Note: Intro -- Preface -- Contents -- Part I: Diversity, Biology, and Ecology -- Chapter 1: Protistan Diversity in Environmental Molecular Surveys -- 1.1 Introduction -- 1.2 Protists in Marine Environments -- 1.3 Identification of Marine Planktonic Protists -- 1.4 Environmental Sequencing of Phylogenetic Marker Genes -- 1.5 Fingerprinting Analysis for Community Comparison -- 1.6 Beyond Sequences and Back to the Cells -- 1.7 The Genomic Era -- 1.8 Closing Remarks -- References -- Chapter 2: Unusual Features of Dinokaryon, the Enigmatic Nucleus of Dinoflagellates -- 2.1 Introduction -- 2.2 Phylogeny of Dinoflagellates -- 2.3 The Dinokaryon -- 2.3.1 Genome, Chromosome, and DNA -- 2.3.2 Transcription and Spliced Leader Trans-Splicing -- 2.3.3 Mitosis -- 2.3.4 Nucleofilament -- 2.3.5 Proposed Models for Chromosome Architecture -- 2.3.6 Nuclear Proteins -- 2.3.7 HCc Family -- 2.3.8 Dinaps and Their Associating Proteins -- 2.3.9 Lamin and Lamin-Like Proteins -- 2.3.10 NP23 and DVNP -- 2.3.11 Histones and Histone-Related Proteins -- 2.3.12 Other Nuclear Proteins -- 2.4 Concluding Remarks -- References -- Chapter 3: Diversity of Microbial Eukaryotes in Deep Sea Chemosynthetic Ecosystems Illuminated by Molecular Techniques -- 3.1 Introduction -- 3.2 Microbial Eukaryotes in the Ecosystems of Hydrothermal Vents -- 3.3 Microbial Eukaryotes in the Ecosystems of Cold Seeps -- 3.4 Perspectives -- References -- Chapter 4: Biology, Diversity and Ecology of Free-Living Heterotrophic Flagellates -- 4.1 Introduction -- 4.2 Opisthokonta -- 4.3 Amoebozoa (Amoebobionta) -- 4.4 Excavata -- 4.5 Archaeplastida (Plantae) -- 4.6 Stramenopiles -- 4.7 Alveolata -- 4.8 Rhizaria -- 4.9 Other Flagellates -- References -- Chapter 5: Basal Lineages of Green Algae - Their Diversity and Phylogeny -- 5.1 Introduction -- 5.2 Classification of Primitive Green Algae -- 5.2.1 Streptophyta. , 5.2.1.1 Class Mesostigmatophyceae Marin et Melkonian 1999 -- 5.2.2 Chlorophyta -- 5.2.2.1 Order Prasinococcales (Clade VI) -- 5.2.2.2 Order Palmophyllales Zechman, Verbruggen, Leliaert, Ashworth, MA Buchheim, Fawley, H Spalding, Pueschel, JA Buchheim, Verghese et Hanisak 2010 -- 5.2.2.3 Pyramimonadales sensu Melkonian 1990 (Clade I) -- 5.2.2.4 Mamiellophyceae Marin et Melkonian 2010 (Clade II) -- 5.2.2.4.1 Mamiellales Moestrup 1984 emend. Marin et Melkonian 2010 -- Mamiellaceae Moestrup 1984 emend. Marin et Melkonian 2010 -- Bathycoccaceae Marin et Melkonian 2010 -- 5.2.2.4.2 Dolichomastigales Marin et Melkonian 2010 -- Dolichomastigaceae Marin et Melkonian 2010 -- Crustomastigaceae Marin et Melkonian 2010 -- 5.2.2.4.3 Monomastigales Marin et Melkonian 2010 -- 5.2.2.5 Clade VII sensu Guillou et al. 2004 -- 5.2.2.5.1 The Picocystis Clade -- 5.2.2.6 Pycnococcaceae Guillard emend. Fawley 1999 (Clade V) -- 5.2.2.7 Nephroselmidophyceae Cavalier-Smith 1993 (Clade III) -- 5.2.2.8 Chlorodendrophyceae Massjuk 2006 (Clade IV) -- 5.2.2.9 Pedinophyceae Moestrup emend. Marin 2012 -- 5.2.2.9.1 Pedinomonadales Moestrup emend. Marin 2012 -- 5.2.2.9.2 Marsupiomonadales Marin 2011 -- 5.2.2.10 Clades VIII and IX -- 5.3 Ecology of Primitive Green Algae -- References -- Chapter 6: Typical Features of Genomes in the Mamiellophyceae -- 6.1 Introduction to Mamiellophyceae -- 6.2 Genome Characteristics of Mamiellales -- 6.2.1 The Genomes of the Mamiellales Are Small -- 6.2.2 Similar Cellular Morphologies Cloak Phylogenomic Divergence -- 6.2.3 Two Outlier Chromosomes Have Enigmatic Functionalities -- 6.3 Metabolic Processes or Life Styles Inferred from Genomes -- 6.4 Organellar Genomes -- 6.4.1 Common Features of Mamiellophyceae Organellar Genomes -- 6.4.2 Variable Features of Mamiellophyceae Organellar Genomes. , 6.4.3 Population Genomic Insights into Organelle Inheritance and Evolution -- 6.5 Metagenomics of Mamiellales -- 6.5.1 Linking Marker Gene Diversity, Physiology and Ecology -- 6.5.2 Whole Genomic Sequence from "Wild" Populations -- 6.6 Viruses -- 6.6.1 Prasinoviruses Are Diverse and Abundant -- 6.6.2 Is the Evolution of Host and Viral Genomes Driven by an Arms Race? -- 6.7 Perspectives -- References -- Chapter 7: Planktic Foraminifera -- 7.1 Introduction -- 7.1.1 What Are Foraminifera? -- 7.1.2 Evolution over Geological Timescales -- 7.1.3 Research History of Living Planktic Foraminifera: An Overview -- 7.2 Shell Morphology and Structure -- 7.2.1 Morphology-Based Classification -- 7.2.2 Shell Structure and Ontogeny -- 7.3 Horizontal and Vertical Distributions -- 7.4 Biology -- 7.4.1 Cytoplasm -- 7.4.2 Predation -- 7.4.3 Symbiosis -- 7.4.4 Reproduction and Life Cycles -- 7.5 Shell Geochemistry -- 7.5.1 Advances in Geochemistry and Paleoceanography -- 7.5.2 Oxygen and Carbon Isotopes -- 7.5.3 Trace Metals in Foraminiferal Shells -- 7.5.4 Sub-micron-Order Geochemical Analysis -- 7.6 Molecular Biology -- 7.6.1 Evolution -- 7.6.2 Origin of the Modern Planktic Foraminifera -- 7.6.3 Genetic Diversity -- 7.6.4 Geographic and Vertical Distribution of Genetic Diversity -- 7.6.5 Reassessment of Shell Morphology -- 7.7 Collection and Cultivation -- 7.7.1 Collection of Living Specimens -- 7.7.2 Preparation in the Laboratory -- 7.7.3 Maintenance of Living Specimens -- 7.7.4 Feeding and Maintenance -- 7.7.5 Sample Fixation -- 7.7.6 Advanced Systems for Ecological Study: A Flow-­Through Culture Approach -- References -- Further Reading Lists -- Chapter 8: Biology and Ecology of Radiolaria -- 8.1 Overview of Radiolarian Features -- 8.2 Acantharia -- 8.2.1 Cell Structure and Taxonomy -- 8.2.2 Reproduction and Motility. , 8.2.3 Trophic Characteristics and Biotic Interactions -- 8.2.4 Environmental Distribution -- 8.3 Taxopodia -- 8.3.1 Cell Structure and Taxonomy -- 8.3.2 Reproduction and Motility -- 8.3.3 Trophic Characteristics and Biotic Interactions -- 8.3.4 Environmental Distribution -- 8.4 Spumellaria -- 8.4.1 Cell Structure and Taxonomy -- 8.4.2 Reproduction and Motility -- 8.4.3 Trophic Characteristics and Biotic Interactions -- 8.4.4 Environmental Distributions -- 8.5 Nassellaria -- 8.5.1 Cell Structure and Taxonomy -- 8.5.2 Reproduction and Motility -- 8.5.3 Trophic Characteristics and Biotic Interactions -- 8.5.4 Environmental Distributions -- 8.6 Collodaria -- 8.6.1 Cell Structure and Taxonomy -- 8.6.2 Reproduction and Motility -- 8.6.3 Trophic Characteristics and Biotic Interactions -- 8.6.4 Environmental Distributions -- 8.7 General Ecology of Radiolaria -- 8.8 Seasonality of Polycystines in Different Regions -- 8.8.1 Upwelling Regions -- 8.8.2 Major Factors Controlling Polycystine Distributions -- 8.8.3 Contributions to Inorganic Biochemical Cycle -- 8.9 Research Perspectives on Living Radiolarians -- References -- Chapter 9: Phaeodaria: Diverse Marine Cercozoans of World-Wide Distribution -- 9.1 Introduction -- 9.1.1 What Are "Phaeodarians"? -- 9.1.2 History -- 9.2 Classification -- 9.2.1 Cercozoa -- 9.2.2 Outline of Taxonomy -- 9.3 Cell Structure -- 9.3.1 Malacoma -- 9.3.2 Scleracoma -- 9.4 Mode of Life -- 9.5 Reproduction -- 9.5.1 Cell Division -- 9.5.2 Swarmer Production -- 9.6 Trophic Interactions -- 9.6.1 Feeding -- 9.6.2 Predators and Symbiosis -- 9.7 Distribution -- 9.7.1 Global Distribution -- 9.7.2 Vertical Distribution -- 9.8 Interactions with the Environment -- 9.8.1 Restricting Factors of Phaeodarian Distribution -- 9.8.2 Biomass -- 9.8.3 Seasonality -- 9.8.4 Importance in the Matter Cycle -- 9.9 Fossil Records -- References. , Chapter 10: Ecology and Evolution of Marine Diatoms and Parmales -- 10.1 Introduction -- 10.2 Diatom -- 10.2.1 History of Study -- 10.2.2 Marine Diatom Phytoplankton Ecology -- 10.2.3 Resting Stages -- 10.2.4 Physiological Response to Stress -- 10.2.5 Iron Limitation -- 10.2.6 Genomics and the Urea Cycle -- 10.2.7 Sinking and Staying in Suspension -- 10.2.8 Life History -- 10.2.9 Diatoms and Bacteria -- 10.2.10 Toxicity -- 10.2.11 Palaeoecology -- 10.2.12 Evolution -- 10.3 Parmales -- 10.3.1 An Insight into Diatom Ancestry? -- 10.3.2 Effects of Silicon Limitation on Growth and Morphology of Parmales -- 10.3.3 Ecology -- References -- Chapter 11: Planktonic Ciliates: Diverse Ecological Function in Seawater -- 11.1 Introduction -- 11.2 Potential Growth Influencing Grazing Impact of Ciliates -- 11.3 Grazing on Picoplankton and Nanoplankton -- 11.3.1 Ciliates as Picoplankton Feeder -- 11.3.2 Ciliates as Nanoplankton Feeders -- 11.3.3 Factors to Influence Feeding Activities of Ciliates -- 11.3.4 Comparison with the Heterotrophic Dinoflagellates -- 11.4 Prey for Meso- and Macrozooplankton -- 11.5 Nutrient Regeneration -- 11.6 Specific Functions Through Prey-Predator Relationships -- 11.6.1 Role of Grazing on HAB Species -- 11.6.2 Role as Food Source for Aurelia aurita -- 11.6.3 Role as Food for Bivalves -- 11.7 Conclusion and Future Subjects -- References -- Chapter 12: Biology and Paleontology of Coccolithophores (Haptophytes) -- 12.1 Introduction -- 12.2 Life Cycle, Biomineralization and Molecular Phylogeny -- 12.3 Biogeography and Seasonality -- 12.4 Coccolithophores in the Geological Past -- 12.5 The Future of Coccolithophores -- References -- Chapter 13: Diversity and Ecology of Thraustochytrid Protists in the Marine Environment -- 13.1 Introduction -- 13.2 Taxonomy, Morphology and Molecular Phylogeny. , 13.3 Methodologies for Detecting Thraustochytrids.

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