The Marine Microbiome

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)
8.3.2 The Relevance of Culturing Marine Bacteria in the -Omics Era
8.3.3 Shedding Light on the Active Microbiome
8.4 What Have we Learnt from the Exploration of the Marine Microbiome?
8.4.1 The Unknown Marine Microbial Diversity
8.4.2 Insights into New Metabolic Capacities of Uncultured Microorganisms
8.4.3 Delineation of Ecological Meaningful Units of Uncultured Microorganisms
8.5 Future Perspectives
References
9: The Pelagic Light-Dependent Microbiome
9.1 Introduction
9.2 Sunlight as the Dominant Source of Energy in the Epipelagic Zone
9.3 UV Radiation (UVR) in the Euphotic Zone and its Effect on the Microbiome
9.3.1 UVR in the Atmosphere
9.3.2 Factors Affecting UVR Absorption in Seawater
9.3.3 Global Distribution of UVR in the Ocean
9.3.4 Detrimental Effects on the Microbiome and Adaptations to UVR
9.3.5 The Overall Effects of UV-B on Net Community Production (NCP) in the Upper Global Ocean
9.4 Macro and Micronutrient Limitation in the Euphotic Zone
9.4.1 Nutrient Limitation
9.4.2 Nitrogen Limitation
9.4.3 Phosphorus Limitation
9.4.4 Silica Limitation
9.4.5 Iron Limitation
9.5 Subsurface Chlorophyll Maximum Layer (SCML) and Subsurface Biomass Maximum Layer (SBML)
9.6 Mixotrophy in the Euphotic Zone
9.6.1 Defining Mixotrophy
9.6.2 Mixotrophy in Bacteria and Archaea
9.6.3 Mixotrophy in Eukaryotic Microbes
9.7 The Fate of the Ocean Pelagic Lit-Zone Microbiome
9.8 The Marine Microbiome of the Euphotic Zone
9.8.1 Central Oligotrophic Gyres
9.8.2 Higher Latitudes
9.9 The Microbiome of the Euphotic Zone in the Future Ocean
References
10: Microbial Inhabitants of the Dark Ocean
10.1 The Dark Ocean: The Largest Habitat in the Biosphere
10.2 The Dark Ocean´s Microbiome
10.2.1 Bacteria Versus Archaea
10.2.2 Diversity and Community Composition of the Dark ocean´s Microbiome
10.2.3 Spatial Heterogeneity of the Dark Ocean Microbiome
10.2.4 Surface: Deep Ocean Connectivity of the Microbiome
10.2.5 Temporal Heterogeneity of the Dark Ocean´s Microbiome
10.3 Functional Diversity of the Dark Ocean´s Microbiome
10.4 Abyssal and Hadal Phylogenetic and Functional Diversity
10.5 Summary
References
11: The Subsurface and Oceanic Crust Prokaryotes
11.1 Introduction
11.2 Deep Subseafloor Exploration
11.3 Deep-Sea Biosphere Bacteria and Archaea
11.4 Deep Subseafloor Archaea
11.5 Deep Subseafloor Bacteria
11.6 Conclusions
References
12: The Microbiome of Coastal Sediments
12.1 Introduction
12.2 Coastal Autotrophic Microbiomes: Microphytobenthic Biofilms
12.2.1 Diversity of Microphytobenthos in Coastal Sediments
12.2.2 Adaptations of Photoautotrophs to Living in Intertidal Sediments
12.2.3 Distribution of MPB Biomass in Coastal Sediments
12.2.4 Interactions between Photoautotrophs and Chemoheterotrophs and the Turnover of Organic Carbon in Coastal Microbiomes
12.3 Nitrogen Cycling in the Marine Coastal Microbiome
12.3.1 Nitrogen Cycling in Aerobic Coastal Sediments: Nitrification and Aerobic Ammonia Oxidation and Comammox
12.3.2 Environmental Factors Influencing Nitrification and Ammonia Oxidation
12.3.3 Nitrogen Cycling in Anaerobic Coastal Sediments: Anammox, Denitrification, and Dissimilatory Reduction of Nitrate to Am...
12.3.4 Environmental Factors Influencing the Anaerobic Nitrogen Cycling Biome
12.3.5 Nitrogen Fixation in Coastal Sediments
12.4 Archaea in Marine Sediment Microbiomes
12.4.1 An Array of Coastal Archaea: Marine Group III (Putative Pontarchaea), Asgard Archaea, Marine Benthic Group D, and Woesa...
12.4.2 Bathyarchaeota (Miscellaneous Crenarchaeota Group) and Thaumarchaeota Are Generally the Most Abundant Archaea in Marine...
12.4.3 Archaea Drive the Methane Cycle in Coastal Sediments
12.4.4 Haloarchaea Are Consistently Present and Locally Abundant in Coastal Sediments
12.5 The Coastal Fungal Microbiome
12.6 Impacts of Oil Pollution on Coastal Microbiomes
12.6.1 Diversity of Hydrocarbon-Degrading Microbes in Coastal Sediments
12.6.2 Association of Hydrocarbon-Degrading Bacteria with Photoautotrophs
12.6.3 Mechanisms of Oil Biodegradation
References
13: Symbiosis in the Ocean Microbiome
13.1 Introduction
13.2 Physical Relationships and the Breadth of Microbial Symbioses
13.2.1 Unattached Microbial Interactions
13.2.2 Ectosymbioses
13.2.3 Endosymbioses
13.3 Mutualistic Nutritional Symbioses: N2 Fixation
13.4 Planktonic Rhizaria and Their Spectrum of Symbioses in the Ocean
13.4.1 Commensalistic and Mutualistic Photosymbioses Among Planktonic Retaria
13.4.2 Photosymbioses, Organelle Acquisition, and the Acantharia-Phaeocystis Symbiosis
13.4.3 Parasitic Symbioses Involving Planktonic Retaria
13.5 Concluding Remarks: Potential Scientific and Technological Benefits of Understanding Symbiosis
References
14: Marine Extreme Habitats
14.1 Hydrothermal Vents
14.1.1 Processes and Microorganisms
14.1.1.1 Sulfur Cycling
14.1.1.2 Hydrogen Oxidation
14.1.1.3 Methanogenesis and Anaerobic Oxidation of Methane
14.1.1.4 Other Chemoautotrophic Processes
14.1.1.5 Carbon Fixation
14.1.2 Symbiosis
14.1.3 Microbial Eukaryotes
14.2 Deep Hypersaline Anoxic Basins
14.2.1 Microbial Diversity of the Red Sea DHABs
14.2.2 Microbial Diversity of the Orca DHAB
14.2.3 Microbial Diversity of the Mediterranean DHABs
14.2.4 Microbial Diversity of the ``Bittern´´ Mediterranean Sea DHABs
14.2.5 Culturing Efforts
14.3 Importance of Polyextreme Environments in Biotechnology
14.4 Relevance of Vents and Deep Hypersaline Anoxic Basins for Astrobiology
References
Part III: Marine Microbiome from Genomes to Phenomes: Biogeochemical Cycles, Networks, Fluxes, and Interaction
15: Marine Biogeochemical Cycles
15.1 Biogeochemistry in the Ocean
15.2 Biogeochemical Cycles
15.2.1 Carbon
15.2.2 Oxygen
15.2.3 Nitrogen
15.2.4 Phosphorus
15.2.5 Sulfur
15.2.6 Trace Gases
15.2.6.1 Methane
15.2.6.2 Nitrous Oxide
15.3 Aggregates and Particles
15.3.1 Particulate Organic Matter
15.3.2 Particulate Inorganic Matter
15.3.3 Remineralization of Organic Material
15.3.4 POM Sedimentation and Associated Elemental Fluxes
15.4 Sediments/Benthic Habitats
15.4.1 Gradients-Depth, Near Versus Offshore
15.4.2 General Biogeochemical Patterns in Sediments
15.4.3 Hot Spots
15.4.4 Deep Biosphere
15.5 Ocean Biogeochemical Cycling in a Changing World
References
16: A Holistic Approach for Understanding the Role of Microorganisms in Marine Ecosystems
16.1 Introduction
16.2 Multi-Omics as a Toolbox to Study Diversity and Function of Microbial Communities
16.2.1 Marine Microbiome Analysis Using rRNA Gene Amplicon Sequencing
16.2.2 Metagenomics
16.2.3 Metatranscriptomics and Metaproteomics
16.2.4 Single-Cell Omics
16.2.5 Single-Cell Transcriptomics
16.3 Integration of Omics and Culturing
16.4 Marine Microbial Ecosystems Beyond Genes and Genomes
References
17: The Hidden Treasure: Marine Microbiome as Repository of Bioactive Compounds
17.1 Introduction
17.2 The Current Status of Marine Microbe-Derived Drug Discovery
17.2.1 Marine Bacteria
17.2.1.1 Early Discoveries of Marine Bacterial Natural Products
17.2.1.2 Recently Discovered Marine Bacterial Natural Products
17.2.2 Marine Fungi
17.2.2.1 Anti-infective Marine Fungal Natural Products
17.2.2.2 Anticancer Marine Fungal Natural Products
17.2.3 Marine Cyanobacteria
17.3 Emerging Strategies for the Exploration of Marine Bioactive Compounds
17.3.1 In-Situ Isolation Technology
17.3.2 Microbial Co-culture
17.3.2.1 Marine Fungal-Bacterial Co-culture
17.3.2.2 Co-culturing of Marine Bacteria
17.3.2.3 Co-culturing of Marine Fungi
17.3.3 The OSMAC (One Strain Many Compounds) Approach
17.3.3.1 OSMAC with Alteration of Food Source
17.3.3.2 OSMAC with Solid and Liquid Media
17.3.3.3 OSMAC with Changes in Physical Factors
17.3.4 Chemical Elicitation
17.3.4.1 Quorum Sensing Elicitors
17.3.4.2 Epigenetic Elicitation
References
18: Ocean Restoration and the Strategic Plan of the Marine Microbiome
18.1 Introduction
18.2 The Marine Microbiome in Ocean Restoration
18.2.1 Importance of the Marine Microbiome
18.2.2 The Potential of the Marine Microbiome in Ocean Restoration
18.2.3 State-of-the-Art in Ocean Restoration
18.2.3.1 Climate Change and Corals
18.2.3.2 Oil Spills
18.2.3.3 Plastic Pollution
Case Study 1: State of the Art Project Generating New Knowledge: MycoPLAST
18.2.3.4 Endocrine Disrupting Chemicals
Case Study 2: State of the Art Project Generating New Knowledge: MER-CLUB
18.3 Policy and Governance. The Current State and Future Expectations
18.4 Strategic Communication Around Usage of the Marine Microbiome in Ocean Restoration
18.5 Ocean Literacy
18.6 Knowledge Transfer
18.7 Discussion and Conclusion
References