Introduction to Marine Biogeochemistry (eBook)

Front Cover 1
Title Page 4
Copyright Page 5
Contents 6
Preface 10
How to Use this Book 12
Acknowledgements 14
Part 1: The Physical Chemistry of Seawater 16
Chapter 1. The Crustal-Ocean-Atmosphere Factory 18
1.1 Introduction 18
1.2 Why the Study of Marine Biogeochemistry is Important 18
1.3 The Crustal-Ocean-Atmosphere Factory and Global Biogeochemical Cycles 19
1.3.1 Steady State, Residence Times, and Turnover Times 21
1.4 Consideration of Time and Space Scales 23
1.5 The History of the Study of Marine Biogeochemistry 26
1.6 New Technologies, New Approaches 28
1.7 The Future of Marine Biogeochemistry 30
Chapter 2. The Waters of the Sea 36
2.1 Introduction 36
2.2 The Hydrological Cycle 36
2.3 Water: A Physically Remarkable Liquid 39
2.3.1 The Molecular Structure of Water 39
2.3.2 The Phases of Water 40
2.3.3 Hydrogen Bonding in Water 43
2.3.4 The Effect of Hydrogen Bonding on the Physical Behavior of Water 45
2.4 Water as the Universal Solvent 51
2.5 The Effect of Salt on the Physical Properties of Water 52
Chapter 3. Seasalt Is More Than NaCl 56
3.1 Introduction 56
3.2 Classifications of Substances in Seawater 56
3.3 Measuring Salt Content 60
3.3.1 Gravimetric Salinity 62
3.3.2 Chlorinity 62
3.3.3 Conductivity 63
3.3.4 Density 65
3.4 The Conservative Nature of the Major Ions 72
3.5 Exceptions to the Rule of Constant Proportions 76
3.5.1 Marginal Seas and Estuaries 76
3.5.2 Anoxic Basins 78
3.5.3 Sea Ice 78
3.5.4 Calcareous Shells and Coral Skeletons 78
3.5.5 Hydrothermal Vents 78
3.5.6 Evaporites 79
3.5.7 Bursting Bubbles 79
3.5.8 Interstitial Waters 79
Chapter 4. Salinity as a Conservative Tracer 80
4.1 Introduction 80
4.2 Global Heat and Water Balance 80
4.2.1 Temperature Distributions 85
4.2.2 Salinity Distributions 87
4.2.3 Density Distributions 93
4.3 Transport of Heat and Salt via Water Movement 97
4.3.1 Advection 99
4.3.2 Turbulent Mixing 103
4.3.3 Conservative Mixing 106
4.3.4 One-Dimensional Advection-Diffusion Model 109
Chapter 5. The Nature of Chemical Transformations in the Ocean 116
5.1 Introduction 116
5.2 Tracking Nonconservative Behavior 117
5.3 Defining Chemical Species 119
5.4 Concentration Units 123
5.5 Modeling Chemical Reactions: Equilibrium versus Kinetic Approaches 123
5.6 Using Equilibrium Models in Seawater 126
5.6.1 Nonspecific versus Specific Effects 128
5.6.2 Handling Nonideal Solution Behavior 130
5.7 Competitive Complexing: Calculating Speciation in a Multi-Ion Solution 134
5.7.1 The “Iron Hypothesis” 134
5.7.2 The Chemical Speciation of Iron: Ion Pairing 138
5.7.3 The Chemical Speciation of Iron: Mineral Precipitation and Dissolution 146
5.7.4 The Chemical Speciation of Iron: Cation Exchange 148
5.7.5 The Chemical Speciation of Iron: Dissolved Organic Matter as a Ligand 149
5.8 Ion Speciation in Seawater 153
5.8.1 Major and Minor Ion Speciation in Seawater 153
5.8.2 Trace Metal Speciation in Seawater 153
5.8.3 Acid and Base Speciation in Seawater 156
5.8.4 Other Speciation Reactions in Seawater 161
Chapter 6. Gas Solubility and Exchange across the Air-Sea Interface 162
6.1 Introduction 162
6.2 Dalton's Law of Partial Pressures 163
6.3 Gas Solubility 165
6.3.1 Deviations from NAEC 168
6.4 Rates of Gas Exchange 173
6.4.1 Thin-Film Model 174
6.4.2 Surface Renewal and Boundary Layer Models 177
6.5 Nonconservative Gases 179
Part 2: The Redox Chemistry of Seawater 184
Chapter 7. The Importance of Oxygen 186
7.1 Introduction 186
7.2 Basic Concepts in Electrochemistry 187
7.2.1 Half-Cell Reactions 187
7.2.2 Energetics of Redox Reactions 189
7.3 The Redox Chemistry of Seawater 197
7.3.1 Relative Redox Intensity 199
7.3.2 Metabolic Classifications of Organisms 204
7.3.3 Electron Transfer on the Intracellular Level 212
7.3.4 Redox Speciation 213
7.3.5 The Global Biogeochemical Redox Cycle 219
7.4 Photochemical Redox Reactions 220
Chapter 8. Organic Matter: Production and Destruction 222
8.1 Introduction 222
8.2 The Production of Organic Matter 223
8.3 The Aerobic Destruction of Organic Matter 226
8.4 Impacts on O2 and Nutrient Concentrations 227
8.4.1 Apparent Oxygen Utilization 227
8.4.2 Why Is the N-to-P Ratio Equal to 16? 230
8.5 The Anaerobic Destruction of Organic Matter 232
8.6 The Influence of Organic Matter on the Global Biogeochemical Oxygen Cycle 234
Chapter 9. Vertical Segregation of the Biolimiting Elements 236
9.1 Introduction 236
9.2 Surface-Water Depletions, Bottom-Water Enrichments 236
9.3 Interpreting Depth Profiles 239
9.4 Broecker Box Model 242
9.5 Biolimiting versus Biointermediate versus Biounlimited 247
Chapter 10. Horizontal Segregation of the Biolimiting Elements 252
10.1 Introduction 252
10.2 Geographic Differences in Depth Profiles 252
10.3 Horizontal Segregation of Nutrients in the Deep Zone 254
10.4 Horizontal Segregation and the Redfield–Richards Ratio 262
10.5 Preformed Nutrients 264
10.6 Feedback Relations in the Marine Biogeochemical Nutrient Cycle 271
Chapter 11. Trace Elements in Seawater 274
11.1 Introduction 274
11.2 Sources of Trace Elements to the Ocean 276
11.2.1 River Runoff 276
11.2.2 Groundwater Seeps 278
11.2.3 Atmospheric lnput 280
11.2.4 Diagenetic Remobilization from Nearshore Sediments 282
11.2.5 Hydrothermal Activity 282
11.2.6 Anthropogenic lnput 283
11.3 Oceanic Sinks of Trace Elements 283
11.3.1 Scavenging 285
11.3.2 Incorporation into Biogenic Materials 288
11.3.3 Hydrothermal Activity 295
11.4 Types of Trace Element Distributions 295
11.4.1 Importance of Speciation 298
11.4.2 Nutrient-Type Distributions 299
11.4.3 Conservative-Type Distributions 303
11.4.4 Scavenged-Type Distributions 303
11.4.5 Other Vertical Profile Shapes 306
Chapter 12. Diagenesis 314
12.1 Introduction 314
12.2 Physical Processes: Particle and Water Transport 315
12.2.1 Sedimentation 315
12.2.2 Pore-Water Advection and Diffusion 316
12.2.3 Bioturbation 317
12.3 Interpreting Depth Profiles in Marine Sediments 319
12.4 The One-Dimensional Advection-Diffusion Model 322
12.5 Redox Conditions in Marine Sediments 325
12.5.1 Oxic Zone Diagenesis 326
12.5.2 Redox Zonation 329
12.5.3 Postdepositional Migration of Metals 334
12.5.4 Diagenetic Overprinting of Fossil Oxidation Fronts 336
12.6 The Relative Importance of Aerobic versus Anaerobic Diagenesis 337
12.7 Chemoautolithotrophy 339
12.8 Clay Minerals and Diagenesis 339
Part 3: The Chemistry of Marine Sediments 340
Chapter 13. Classification of Sediments 342
13.1 Introduction 342
13.2 Sediments: Classification Schemes 342
13.2.1 Geographic Distribution 343
13.2.2 Grain Size 343
13.2.3 Origin, Chemical Composition, and Mineralogy 343
13.2.4 Sedimentation Rate and Thickness 345
13.3 Particle Sinking Rates and Pelagic Sedimentation 346
13.4 Pelagic Sediments 354
13.4.1 Lithogenous Sediments 354
13.4.2 Biogenous Sediments 355
13.4.3 Hydrogenous Sediments 356
13.4.4 Cosmogenous Sediments 357
13.4.5 Anthropogenic Sediments 359
13.5 Nonpelagic Sediments 359
13.5.1 Gravity-Driven Sediment Transport 359
13.5.2 Sediment Transport Driven by Bottom-Water Currents 362
13.5.3 Volcanism 362
13.5.4 Ice-Driven Transport 364
Chapter 14. Clay Minerals and Other Detrital Silicates 366
14.1 Introduction 366
14.2 The Structure of Crystalline Silicate Minerals 367
14.2.1 Crystalline Structure of Clay Minerals 369
14.2.2 Cation Exchange Capacity 370
14.3 The Production of Clay Minerals from Terrestrial Weathering 373
14.4 The Production of Clay Minerals from Authigenic Processes 377
14.5 Transport Pathways 379
14.5.1 Rivers and Oceanic Currents 379
14.5.2 Winds 382
14.5.3 lce 382
14.5.4 Organisms 383
14.6 Global Patterns of Quartz and Clay Mineral Distributions 383
Chapter 15. Calcite, Alkalinity, and the pH of Seawater 388
15.1 Introduction 388
15.2 The Biogenic Inorganic Carbon Pump 389
15.2.1 Planktonic Calcifiers 390
15.2.2 Benthic Calcifiers 393
15.2.3 Biomineralization of Calcium Carbonate 394
15.3 Calcium Carbonate Dissolution 395
15.3.1 Thermodynamic Controls on Solubility 396
15.3.2 Kinetic Controls on Solubility 404
15.4 The Effect of POC and PIC Formation and Degradation on the pH, Carbonate Alkalinity, and ?CO2 of Seawater 404
15.4.1 Vertical Segregation of ?CO2 and Alkalinity 405
15.4.2 Horizontal Segregation of ?CO2 and Alkalinity 407
15.5 The Preservation of Calcium Carbonate in Marine Sediments 409
15.5.1 Thermodynamic Considerations 409
15.5.2 Kinetic Considerations 413
15.6 The Role of Marine Carbonates in the Crustal-Ocean-Atmosphere Factory's Geochemical Evolution, Stabilization, and Future 415
Chapter 16. Biogenic Silica 418
16.1 Introduction 418
16.2 The Production of Biogenic Silica 419
16.3 Preservation versus Dissolution of Sinking Detrital Biogenic Silica 424
16.4 Accumulation and Preservation in the Sediments 429
16.5 The Formation of Chert 432
16.6 The Crustal-Ocean-Atmosphere Perspective 433
16.6.1 Global Marine Silica Budget 433
16.6.2 Feedbacks in the Crustal-Ocean-Atmosphere Factory for Silica? 434
Chapter 17. Evaporites 438
17.1 Introduction 438
17.2 Formation of Evaporites by Evaporation of a Fixed Volume of Seawater 439
17.3 Meteorological and Geological Settings 441
17.4 Modern Evaporites 442
17.5 Ancient Evaporites 447
17.5.1 Geologic Variations in the Rate of Evaporite Deposition 447
17.5.2 Modes of Formation 448
17.5.3 Diapirs 452
17.5.4 The “Dolomite Problem” 452
17.6 The Great Salinity Crisis of the Mediterranean Sea 453
Chapter 18. Iron-Manganese Nodules and Other Hydrogenous Minerals 456
18.1 Introduction 456
18.2 Iron-Manganese Oxides 457
18.2.1 Iron-Manganese Nodules 462
18.3 Other Hydrogenous Minerals 477
18.3.1 Phosphorites 477
18.3.2 Barite 482
18.3.3 Oolitic Calcite and Aragonite Needles 483
18.3.4 Glauconite and Green Clays 484
Chapter 19. Metalliferous Sediments and Other Hydrothermal Deposits 486
19.1 Introduction 486
19.2 The Physical Setting 487
19.2.1 Spreading Centers 488
19.2.2 Subduction Zones 491
19.2.3 Mantle Hot Spots 492
19.3 Hydrothermal System Evolution 493
19.4 Chemical Reactions That Occur in Hydrothermal Systems 495
19.4.1 Seawater Recharge Reactions 496
19.4.2 High-Temperature Reactions in Upper Crust 497
19.4.3 Phase Separation: Changing Impact on Ion Speciation 501
19.4.4 Discharge via Venting from Mid Ocean Ridge Systems 502
19.4.5 Off-Axis Discharges 509
19.4.6 Formation of Metalliferous Sediments 511
19.5 Role of Hydrothermal Chemistry in the Crustal-Ocean-Atmosphere Factory 513
19.5.1 Estimates of Global Hydrothermal Fluxes 513
19.5.2 Feedbacks between Elemental Cycles 516
19.6 Biology of Hydrothermal Systems and Cold Seeps 517
19.6.1 Ridge Crest Hydrothermal Systems 521
19.6.2 Off-Axis Hydrothermal Systems 524
19.6.3 Cold Seeps 524
19.6.4 Evolution of Life 527
Chapter 20 Global Pattern of Sediment Distribution 530
20.1 Introduction 530
20.2 General Model of Surface Sediment Distributions 531
20.2.1 Continental Margins 531
20.2.2 Abyssal Plains 534
20.2.3 Polar Seas 535
20.2.4 Mid-ocean Ridges and Rises 536
20.3 Distribution Pattern of Sediments in the World Ocean 536
20.3.1 Atlantic Ocean Sediments 536
20.3.2 Pacific Ocean Sediments 538
20.3.3 Indian Ocean Sediments 539
20.3.4 Arctic Ocean Sediments 539
20.3.5 Southern Ocean Sediments 539
Chapter 21. Why Seawater Is Salty but Not Too Salty 540
21.1 Introduction 540
21.2 The Crustal-Ocean-Atmosphere Factory 541
21.3 Sources and Transport Processes 542
21.3.1 Terrestrial Weathering and River Transport 542
21.3.2 Volcanic Gases and Hydrothermal Emissions 547
21.4 Storage Reservoirs and Removal Mechanisms 549
21.4.1 Deposition of Biogenic Materials 554
21.4.2 Pyrite Deposition 555
21.4.3 Deposition of Evaporites 555
21.4.4 Plate Tectonics and Hydrothermal Activity 556
21.4.5 Cation Exchange 560
21.4.6 Reverse Weathering 560
21.4.7 Burial and Subduction of Pore Waters 560
21.5 The Whole Picture: Integrated Models of Seawater Composition 561
21.5.1 Equilibrium Models 562
21.5.2 Steady-State Mass Balance Models 563
21.5.3 Dynamical Models 567
21.6 Mean Oceanic Residence Times and Reactivity 568
21.7 Evolution of Seawater 571
21.8 Why Is the Salinity of Seawater around 35‰? 571
Part 4: Organic Biogeochemistry 574
Chapter 22. Marine Biogeochemistry: An Overview 576
22.1 Introduction 576
22.2 The Importance of Organic Compounds in the Marine Environment 577
22.3 Conceptual and Analytical Approaches Used to Study the Marine Biogeochemistry of Organic Compounds 578
22.3.1 Analyses of Operationally Defined Fractions 578
22.3.2 Biomarkers: Tracers of Organic Matter Source and History 583
22.3.3 Isotopes as Tracers of the Source and Fate of Marine Organic Compounds 586
22.3.4 Artificial Ecosystems 588
22.4 General Classes of Organic Compounds 590
22.4.1 Hydrocarbons 596
22.4.2 Simple Sugars and Complex Carbohydrates 597
22.4.3 Complex and Simple Lipids 599
22.4.4 Nucleotides and Nucleic Acids 610
22.4.5 Amino Acids and Proteins 611
22.4.6 Pyrroles and Porphyrins 616
22.4.7 Low-Molecular-Weight Nitrogenous Compounds 618
22.4.8 Low-Molecular-Weight Carboxylic Acids 618
22.4.9 Low-Molecular-Weight Phosphorus- and Sulfur-Containing Compounds 618
22.4.10 Organohalogens 621
22.4.11 Humic Substances 621
Chapter 23. The Production and Destruction of Organic Compounds in the Sea 624
23.1 Introduction 624
23.2 Technical Limitations in the Study of Marine Organic Matter and Various Work-Arounds 625
23.2.1 Elemental Analysis 625
23.2.2 Analysis by Biomolecule Class 626
23.2.3 Classification by Molecular Size: Ultrafiltered DOM 626
23.2.4 Classification by Solubility: Humic Substances 628
23.2.5 Classification by Light Absorption: Chromophoric DOM 629
23.3 The Fate of Terrestrial Organic Matter in the Ocean 629
23.4 Production and Consumption of Organic Compounds by Marine Organisms 631
23.4.1 Primary Producers 631
23.4.2 Elemental Composition of Biomolecules 631
23.4.3 Molecular Composition of Bacterial Cell Walls and Membranes 631
23.4.4 Consumption of Organic Matter: The Marine Food Web 632
23.4.5 Seasonal Fluctuations in Organic Matter Production and Export 636
23.4.6 Abiotic Processes 636
23.5 The Chemical and Physical Transformation of Detrital Particulate Organic Matter 638
23.5.1 Bacterial Processing 638
23.5.2 Zooplankton and the Fecal Pellet Express 641
23.5.3 Formation of Marine Snow 641
23.5.4 Ballasting of Sinking POM 641
23.5.5 Degradation of Sinking Particles: Horizontal, Vertical, and Temporal Trends 642
23.6 Dissolved Organic Compounds 643
23.6.1 Importance of DOM 643
23.6.2 Sources of DOM 645
23.6.3 The Ecological Role of DOM 645
23.6.4 Molecular Composition 646
23.6.5 Cycling of DOM 648
23.6.6 Humic Substances 650
23.6.7 Sea Surface Microlayer and the Role of Abiotic Photochemistry 655
23.6.8 Export of DOM into Deep Ocean and Horizontal Segregation 657
23.7 Sedimentary Organic Compounds: Diagenesis and Preservation 660
23.7.1 Diagenetic and Catagenic Transformations 662
23.7.2 Sedimentary Organic Matter as a Paleoceanographic Record 664
23.7.3 Mechanisms of Preservation 666
23.8 Global Patterns in Organic Matter Distributions 667
23.8.1 Surface Production and Organic Matter Export from the Photic Zone 668
23.8.2 Sedimentary Organic Matter 673
Chapter 24. The Marine Nitrogen and Phosphorus Cycles 676
24.1 Introduction 676
24.2 Nitrogen Species 677
24.3 The Global Nitrogen Cycle 679
24.4 Redox Cycling of Nitrogen 681
24.4.1 Inorganic Nitrogen Assimilation 682
24.4.2 Nitrogen Fixation 685
24.4.3 Solubilization and Ammonification 688
24.4.4 Ammonium Oxidation 688
24.4.5 Dissimilatory Reductions under Suboxic and Anoxic Conditions 691
24.5 Geographic and Temporal Variations in Nutrient Limitation 695
24.5.1 Seasonal Variations 696
24.5.2 Decadal Variations 702
24.5.3 Millennial Variations 704
24.6 The Global Phosphorus Cycle 706
24.7 Sedimentary Nitrogen and Phosphorus Transformations 707
24.8 Are the Marine Nitrogen and Phosphorus Cycles in a Steady State? 711
24.9 Anthropogenic Perturbations of the Marine Nitrogen and Phosphorus Cycles 714
Chapter 25. The Marine Carbon Cycle and Global Climate Change 724
25.1 The Global Carbon Cycle 725
25.1.1 The Oceanic Carbon Cycle 729
25.1.2 The Atmospheric Reservoir and Its Greenhouse Problem 732
25.2 The Greenhouse Effect and Increasing Atmospheric Temperatures 735
25.3 How the Modern Ocean Takes Up Carbon—the Three Pumps 739
25.3.1 The Solubility or Gas Exchange Pump 739
25.3.2 The Biological Pumps 742
25.3.3 CO2 Fluxes across the Air-Sea Interface 743
25.4 Past Variations in Climate and Atmospheric Carbon Dioxide Levels 750
25.5 The Ocean’s Response(s) to Increased Anthropogenic CO2 Emissions 753
25.5.1 Past to Present Emissions 753
25.5.2 Response of the Solubility Pump to Future Emissions 757
25.5.3 Response of the Biological Pumps to Future Emissions 758
25.5.4 Response of the Coastal Ocean and Estuaries to Future Emissions 759
25.5.5 Climate Feedbacks and Tipping Points 761
25.5.6 Climatic Predictions for the Next Century 764
25.6 Using the Ocean to Solve the CO2 Problem 769
Chapter 26. The Origin of Petroleum in the Marine Environment 774
Chapter 27. Organic Products from the Sea: Pharmaceuticals, Nutraceuticals, Food Additives, and Cosmoceuticals 776
Part 5: Marine Pollution 778
Chapter 28. Marine Pollution: The Oceans as a Waste Space 780
28.1 Introduction 780
28.2 Why Has the Ocean Been Used for Waste Disposal? 782
28.3 What Is Marine Pollution? 782
28.4 Why Pollution Is Hard to Measure 783
28.5 Land-Use Impacts on the Coastal Zone 788
28.6 Contaminants 793
28.6.1 Sediment Mobilization 793
28.6.2 Nutrient Pollution 797
28.6.3 Hypoxia 802
28.6.4 Harmful Algal Blooms 810
28.6.5 Microorganisms 811
28.6.6 Petroleum 811
28.6.7 Radioactivity 821
28.6.8 Trace Metals 822
28.7 Synthetic Organic Compounds 842
28.7.1 Persistent Organic Pollutants 843
28.7.2 Other Semivolatile Synthetic Organic Compounds of Concern 855
28.7.3 Volatile Organic Compounds 856
28.7.4 Organometallic Paints 856
28.7.5 Marine Litter 858
28.8 The Future of the Ocean as a Waste Space 864
Appendix 1. The Periodic Table of the Elements 
868 
Appendix 2. Common Names and Chemical Formulae 870
Appendix 3. Metric Units and Equivalents 872
Appendix 4. Symbols, Constants, and Formulae 876
Appendix 5. Geologic Time Scales 878
Glossary 880
Index 908