Evolution of Primary Producers in the Sea (eBook)

Cover 1
Contents 6
List of Contributors 12
Preface 14
Chapter 1: An Introduction to Primary Producers in the Sea: Who They Are, What They Do, and When They Evolved 15
I. What Is Primary Production? 16
II. How Is Photosynthesis Distributed in the Oceans? 17
III. What Is the Evolutionary History of Primary Production in the Oceans? 18
IV. Concluding Comments 19
References 19
Chapter 2: Oceanic Photochemistry and Evolution of Elements and Cofactors in the Early Stages of the Evolution of Life 21
I. Energy Requirements for Life 22
II. Prebiotic Photochemistry-UV and Oceanic Photochemistry 22
III. Evolution of Cofactors 24
A. Metals 24
B. Cofactors 26
IV. Conclusions 31
Acknowledgments 31
References 31
Chapter 3: The Evolutionary Transition from Anoxygenic to Oxygenic Photosynthesis 35
I. Earliest Evidence for Photosynthesis and the Nature of the Earliest Phototrophs 36
II. Structural Conservation of the Core Structure of Photosynthetic Reaction Centers During Evolution 39
III. The Structural and Mechanistic Differences Between the Anoxygenic Reaction Centers of Type II and Photosystem II of Oxygenic Organisms 42
IV. Evolutionary Scenarios for How the Transition from Anoxygenic to Oxygenic Photosynthesis May Have Taken Place 43
V. Conclusions and Prospects for the Future 47
Acknowledgments 47
References 47
Chapter 4: Evolution of Light-Harvesting Antennas in an Oxygen World 51
I. How Cyanobacteria Changed the World 52
II. Light-Harvesting Antennas and the Evolution of the Algae 53
III. Phycobilisomes 54
IV. The ISIA/PCB Family 56
V. About Chlorophylls 58
VI. The LHC Superfamily 59
A. The Light-Harvesting Antennas 59
B. The Stress-Response Connection 61
C. Prokaryotic Ancestry of the LHC Superfamily 62
VII. Overview 63
Acknowledgments 63
References 64
Chapter 5: Eukaryote and Mitochondrial Origins: Two Sides of the Same Coin and Too Much Ado About Oxygen 69
I. Cell Evolution With and Without Endosymbiosis 69
II. The Standard Model of How and Why the Mitochondrion Become Established 71
III. There are at Least 12 Substantial Problems with the Standard Model 72
IV. The Same 12 Issues from the Standpoint of an Alternative Theory 78
V. Criticism and Defense of the Hydrogen Hypothesis 80
VI. Intermezzo 82
VII. Conclusions 83
Acknowledgments 84
References 84
Chapter 6: Photosynthesis and the Eukaryote Tree of Life 89
I. The Eukaryotes 90
II. Overview of the Tree 91
A. Opisthokonts 92
B. Amoebozoa 94
C. Rhizaria (Formerly Cercozoa) 95
D. Archaeplastida 97
E. Chromalveolates 98
F. Excavates 100
G. Incertae Sedis 102
III. The Eukaryote Root 102
IV. Oxygenic Photosynthesis Across the Eukaryote Tree of Life 103
A. Opisthokonts 107
B. Amoebozoa 107
C. Rhizaria 108
D. Archaeplastida 109
E. Chromalveolates 109
F. Excavates and Incertae Sedis 111
V. Conclusions 112
References 113
Chapter 7: Plastid Endosymbiosis: Sources and Timing of the Major Events 123
I. General Introduction to Plastid Endosymbiosis 123
II. Primary Plastid Origin and Plantae Monophyly 128
A. Generating the Eukaryotic Phylogeny 128
B. Molecular Clock Analyses 131
C. Conclusions of Plantae Phylogenetic and Molecular Clock Analyses 134
III. Secondary Plastid Endosymbiosis 135
IV. Tertiary Plastid Endosymbiosis 138
V. Summary 141
References 142
Chapter 8: The Geological Succession of Primary Producers in the Oceans 147
I. Records of Primary Producers in Ancient Oceans 148
A. Microfossils 148
B. Molecular Biomarkers 148
II. The Rise of Modern Phytoplankton 156
A. Fossils and Phylogeny 156
B. Biomarkers and the Rise of Modern Phytoplankton 157
C. Summary of the Rise of Modern Phytoplankton 160
III. Paleozoic Primary Production 160
A. Microfossils 160
B. Paleozoic Molecular Biomarkers 161
C. Paleozoic Summary 162
IV. Proterozoic Primary Production 162
A. Prokaryotic Fossils 162
B. Eukaryotic Fossils 163
C. Proterozoic Molecular Biomarkers 165
D. Summary of the Proterozoic Record 166
V. Archean Oceans 166
VI. Conclusions 169
A. Directions for Continuing Research 170
Acknowledgments 171
References 171
Chapter 9: Life in Triassic Oceans: Links Between Planktonic and Benthic Recovery and Radiation 179
I. Benthos 183
A. Benthic Wastelands of the Early Triassic 183
B. Middle Triassic Recovery of Benthic Ecosystems 184
C. Late Triassic Benthic Boom: Supersize Me 187
II. Plankton 188
A. Early Triassic Disaster Species 188
B. Middle Triassic Oxygen and Evolution 189
C. Late Triassic Rise of Modern Phytoplankton 191
III. Benthic-Planktonic Coupling in Triassic Oceans 194
A. Common Driver 194
B. Plankton Control 195
C. Feedback from the Benthos 195
D. Assistance from the Plankton 196
IV. Conclusions 196
Acknowledgments 197
References 197
Chapter 10: The Origin and Evolution of Dinoflagellates 205
I. Paleontological Data 207
II. Phylogeny of Dinoflagellates 208
A. Sources of Information 208
B. The Phylogeny 210
C. Reconciling Molecular and Morphological Phylogenies 211
III. The Plastids of Dinoflagellates 212
IV. Dinoflagellates in the Plankton 214
References 216
Chapter 11: The Origin and Evolution of the Diatoms: Their Adaptation to a Planktonic Existence 221
I. The Hallmark of the Diatoms: The Silica Frustule 224
A. Frustule Shape and Ornamentation and Their Bearings on Diatom Taxonomy 224
B. Frustule Construction 225
II. Diatom Phylogeny 225
A. The Heterokont Ancestry of the Diatoms 227
B. Diatom Phylogenies 228
C. The Life Cycle and Its Bearings on Phylogeny 230
III. The Origin of the Frustule 233
A. The Origin of Silica Sequestering and Metabolism 233
B. The Evolution of the Frustule in Vegetative Cells 234
IV. The Fossil Record 235
A. The Early Fossil Record of the Heterokontophytes 235
B. The Fossil Record of the Diatoms 236
V. The Success of the Diatoms in the Plankton 241
A. The Paleo-Environmental Settings and the Fates of the Various Phytoplankton Lineages 241
B. Why Did Chromists Win Over Prasinophytes or Red Microalgae? 243
C. Why Did Heterokontophytes Win Over Haptophytes and Dinoflagellates? 245
D. Why Did Diatoms Win Over Other Heterokontophytes? 247
VI. Cryptic Diversity in Planktonic Diatoms and Its Bearing on Evolution 251
VII. The Dawning Future of Diatom Research: Genomics 253
Acknowledgments 255
References 255
Chapter 12: Origin and Evolution of Coccolithophores: From Coastal Hunters to Oceanic Farmers 265
I. Coccolithophores and the Biosphere 265
II. What Is a Coccolithophore? 267
A. Coccoliths and Coccolithogenesis 269
III. The Haptophytes 270
IV. Tools and Biases in the Reconstruction of Coccolithophore Evolution 273
V. The Evolution of Haptophytes up to the Invention of Coccoliths: From Coastal Hunters to Oceanic Farmers? 275
A. The Origin of the Haptophytes and Their Trophic Status 275
B. Paleozoic Haptophytes and the Ancestors of the Coccolithophores 279
VI. The Origin of Calcification in Haptophytes: When, How Many Times, and Why? 281
A. Genetic Novelties? 282
B. Multiple Origins for Coccolithogenesis? 282
C. Environmental Forcing on the Origin of Haptophyte Calcification 286
D. Why Were Coccoliths Invented? 286
VII. Macroevolution Over the Last 220 Million Years 289
A. Forces Shaping the Evolution of Coccolithophores and Coccolithogenesis 289
B. Broad Patterns of Morphological Diversity 290
C. Oligotrophy and Water Chemistry 290
D. Changes in Morphostructural Strategies 292
VIII. The Future of Coccolithophores 293
Acknowledgments 294
References 295
Chapter 13: The Origin and Early Evolution of Green Plants 301
I. Green Plants Defined 302
II. Green Plant Body Plans 305
A. Green Plant Life Histories 307
III. The Core Structure of the Green Plant Phylogenetic Tree 308
A. The Archegoniate Line 308
B. The Chlorophyte Line 310
C. The Prasinophytes 312
IV. Difficulties in the Green Plant Phylogenetic Tree 315
A. The Identity of the Lineage Ancestral to Green Plants 315
B. The Early Diversification of the SeaweedŽ Orders 316
V. Green Plants in the Modern Marine Environment 317
VI. Conclusions 318
Acknowledgments 318
References 318
Chapter 14: Armor: Why, When, and How 325
I. Why Armor 326
A. History of The Concept ArmorŽ Applied to Plankton 326
B. Why Should Protists and the Pelagial Be Different? 329
C. Form and Function in Sessile and Drifting Photoautotrophs 330
D. Attacking Organisms/Attacking Tools 332
E. Ingestors or Predators 335
II. When 337
III. How 338
A. Material 339
B. The Geometry 340
C. Lightweight Constructions of Phytoplankton Armor 341
D. Spines and Large Size 342
E. Other Functional Explanations 343
IV. Conclusions 343
Acknowledgments 344
References 344
Chapter 15: Does Phytoplankton Cell Size Matter? The Evolution of Modern Marine Food Webs 347
I. Size Matters: From Physiological Rates to Ecological and Evolutionary Patterns 348
A. Size Scaling of Physiological Rates 348
B. Size–Abundance Relationship 349
C. Size–Diversity Relationship 349
D. Size Matters: Food Web Structure and Function 350
II. Resource Availability, Primary Production, and Size Structure of Planktonic and Benthic Food Webs 353
III. Size and the Evolution of Marine Food Webs 354
A. Increase in the Maximum Size of Living Organisms Through Time 354
B. Organism Size Within Lineages Through Time (Cope’s Rule) 355
C. Climatically Driven Macroevolutionary Change in Organism Size 355
D. The Evolution of the Modern Marine Food Web 356
Acknowledgments 359
References 359
Chapter 16: Resource Competition and the Ecological Success of Phytoplankton 365
I. Resource Acquisition and Measures of Competitive Ability 366
A. Nutrients 366
B. Light 367
II. The Role of Spatial and Temporal Heterogeneity in Resource Competition in Phytoplankton 369
A. Heterogeneity in Nutrient Distribution 369
B. Heterogeneity in Light Distribution 371
C. Vertical Heterogeneity in Phytoplankton Distribution 372
III. Physiological Trade-Offs 373
A. Nutrient Utilization Trade-Offs 374
B. Light Utilization Trade-Offs 374
C. Trade-Offs in Nutrient Competitive Ability Versus Light Competitive Ability 374
D. Trade-Offs in Growth Rate Versus Competitive Ability 375
E. Trade-Offs in Grazing Resistance Versus Competitive Ability 375
IV. Ecological Strategies of Resource Utilization in Major Functional Groups 375
A. Diatoms 376
B. Coccolithophores 377
C. Green Algae 377
D. Dinoflagellates and the Role of Mixotrophy 379
E. The Role of Size 380
F. Clonal Differences in Resource Utilization 380
V. Future Phytoplankton Communities 380
VI. Challenges and Future Directions 381
A. Dynamic Regulation of Resource Utilization and Competitive Ability 381
B. Resource Interaction 382
C. Evolution of Competitive Ability 382
D. Phylogenetic Relationships 383
E. Concluding Remarks 383
Acknowledgments 384
References 384
Chapter 17: Biological and Geochemical Forcings to Phanerozoic Change in Seawater, Atmosphere, and Carbonate Precipitate Composition 391
I. Continental Weathering Fluxes and CO2 392
II. The Global Biogeochemical Cycles of Calcium, Magnesium, Carbon, Sulfur, Silica, and Phosphorus 396
A. Calcium-Magnesium-Silicate-Carbonate-CO2 Cycle 396
B. Organic Carbon and Phosphorus Subcycles 397
C. Sulfur Subcycle 398
III. Oceanic Sinks 398
A. The Major Sink Processes 398
B. Sink Trends Through Time 401
IV. Some Trends in Carbonate Rock Features 406
V. Atmosphere and Seawater Composition 407
VI. Discussion and Conclusions 411
Acknowledgments 414
References 414
Chapter 18: Geochemical and Biological Consequences of Phytoplankton Evolution 419
I. Introduction 419
A. The Two Carbon Cycles 420
B. The Great Oxidation EventŽ and the Wilson Cycle 421
II. The Role of Phytoplankton in the Geological Carbon Cycle 422
A. Early Phytoplankton Evolution 422
B. The Rise of the Red Lineage 424
C. Biological Overprint of the Geological Carbon Cycle 426
III. The Phanerozoic Carbon Isotope Record 427
A. Jurassic to Mid-Miocene 1.1permil delta13Ccarb Increase 429
B. 2.5permil delta13Ccarb Decrease Since the Mid-Miocene 430
IV. Feedbacks in Biogeochemical Cycles 431
A. Phytoplankton Community Structure and the Wilson Cycle 431
B. Biological Impact on Global Sedimentation Patterns 433
C. Effects of Carbon Burial on Atmospheric Gases 434
V. Concluding Remarks 438
Acknowledgments 439
References 439
Index 445
Color Plates 457