Note: Intro -- Foreword -- Preface -- References -- Contents -- 1: A Sea of Microbes: What´s So Special about Marine Microbiology -- 1.1 Introduction -- 1.2 Planet Ocean -- 1.2.1 Salinity -- 1.2.2 Origin of Salinity and Early Ocean -- 1.2.3 Microorganisms in the Ocean -- 1.2.4 The Oceanic Habitat -- 1.3 What Is a Marine Microorganism? -- 1.3.1 What Is a Microorganism? -- 1.3.2 Do Marine Microorganisms Exist? -- 1.3.3 How Many Species of Marine Microorganisms Exist? -- 1.4 (Some) Milestones of Marine Microbiology -- 1.5 Selected Aspects of the Marine Microbial System -- 1.5.1 The Redfield Ratio -- 1.5.2 Nitrogen Fixation -- 1.5.3 Adaptation to Salt -- 1.5.4 Sulfate -- 1.5.5 Freshwater- and Marine Microbiomes: What Are the Boundaries? -- 1.6 On a Personal Note: How Did I Become a Marine Microbiologist -- 1.7 Concluding Remarks -- References -- Part I: Diversity and Evolution of Marine Microorganisms -- 2: Survival in a Sea of Gradients: Bacterial and Archaeal Foraging in a Heterogeneous Ocean -- 2.1 Introduction -- 2.2 The Physics of Marine Microenvironments -- 2.2.1 Diffusion and Flow Shape Microscale Nutrient Seascapes -- Box 2.1 The Batchelor Scale -- Box 2.2 The Péclet Number -- 2.2.2 A Bacterial View of the Microscale Ocean -- 2.3 Sources and Nature of Microscale Gradients in the Ocean -- 2.3.1 The Phycosphere -- 2.3.2 Zooplankton Excretion and Sloppy Feeding -- 2.3.3 Cell Lysis Events -- 2.3.4 Particles -- 2.3.5 Transparent Exopolymer Particles -- 2.3.6 Larger Organisms -- 2.3.7 Molecular Diversity of Chemoattractants -- 2.4 Motility and Chemotaxis as Microbial Adaptations to Microscale Heterogeneity in the Ocean -- 2.4.1 The Molecular Machinery of Chemotaxis -- 2.4.2 The Roles of Chemotaxis -- 2.4.3 Mechanics of Motility -- 2.4.4 Abundance of Motile Prokaryotes -- 2.4.5 Swimming Speed -- 2.4.6 Why Do Marine Bacteria Swim Fast?. , 2.4.7 Energetic Costs and Benefits of Motility -- 2.4.8 Swimming Patterns -- 2.5 Recent Insight from Omics Data -- 2.5.1 Genomes of Marine Bacteria -- 2.5.2 Metagenomics -- 2.5.3 Metatranscriptomics -- 2.6 Influence of Microscale Gradients on Large-Scale Processes -- 2.6.1 Impacts on Oceanic Primary Production -- 2.6.2 Impacts on Symbiont Recruitment -- 2.6.3 Impacts on Rates of Chemical Transformations -- 2.6.4 Impacts on Exchanges Between Ocean and Atmosphere -- 2.6.5 Impacts on Exchanges Between Ocean and Sediments -- 2.7 Summary and Future Directions -- References -- 3: Marine Cyanobacteria -- 3.1 Introduction -- 3.2 Marine Cyanobacteria and the Next Generation Sequencing Revolution -- 3.3 Cyanobacterial Origin and Evolution -- 3.3.1 The Advent of Cyanobacteria and Oxygenic Photosynthesis -- 3.3.2 Evolutionary History of Marine Cyanobacteria -- 3.3.3 Adaptation to Salinity -- 3.3.4 Adaptation to Nitrogen Depletion -- 3.3.5 Adaptation to Spectral Niches -- 3.4 Prochlorococcus and Synechococcus -- 3.4.1 Interest as Model Organisms in Marine Biology and Ecology -- 3.4.2 Global Abundance and Distribution -- 3.4.3 Phylogeny -- 3.4.4 The Wide Genomic Diversity of Marine Picocyanobacteria and Its Taxonomic Implications -- 3.4.5 Role of Environmental Factors in Genetic and Functional Diversification -- 3.4.5.1 Prochlorococcus -- 3.4.5.2 Synechococcus -- 3.4.6 Prochlorococcus Genome Streamlining -- 3.4.7 Core, Accessory, and Pangenomes -- 3.4.8 Potential Biotechnological Value -- 3.5 Nitrogen-Fixing Cyanobacteria -- 3.5.1 Ecological Role and Importance of Diazotrophy in Marine Ecosystems -- 3.5.2 Filamentous Marine Diazotrophs -- 3.5.2.1 Trichodesmium -- 3.5.2.2 Nodularia, a Bloom-Forming Cyanobacterium Specifically Adapted to Salinity Gradients -- 3.5.2.3 Richelia and Calothrix -- 3.5.3 Unicellular Marine Diazotrophs -- 3.6 Concluding Remarks. , References -- 4: Marine Protists: A Hitchhiker´s Guide to their Role in the Marine Microbiome -- 4.1 Introduction: The Poetry and Beauty of Protists Through Time -- Box 4.1 -- Box 4.2 -- 4.2 Evolutionary Relationships among Protists -- 4.2.1 A Historical Perspective on Protistan Diversity -- Box 4.3 -- 4.2.2 Developments in the Understanding of Evolution of Protists -- 4.2.3 Major Groups of Eukaryotes as of ``Currently´´ -- 4.2.4 The Contribution of Plastid Acquisition and Evolution to the Generation of Eukaryotic Diversity -- 4.3 Traits Distinguishing Protists from Other Marine Microbiome Members: Size and Cell Structure -- 4.3.1 Cell Size of Marine Protists -- Box 4.4 -- 4.3.2 Cellular Structure and Mosaic Genomes -- Box 4.5 -- 4.4 Metabolic Exchanges Between Microbiome Members -- 4.4.1 Symbioses: Manifestation Is a Status Not an Identity -- 4.4.2 Phycosphere and Metabolic Exchanges -- 4.4.3 The Holobiont Concept -- 4.5 Shifting from a Functional Dichotomy to Recognizing the True Complexity of Marine Protists -- Box 4.6 -- 4.5.1 Pursuing Lines of Protistan Heterotrophy in the Sea -- 4.5.2 Non-constitutive Mixotrophy (Via Photosynthetic Endosymbionts and Kleptoplasty) -- Box 4.7 -- 4.5.3 Constitutive Mixotrophy -- 4.5.4 Diversity and Importance of Photosynthetic Protists -- 4.6 Distribution and Vertical Dimension of Protistan Diversity and Ecology: From the Sea Surface to Sediments -- 4.6.1 Protists in the Photic Zone -- 4.6.2 Protists in the Dark Ocean: Oxygen Minimum Zones and Sediments -- 4.6.3 Diversity of Marine Protists in the Vertical Dimension -- 4.7 Forces of Mortality -- 4.7.1 Timeline of Virus Discovery -- 4.7.2 Current Perspectives on Viruses of Marine Protists -- 4.7.3 Diversity of Viruses Infecting Marine Protists -- 4.7.4 Death of a Protist Via Predation -- 4.8 Looking Forward -- 4.8.1 Classics: The Delineation of Protistan Species. , 4.8.2 Classics: Everything Is Everywhere, but, the Environment Selects Versus Endemism -- 4.8.3 Classics: Diversity and Stability of Plankton Communities -- 4.8.4 The Uncultured Majority: Quantifying Activities and Trophic Transfer -- 4.8.5 Bringing Cell Biology to Bear on the Protistan Role in the Marine Microbiome -- 4.8.6 Connecting Microbiome Members and Interactions to Ocean Physics and Chemistry -- 4.8.7 Climate Change and Conservation -- Box 4.8 -- References -- 5: Marine Fungi -- 5.1 Introduction -- 5.2 From Culture-Based to Next-Generation Sequencing Methods to Access Marine Fungal Life -- 5.3 Habitat Specific Community Composition or over-Dispersion? -- 5.3.1 Plant-Based Habitats -- 5.3.2 Coastal Waters -- 5.3.3 Algae -- 5.3.4 Deep-Sea and Deep Subsurface -- 5.3.4.1 Deep-Sea Habitats -- 5.3.4.2 Deep Subsurface Sediments and Oceanic Crust -- 5.3.5 Polar Waters -- 5.4 Adaptation of Marine Fungi -- 5.5 Accessing the Bioremediation Potential of Marine Fungi -- 5.5.1 Degradation of Hydrocarbons -- 5.5.2 Degradation of Plastics -- 5.6 Hints to Ecological Roles Inferred from Secondary Metabolites -- 5.6.1 Secondary Metabolites (or Specialized Metabolites): A Definition -- 5.6.2 Marine Fungal Chemodiversity -- 5.6.3 Marine Fungal SMs and Specificity to the Marine Environment -- 5.6.4 New Methods to Access the Marine Fungal Metabolome -- 5.6.5 Marine Fungal Chemical Ecology: Ecological Role of Marine Fungal Metabolites -- 5.7 From (Meta)Genomes to Bioactive Molecules -- References -- 6: Marine Viruses: Agents of Chaos, Promoters of Order -- 6.1 Introduction -- 6.2 Consolidating the Role of Marine Viruses -- 6.2.1 Revisiting the Evidence -- 6.2.2 The Nutrient Connexion -- 6.3 Marine Viruses Reviewed -- 6.3.1 The Ecology of Marine Viruses -- 6.3.2 Methodological Approaches -- 6.3.3 Numerical Modelling -- 6.4 The Omnipresence of Virus in the Sea. , 6.4.1 Different Environments, Same Incidence -- 6.4.2 From Surface to Bottom, and deeper -- 6.5 Recent Developments in Viral Research -- 6.5.1 The Endless Harvest in the Field of Metagenomics -- 6.5.2 Novel Applications, Innovative Methodologies, New Protocols -- 6.5.3 Tackling Omics-Data -- 6.6 Emergent Themes -- 6.6.1 Resistance to Infection -- 6.6.2 Ocean Acidification -- 6.6.3 Response to Climate Change -- 6.6.4 Viral Action during Harmful Algal Blooms -- 6.7 Viruses and Marine Models -- 6.7.1 Different Modelling Approaches -- 6.7.2 Challenges Ahead -- 6.8 Concluding Remarks -- References -- 7: Evolutionary Genomics of Marine Bacteria and Archaea -- 7.1 Introduction -- 7.2 The Origins of Genomic Diversity in Marine Microbial Populations -- Box 7.1 Effective population size and its role on microbial evolution -- 7.3 Streamlining: Genome Simplification in the Open Ocean -- 7.4 Ecological Factors Influencing Genome Composition -- 7.5 Genome Evolution in the Dark Ocean -- 7.6 Virus-Host Interactions Influencing Genome Evolution in Bacteria and Archaea -- 7.7 Outlook -- References -- Part II: Marine Habitats -- 8: Towards a Global Perspective of the Marine Microbiome -- 8.1 Marine Microbial Ecology: Opening the Black Box -- 8.1.1 Major Breakthroughs before the -Omics Revolution -- 8.1.2 It Is Not Always Black and White: The Discovery of Photoheterotrophs -- 8.1.3 Are all Microorganisms Equally Active in the Ocean? -- 8.2 The Marine Microbiome over Space and Time -- 8.2.1 The Beginning of the Global Exploration of the Marine Microbiome -- 8.2.2 Seasonality and Temporal Dynamics of Marine Microbial Communities -- 8.3 Approaches to Link Taxonomy and Function of Marine Bacteria and Archaea -- 8.3.1 The Genome-Centric Approaches: Single Amplified Genomes (SAGs) and Metagenome Assembled Genomes (MAGs) -- 8.3.1.1 Single-Amplified Genomes (SAGs). , 8.3.1.2 Metagenome Assembled Genomes (MAGs).