Systems Biogeochemistry of Major Marine Biomes

Cover
Title Page
Copyright Page
Contents
List of Contributors
Preface
Biome I Continental Margins
	1 Biogeochemistry of Marine Oxygen Minimum Zones with Special Emphasis on the Northern Indian Ocean
		1.1 Introduction
			1.1.1 The Arabian Sea Oxygen Minimum Zone
			1.1.2 The Bay of Bengal Oxygen Minimum Zone
		1.2 Preservation of Organic matter and Sediment Biogeochemistry
		1.3 Pore Fluid Geochemistry
		1.4 Sedimentary Sulfidization and Sulfurization
		1.5 Benthic Biology
		1.6 Microbial Metabolism in the Marine Oxygen Minimum Zone Water Column and Sediment
		1.7 Nitrogen Metabolism in the Marine Marine Oxygen Minimum Zone Water Column
		1.8 Microbiological Perspective of Sulfur Metabolism in the Marine Oxygen Minimum Zone Water Column
		1.9 Microbiology of Methane Cycling in the Oxygen Minimum Zone Water Column
		1.10 Microbial Metabolism in Marine Oxygen Minimum Zone Sediments
		1.11 Oxygen Minimum Zone expansion
		1.12 Conclusion
		Acknowledgment
		References
	2 Sedimentary Records of Present and Past Marine Sulfur Cycling
		2.1. Introduction
		2.2. Stable Sulfur Isotopes – a Tool for Reconstructing Spatial and Temporal Changes in Sulfur Cycling
		2.3. The Modern Marine Realm
		2.4. Oceanic Sulfate and its Evolution Through Time
		2.5. Pyrite and Organic-Bound Sulfur as Recorders of Microbial Sulfur Cycling in the Past
		2.6. Mass-Independently Fractionated Sulfur Isotopes – a record of Earth’s Oxygenation
		2.7. Summary and Direction of Future Research
		Acknowledgments
		References
	3 The Role of Microorganisms in Iron Reduction in Marine Sediments
		3.1. INTRODUCTION
		3.2. THE REDOX ZONES IN SHALLOW MARINE SEDIMENTS
		3.3. BIOCHEMICAL PATHWAYS OF IRON REDUCTION
			3.3.1. The Specificity of Microbial Pathways with Respect to Iron
			3.3.2. Microbial Strategies to Reduce Solid Iron Phases
			3.3.3. Uptake of Iron as a Nutrient
		3.4. DIVERSITY OF POTENTIAL IRON-REDUCING AND IRON-OXIDIZING ORGANISMS
			3.4.1. Correlation of Phylogenetic Abundances with Porewater Chemistry Data
			3.4.2. Diversity of Iron Reducers in Suboxic Zones
			3.4.3. Methanogenic Zones
			3.4.4. The Phylogenetic Tree of Marine Iron Reducers
		3.5. SUMMARY AND CONCLUSIONS
		References
	4 Biogeochemistry of Nitrogen in the Marine System with Special Emphasis on the Arabian Sea and Bay of Bengal
		4.1 Introduction
		4.2 Sources of Nitrogen for the Ocean
			4.2.1 Riverine and Groundwater Input
			4.2.2 Atmospheric Deposition
			4.2.3 Volcanic Input
			4.2.4 Marine Upwelling
		4.3 Marine Nitrogen Biogeochemistry
			4.3.1 Biological Nitrogen Fixation
			4.3.2 Nitrogen Assimilation
			4.3.3 Nitrification
			4.3.4 Denitrification
			4.3.5 Ammonium Production in the Marine Realm
			4.3.6 Dissimilatory Nitrate Reduction to Ammonia
			4.3.7 Anammox
			4.3.8 Nitrate/Nitrite-Dependent Anaerobic Methane Oxidation
		4.4. N-cycle in Marine Sediments
			4.4.1 Nitrogen Fixation in Sediments
			4.4.2 Nitrification in Marine Sediments
			4.4.3 Denitrification in Marine Sediments
			4.4.4 Anammox in Marine Sediments
			4.4.5 Dissimilatory Nitrate Reduction to Ammonia In Marine Sediments
		4.5 Nitrogen Cycling in the Northern Indian Ocean
			4.5.1 Pelagic Nitrogen Cycle in Oxygen Minimum Zones
			4.5.2 Sedimentary Denitrification and Anammox Rates in the Arabian Sea
		4.6 Nitrogen isotopic values in sinking particulates
			4.6.1 15N in Marine Sediments from the Arabian Sea and Bay of Bengal
		4.7 Summary
		Acknowledgement
		References
	5 Organic Carbon in Sediments of the Western Indian Margin
		5.1. Introduction
		5.2. Organic Matter and Organic Carbon
		5.3. Organic Carbon Distribution in the World Ocean and the Arabian Sea
		5.4. Methods Adopted to Determine OC in the Arabian Sea
		5.5. Processes Responsible for Primary Productivity and Transport of Organic Carbon
		5.6. Oxygen Minimum Zone and Organic Carbon
		5.7. Studies Carried out on Organic Carbon from the Western Margin of India
			5.7.1. Particulate/Dissolved Organic Carbon from the Water Column
			5.7.2. Organic Carbon in Surface Sediments
			5.7.3. Variations in Organic Carbon in the Sediment Cores
			5.7.4. Early Diagenesis of Organic Matter and the Sedimentary Environment
		5.8. Summary and Future Work
		Acknowledgement
		References
Biome II Ocean Depths
	6 Deep Subsurface Microbiomes of the Marine Realm
		6.1. INTRODUCTION
		6.2. ECOSYSTEM CONSTRAINTS IN THE MARINE DEEP SUBSURFACE
		6.3. FACTORS CONSTRAINING THE STUDY OF MARINE DEEP SUBSURFACES
		6.4. BIOGEOCHEMISTRY OF MARINE DEEP SUBSURFACES
			6.4.1. Major Sites of Exploration and Their Geological Contexts
			6.4.2. Geomicrobiology of Marine Deep Subsurfaces
			6.4.3. Geomicrobiology of Marine Subsurfaces >5 mbsf
		6.5. SUMMING UP THE GEOMICROBIOLOGY OF THE MARINE DEEP SUBSURFACE
		6.6. ULTRASLOW METABOLISM AND SUSTAINABILITY OF DEEP LIFE: IMPLICATIONS FOR EVOLUTION AND ASTROBIOLOGY
		REFERENCES
	7 Biogeochemistry of Marine Petroleum Systems
		7.1. INTRODUCTION
		7.2. FORMATION OF OIL RESERVOIRS
		7.3. ECOSYSTEM CONSTRAINTS AND HABITABILITY OF PETROLEUM BASINS
		7.4. MICROBIOME FRAMEWORK OF PETROLEUM RESERVOIRS
		7.5. MICROBIAL COMMUNITY STRUCTURES AND FUNCTIONS IN MARINE OIL RESERVOIRS
			7.5.1. Anaerobic Breakdown of Hydrocarbons and Fermentation
			7.5.2. Methanogenesis
			7.5.3. Sulfate Reduction
		7.6. SUMMARY VIEW OF THE POTENTIAL NETWORK OF BIOGEOCHEMICAL PROCESSES IN OFFSHORE OIL RESERVOIRS
		7.7. EFFECTS OF BIODEGRADATION ON PETROLEUM PROPERTIES
		7.8. DELETERIOUS MICROBIAL ACTIVITIES: HYDROGEN SULFIDE PRODUCTION (SOURING) AND ITS REMEDIATION WITH NITRATE
		7.9. IN SITU MICROBIAL PROCESSES BENEFICIAL TO OIL RECOVERY
		7.10. CONCLUDING REMARKS
		ACKNOWLEDGEMENTS
		REFERENCES
Biome III Polar Oceans
	8 Biogeochemical Processes in the Arctic Ocean
		8.1. Introduction
		8.2. The Arctic Ocean and its Biogeochemistry
		8.3. Response of the Arctic Ocean and Arctic Fjords to Climate Change
		8.4. Biochemical Effects of Glacial Discharge on Marine Resources
		8.5. Effect of Biochemical Changes on Primary and Secondary Production
		8.6. Arctic Permafrost
			8.6.1 Biogeochemistry and Significance of Arctic Permafrost
			8.6.2 Impact of Thawing Permafrost on Arctic Environment
		8.7. Summary and Future Perspectives
		Acknowledgements
		References
	9 Biogeochemistry and Ecology of the Indian Sectorof the Southern Ocean
		9.1. Introduction
		9.2. Role of Currents and Oceanic Fronts in the Southern Ocean
		9.3. Nutrients in the Southern Ocean
		9.4. Southern Ocean Plankton Ecology
		9.5. Ocean Carbonate Chemistry
		9.6. Sea Ice and Implications for Future Global Change
		9.7. Summary
		Acknowledgements
		References
	10 Benthic Biome of the Southern Ocean: Present State of Knowledge and Future Perspectives
		10.1 Introduction
		10.2 Biogeochemistry of the Southern Ocean
			10.2.1 The High-Nutrient Low-Chlorophyll Zone and Productivity
			10.2.2 Antarctic Circumpolar Current
			10.2.3 Carbon Immobilization and Benthic Carbon Flux
			10.2.4 Retreat of Sea Ice and Benthic Blue Carbon
		10.3 Benthic Ecoregions and Biodiversity
			10.3.1 Meiobenthos
			10.3.2 Macrobenthos
			10.3.3 Megabenthos
			10.3.4 Functional Types
		10.4 Evolutionary Setting and Unique Trait Modalities
		10.5 Biotic interaction
		10.6 Dispersal and Endemism
		10.7 Climate Change and Benthos
		10.8 Conservation and Future Perspectives
		10.9 Conclusions
		Acknowledgments
		References
	11 Biogeochemistry of the Antarctic Coasts: Implications for Biodiversity and Climate Change
		11.1 Introduction
		11.2 Biogeochemical Cycles on the Antarctic Coast
		11.3 Antarctic Coastal Features in the Context of Biogeochemistry and Climate Change
			11.3.1 Sea Ice
			11.3.2 Coastal Polynyas
			11.3.3 Fast Ice
			11.3.4 Ice Shelves
			11.3.5 Ice Sheets
		11.4 Interlink Between Biogeochemical Cycles and Climate Change
		11.5 Floral and microbial diversity of Antarctica: Distribution and Implications for Climate Change
			11.5.1 Diversity of Bacteria and Archaea
			11.5.2 Diversity of Fungi
			11.5.3 Diversity of Lichens
			11.5.4 Diversity of Cyanobacteria
			11.5.5 Diversity of Seaweeds
			11.5.6 Diversity of Snow Algae
		11.6 Climate Change and its Effect on Algal Biodiversity
		11.7 Summary
		Acknowledgment
		References
Biome IV Extreme Environments
	12 Geomicrobiology at a Physicochemical Limit for Life: Deep-sea Hypersaline Anoxic Basins
		12.1. Introduction
		12.2. Geographical and Geological Overview of Deep-sea Hypersaline Anoxic Basins
		12.3. Deep-sea Hypersaline Anoxic Basins as Physicochemical Limits of the Earth’s Biosphere
		12.4. Geomicrobial Dynamics in Deep-sea Hypersaline Anoxic Basins Across the Global Ocean
			12.4.1. Deep-sea Hypersaline Anoxic Basins of the Mediterranean Sea
			12.4.2. Deep-sea Hypersaline Anoxic Basins of the Red Sea
			12.4.3. Deep-sea Hypersaline Anoxic Basins of the Gulf of Mexico
			12.4.4. The Solitary Deep-sea Hypersaline Anoxic Basin of the Black Sea
		12.5. A Universal Biogeochemical Framework for all Deep-sea Hypersaline Anoxic Basins (and Other High-Entropy O2-Scarce Marine Microbiomes?)
		12.6. Astrobiological Implications of Deep-sea Hypersaline Anoxic Basins
		References
	13 Ecology of Cold Seep Habitats
		13.1. Introduction
		13.2. Distribution and Diversity
		13.3. Biogeochemical Cycle of Cold Seep Sediment
		13.4. Symbiosis
		13.5. Symbionts and Adaptations
		13.6. Genetics and Global Connectivity
		13.7. Chemosynthesis and Trophic Transfer
		13.8. Impact of Cold Seep Habitats on Surrounding Oceans
		13.9. Societal Relevance of Cold Seeps
		13.10. Anthropogenic Impacts on Global Seep Ecosystems
		Acknowledgment
		References
	14 Biogeochemical Characteristics of Hydrothermal Systems in the Indian Ocean
		14.1. INTRODUCTION
			14.1.1. Hydrothermal Circulation: Evolution of Fluids and Associated Chemosynthetic Ecosystem
		14.2. GEOLOGICAL AND OCEANOGRAPHIC SETTINGS OF THE INDIAN OCEAN
		14.3. HYDROTHERMAL VENT FIELDS IN THE INDIAN OCEAN
			14.3.1. Chemical and Microbiological Aspects of Vent Fluids and Plume Waters
			14.3.2. Other Active Fields
			14.3.3. Inactive Vent Fields
			14.3.4. Hydrothermal Plume Signatures in Water Column/Sediments/Ferromanganese Crusts
			14.3.5. Vent Fauna Associated with Hydrothermal Vents in the Indian Ocean
		14.4. NATURE OF VENT-ASSOCIATED CHEMOAUTOTROPHS: ARE THEY LINKED WITH COLD-SEEP ECOSYSTEMS IN THE INDIAN OCEAN?
		14.5. CONCLUSION
		ACKNOWLEDGMENTS
		References
Index
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