 Introduction
		15.2 Up and Downstream Processing of Cyanobacteria to Obtain Metabolites
			15.2.1 Upstream Challenges and Techno-economics
			15.2.2 Downstream Processing Challenges
				15.2.2.1 Cell Concentration
				15.2.2.2 Cell Disruption
				15.2.2.3 Recovery and Purification of Metabolites
		15.3 Metabolites
			15.3.1 Phycobilins
			15.3.2 Carotenoids
			15.3.3 Polysaccharides
			15.3.4 Proteins and Peptides
			15.3.5 Nonribosomal Peptides
			15.3.6 Lipids and Fatty Acids
			15.3.7 Cyanotoxins
			15.3.8 Sunscreens
			15.3.9 Polyhydroxyalkanoates (PHAs)
			15.3.10 Isoprenoids (Terpenes)
			15.3.11 Platform Chemicals
			15.3.12 Stable Isotopes
		15.4 Systems Biology
		15.5 Biorefinery Approaches
		15.6 Conclusion
		References
	Chapter 16: European Union Legislation and Policies Relevant for Algae
		16.1 Introduction
		16.2 Policies
		16.3 Harvest and Production
		16.4 Food, Feed and Pharmaceuticals
		16.5 Chemicals (Including Fertilisers and Cosmetics)
		16.6 Energy and Trade
		16.7 Conclusion: Challenges and Opportunities
		References