Handbook of Microalgal Culture Applied Phycology and Biotechnology -- Contents -- List of Contributors -- Acknowledgments -- Introduction -- Part 1 The Microalgal Cell with Reference to Mass Cultures -- 1 The Microalgal Cell -- 1.1 INTRODUCTION -- 1.2 GROSS MORPHOLOGY -- 1.3 SEXUAL REPRODUCTION -- 1.4 ULTRASTRUCTURE -- 1.4.1 Chloroplast -- 1.4.2 Mitochondrion -- 1.4.3 Nucleus and mitosis -- 1.4.4 Golgi body and endoplasmic reticulum -- 1.4.5 Vacuoles -- 1.4.6 Flagella and eyespots -- 1.4.7 Cell walls and coverings -- 1.5 BIOCHEMICAL ASPECTS -- 1.5.1 Carbohydrates -- 1.5.2 Lipids -- 1.5.3 Proteins -- 1.6 BIODIVERSITY -- 1.7 EVOLUTION AND SYSTEMATIC BIOLOGY -- 1.7.1 Evolutionary origins -- 1.7.2 Cyanobacteria -- 1.7.3 Eukaryotic super groups -- 1.7.4 Glaucophyte algae -- 1.7.5 Green algae -- 1.7.6 Red algae -- 1.7.7 Heterokont algae -- 1.7.8 Dinoflagellates -- 1.7.9 Haptophytes -- 1.7.10 Cryptophytes -- 1.7.11 Euglenoids -- 1.7.12 Chlorarachniophytes -- 1.7.13 Other photosynthetic alga-like organisms -- 1.8 ECOLOGY -- ACKNOWLEDGMENT -- REFERENCES -- 2 Photosynthesis in Microalgae -- 2.1 THE PROCESS OF PHOTOSYNTHESIS -- 2.2 THE NATURE OF LIGHT -- 2.3 PHOTOSYNTHETIC PIGMENTS -- 2.4 THE LIGHT REACTIONS OF PHOTOSYNTHESIS -- 2.4.1 The photosynthetic membranes -- 2.4.2 Photosynthetic electron transport and phosphorylation -- 2.4.3 The outer light-harvesting antennae -- 2.4.4 Photosystem II -- 2.4.5 Plastoquinone, the cytochrome b6/f complex, and plastocyanin -- 2.4.6 Photosystem I -- 2.4.7 ATP synthase/ATPase -- 2.5 THE DARK REACTIONS OF PHOTOSYNTHESIS -- 2.5.1 Carbon assimilation -- 2.5.2 Photorespiration -- 2.6 LIGHT ACCLIMATION -- 2.7 SELECTED MONITORING TECHNIQUES USED IN MICROALGAL BIOTECHNOLOGY -- 2.7.1 Measurement of photosynthetic oxygen evolution -- 2.7.2 Measurement of photosynthetic carbon fixation -- 2.7.3 Chlorophyll fluorescence.

2.8 THEORETICAL LIMITS OF MICROALGAL PRODUCTIVITY -- ACKNOWLEDGEMENT -- REFERENCES -- 3 Basic Culturing and Analytical Measurement Techniques -- 3.1 ISOLATION OF MICROALGAE -- 3.1.1 Selection of sources of microalgae -- 3.1.2 Enrichment of a culture -- 3.1.3 Direct isolation -- 3.1.4 Producing axenic cultures -- 3.2 SCREENING OF MICROALGAE FOR BIOACTIVE MOLECULES -- 3.2.1 Direct assays -- 3.2.2 Indirect assays -- 3.3 MAINTENANCE AND PRESERVATION OF MICROALGAL STRAINS -- 3.4 MEASUREMENT OF GROWTH PARAMETERS -- 3.4.1 Cell count -- 3.4.2 Optical density method for determination of microalgal biomass -- 3.4.3 Dry and wet mass -- 3.4.4 Moisture content and ash content -- 3.4.5 Chlorophyll determination -- 3.4.6 Total organic carbon (TOC) measurement -- 3.4.7 Doubling time, specific growth rate, and output rate -- 3.4.8 Growth yield -- 3.4.9 Maintenance energy requirement -- 3.5 MODES OF CULTURE -- 3.5.1 Batch culture -- 3.5.2 Continuous cultures -- 3.5.3 Immobilized cultures -- 3.6 ADVANCED BIOCHEMICAL ANALYSIS -- 3.6.1 Carbohydrates -- 3.6.2 Proteins -- 3.6.3 Lipids -- 3.6.4 Fatty acid composition analysis -- 3.6.5 Lipid determination using fluorescence spectroscopy and microscopy -- ACKNOWLEDGMENT -- REFERENCES -- 4 Strategies for Bioprospecting Microalgae for Potential Commercial Applications -- 4.1 INTRODUCTION -- 4.2 UNIVARIATE APPROACHES TO DESIGN AND IMPLEMENTATION OF STRAIN COLLECTION STRATEGIES -- 4.2.1 Collection strategies focused on broad collection of all algae in general -- 4.2.2 Collection strategies focused on specific habitat types -- 4.2.3 Collection strategies focused on a targeted chemical composition or product -- 4.2.4 Collection strategies centered on physiological or chemical attributes of the strains -- 4.3 MULTIVARIATE APPROACHES TO DESIGN AND IMPLEMENTATION OF STRAIN COLLECTION STRATEGIES.

4.3.1 Sample collection and enrichment for targeted strain capabilities -- 4.3.2 Simultaneous collection and screening for two or more targeted capabilities -- REFERENCES -- 5 Maintenance of Microalgae in Culture Collections -- 5.1 INTRODUCTION -- 5.2 THE DIVERSITY OF MICROALGAE IN CULTURE COLLECTIONS -- 5.3 THE CONCEPT OF STRAINS VERSUS SPECIES OF MICROALGAE -- 5.4 MAINTENANCE OF ACTIVELY GROWING CULTURES -- 5.4.1 Purity of cultures -- 5.4.2 Quality control and financial considerations -- 5.4.3 Cryopreservation -- 5.4.4 Identifying and authenticating strains of microalgae in culture collections -- 5.4.5 The future of culture collections -- ACKNOWLEDGMENT -- REFERENCES -- 6 Environmental Stress Physiology with Reference to Mass Cultures -- 6.1 INTRODUCTION -- 6.2 LIGHT AND PHOTOSYNTHESIS RATE -- 6.2.1 P versus I curve -- 6.2.2 Photoacclimation -- 6.2.3 Photoinhibition -- 6.2.4 Photoinhibition in outdoor cultures -- 6.2.5 Some practical considerations -- 6.3 SALINITY STRESS -- 6.4 CONCLUDING REMARKS -- 6.5 SUMMARY -- ACKNOWLEDGMENT -- REFERENCES -- 7 Environmental Effects on Cell Composition -- 7.1 INTRODUCTION -- 7.2 ENVIRONMENTAL FACTORS -- 7.2.1 Light -- 7.2.2 Temperature -- 7.3 NUTRITIONAL FACTORS -- 7.3.1 Nitrogen -- 7.3.2 Phosphorus -- 7.3.3 Iron -- 7.4 SALINITY -- 7.5 SYNERGISTIC EFFECTS OF COMBINATIONS OF CHEMICAL AND PHYSICAL FACTORS ON CELL COMPOSITION -- 7.6 BIOTECHNOLOGICAL APPROACHES TO CONTROL CELL COMPOSITION -- REFERENCES -- 8 Inorganic Algal Nutrition -- 8.1 NUTRITIONAL MODES -- 8.2 NUTRIENT REQUIREMENTS -- 8.3 CARBON -- 8.4 NITROGEN -- 8.5 PHOSPHORUS -- 8.6 OTHER MACRO- AND MICRONUTRIENTS, CHELATES, AND WATER -- 8.7 RECIPES FOR ALGAL GROWTH NUTRIENT MEDIA -- 8.8 UPTAKE OF N AND P -- 8.8.1 Competition for limiting resources (nutrients) -- 8.9 NUTRIENT RATIOS -- 8.10 PHYSICAL FACTORS INFLUENCING NUTRIENT UPTAKE -- 8.10.1 Bioremediation.

REFERENCES -- 9 Commercial Production of Microalgae via Fermentation -- 9.1 INTRODUCTION -- 9.2 WHY HETEROTROPHIC PRODUCTION OF ALGAE? -- 9.3 THE HETEROTROPHIC CAPACITY OF MICROALGAE -- 9.4 EARLY HISTORY OF THE PRODUCTION OF MICROALGAE IN COMMERCIAL-SCALE FERMENTORS -- 9.5 COMMERCIAL SUCCESS: CHLORELLA FERMENTATION FOR NUTRITIONAL SUPPLEMENTS -- 9.6 COMMERCIAL SUCCESS: CRYPTHECODINIUM FERMENTATION FOR DHA -- 9.7 COMMERCIAL SUCCESS: SCHIZOCHYTRIUM FERMENTATION FOR DHA -- 9.8 HETEROTROPHIC CHLORELLA: FUTURE DIRECTIONS -- 9.8.1 Biodiesel from heterotrophic Chlorella -- 9.8.2 Food ingredients from heterotrophic Chlorella -- 9.8.3 Renewable chemicals from heterotrophic Chlorella -- 9.9 CRYPTHECODINIUM: FUTURE DIRECTIONS -- 9.10 SCHIZOCHYTRIUM: FUTURE DIRECTIONS -- 9.10.1 Biodiesel from Schizochytrium -- 9.10.2 New food ingredients from Schizochytrium -- 9.11 OTHER HETEROTROPHIC MICROALGAE: FUTURE DIRECTIONS -- REFERENCES -- 10 Molecular Genetic Manipulation of Microalgae: Principles and Applications -- 10.1 GENE STRUCTURE AND CONTROL OVER EXPRESSION -- 10.1.1 Control elements affecting mRNA levels -- 10.2 SELECTION MARKERS -- 10.3 TRANSFORMATION METHODS -- 10.3.1 Comparison of transformation efficiencies -- 10.4 GENE TARGETING AND KNOCKDOWNS -- 10.4.1 Insertional mutagenesis -- 10.4.2 Homologous recombination -- 10.4.3 RNAi- and antisense RNA expressionmediated gene knockdown -- 10.5 PROBLEMS IN ALGAL TRANSGENICS -- 10.5.1 Gene silencing -- 10.5.2 Codon usage -- 10.5.3 Introns and other elements -- 10.6 NUCLEAR VERSUS CHLOROPLAST TRANSFORMATION -- 10.7 METABOLIC ENGINEERING -- 10.7.1 Selection of gene targets for metabolic engineering -- 10.8 MICROALGAE AS PROTEIN EXPRESSION SYSTEMS -- 10.9 BREEDING, MUTAGENESIS, AND SELECTION -- 10.10 SUMMARY AND FUTURE DIRECTIONS -- ACKNOWLEDGMENT -- REFERENCES -- Part 2 Mass Cultivation and Processing of Microalgae.

11 Biological Principles of Mass Cultivation of Photoautotrophic Microalgae -- 11.1 LIGHT: THE MAJOR FACTOR IN GROWTH AND PRODUCTIVITY -- 11.2 CELL CONCENTRATION: A PROMINENT FACTOR OF THE LIGHT REGIME OF CELLS IN THE CULTURE -- 11.2.1 Areal and population densities -- 11.2.2 Light penetration depth -- 11.2.3 Effect of cell density on cellular ultrastructure and composition -- 11.3 MIXING PHOTOAUTOTROPHIC CULTURES -- 11.4 LIGHT-DARK CYCLE FREQUENCIES -- 11.5 THE OPTICAL PATH, A DECISIVE PARAMETER IN GROWTH AND PRODUCTIVITY OF PHOTOAUTOTROPHIC CULTURES -- 11.6 ULTRAHIGH CELL DENSITY CULTURES -- 11.6.1 Growth inhibitory substances and conditions -- 11.6.2 Areal density in relation to the optical path -- 11.7 REACTION TIMESCALES IN PHOTOSYNTHESIS, IN RELATION TO THE EFFECT OF THE OPTICAL PATH ON CULTURE PRODUCTIVITY -- 11.7.1 Reaction timescales in photosynthesis -- 11.7.2 Cell travel times between the lit and dark volumes in the reactor -- 11.7.3 Long optical paths -- 11.7.4 Short optical paths -- 11.7.5 Radiation dependence of the photosynthetic reaction center - turnover time -- 11.8 THE AVERAGE RADIATION INTENSITY -- 11.9 EFFECTIVE USE OF SUNLIGHT AND HIGH IRRADIANCE FOR PHOTOSYNTHETIC PRODUCTIVITY -- 11.9.1 Response to changing irradiance outdoors -- 11.9.2 Tilting reactor surfaces in adjustment to the solar angle -- 11.10 PHOTOSYNTHETIC EFFICIENCY IN MASS CULTURES (SEE CHAPTER 2) -- 11.10.1 Appraising algal productivity and assessment of reactor efficiency (see also Chapter 12) -- 11.11 MAINTENANCE OF MASS CULTURES -- 11.11.1 Online monitoring of photosynthetic activity -- 11.11.2 Measurement of cell growth and culture productivity -- 11.11.3 Night biomass loss -- 11.11.4 Maintaining OPD -- 11.11.5 Preventing nutritional deficiencies -- 11.11.6 Maintenance of monoalgal cultures and combating contamination -- REFERENCES.

12 Theoretical Analysis of Culture Growth in Flat-Plate Bioreactors: The Essential Role of Timescales.