Fundamentals of Geobiology

Contributors, xi

1. What is Geobiology?, 1
Andrew H. Knoll, Donald E. Canfield, and Kurt O. Konhauser

1.1 Introduction, 1

1.2 Life interacting with the Earth, 2

1.3 Pattern and process in geobiology, 2

1.4 New horizons in geobiology, 3

2. The Global Carbon Cycle: Biological Processes, 5
Paul G. Falkowski

2.1 Introduction, 5

2.2 A brief primer on redox reactions, 5

2.3 Carbon as a substrate for biological reactions, 5

2.4 The evolution of photosynthesis, 8

2.5 The evolution of oxygenic phototrophs, 11

2.6 Net primary production, 13

2.7 What limits NPP on land and in the ocean?, 15

2.8 Is NPP in balance with respiration?, 16

2.9 Conclusions and extensions, 17

3. The Global Carbon Cycle: Geological Processes, 20
Klaus Wallmann and Giovanni Aloisi

3.1 Introduction, 20

3.2 Organic carbon cycling, 20

3.3 Carbonate cycling, 22

3.4 Mantle degassing, 23

3.5 Metamorphism, 24

3.6 Silicate weathering, 24

3.7 Feedbacks, 25

3.8 Balancing the geological carbon cycle, 26

3.9 Evolution of the geological carbon cycle through Earth's history: proxies and models, 27

3.10 The geological C cycle through time, 30

3.11 Limitations and perspectives, 32

4. The Global Nitrogen Cycle, 36
Bess Ward

4.1 Introduction, 36

4.2 Geological nitrogen cycle, 36

4.3 Components of the global nitrogen cycle, 38

4.4 Nitrogen redox chemistry, 40

4.5 Biological reactions of the nitrogen cycle, 40

4.6 Atmospheric nitrogen chemistry, 45

4.7 Summary and areas for future research, 46

5. The Global Sulfur Cycle, 49
Donald E. Canfield and James Farquhar

5.1 Introduction, 49

5.2 The global sulfur cycle from two perspectives, 49

5.3 The evolution of S metabolisms, 53

5.4 The interaction of S with other biogeochemical cycles, 55

5.5 The evolution of the S cycle, 59

5.6 Closing remarks, 61

6. The Global Iron Cycle, 65
Brian Kendall, Ariel D. Anbar, Andreas Kappler and Kurt O. Konhauser

6.1 Overview, 65

6.2 The inorganic geochemistry of iron: redox and reservoirs, 65

6.3 Iron in modern biology and biogeochemical cycles, 69

6.4 Iron through time, 73

6.5 Summary, 83

7. The Global Oxygen Cycle, 93
James F. Kasting and Donald E. Canfield

7.1 Introduction, 93

7.2 The chemistry and biochemistry of oxygen, 93

7.3 The concept of redox balance, 94

7.4 The modern O2 cycle, 94

7.5 Cycling of O2 and H2 on the early Earth, 98

7.6 Synthesis: speculations about the timing and cause of the rise of atmospheric O2, 102

8. Bacterial Biomineralization, 105
Kurt Konhauser and Robert Riding

8.1 Introduction, 105

8.2 Mineral nucleation and growth, 105

8.3 How bacteria facilitate biomineralization, 106

8.4 Iron oxyhydroxides, 111

8.5 Calcium carbonates, 116

9. Mineral–Organic–Microbe Interfacial Chemistry, 131
David J. Vaughan and Jonathan R. Lloyd

9.1 Introduction, 131

9.2 The mineral surface (and mineral–bio interface) and techniques for its study, 131

9.3 Mineral-organic-microbe interfacial processes: some key examples, 140

10. Eukaryotic Skeletal Formation, 150
Adam F. Wallace, Dongbo Wang, Laura M. Hamm, Andrew H. Knoll and Patricia M. Dove

10.1 Introduction, 150

10.2 Mineralization by unicellular organisms, 151

10.3 Mineralization by multicellular organisms, 164

10.4 A brief history of skeletons, 173

10.5 Summary, 175

11. Plants and Animals as Geobiological Agents, 188
David J. Beerling and Nicholas J. Butterfield

11.1 Introduction, 188

11.2 Land plants as geobiological agents, 188

11.3 Animals as geobiological agents, 195

11.4 Conclusions, 200

12. A Geobiological View of Weathering and Erosion, 205
Susan L. Brantley, Marina Lebedeva and Elisabeth M. Hausrath

12.1 Introduction, 205

12.2 Effects of biota on weathering, 207

12.3 Effects of organic molecules on weathering, 209

12.4 Organomarkers in weathering solutions, 211

12.5 Elemental profiles in regolith, 213

12.6 Time evolution of profile development, 217

12.7 Investigating chemical, physical, and biological weathering with simple models, 218

12.8 Conclusions, 222

13. Molecular Biology’s Contributions to Geobiology, 228
Dianne K. Newman, Victoria J. Orphan and Anna-Louise Reysenbach

13.1 Introduction, 228

13.2 Molecular approaches used in geobiology, 229

13.3 Case study: anaerobic oxidation of methane, 238

13.4 Challenges and opportunities for the next generation, 242

14. Stable Isotope Geobiology, 250
D.T. Johnston and W.W. Fischer

14.1 Introduction, 250

14.2 Isotopic notation and the biogeochemical elements, 253

14.3 Tracking fractionation in a system, 255

14.4 Applications, 258

14.5 Using isotopes to ask a geobiological question in deep time, 261

14.6 Conclusions, 265

15. Biomarkers: Informative Molecules for Studies in Geobiology, 269
Roger E. Summons and Sara A. Lincoln

15.1 Introduction, 269

15.2 Origins of biomarkers, 269

15.3 Diagenesis, 269

15.4 Isotopic compositions, 270

15.5 Stereochemical considerations, 272

15.6 Lipid biosynthetic pathways, 273

15.7 Classification of lipids, 273

15.8 Lipids diagnostic of Archaea, 277

15.9 Lipids diagnostic of Bacteria, 280

15.10 Lipids of Eukarya, 283

15.11 Preservable cores, 283

15.12 Outlook, 287

16. The Fossil Record of Microbial Life, 297
Andrew H. Knoll

16.1 Introduction, 297

16.2 The nature of Earth’s early microbial record, 297

16.3 Paleobiological inferences from microfossil morphology, 299

16.4 Inferences from microfossil chemistry and ultrastructure (new technologies), 302

16.5 Inferences from microbialites, 306

16.6 A brief history, with questions, 308

16.7 Conclusions, 311

17. Geochemical Origins of Life, 315
Robert M. Hazen

17.1 Introduction, 315

17.2 Emergence as a unifying concept in origins research, 315

17.3 The emergence of biomolecules, 317

17.4 The emergence of macromolecules, 320

17.5 The emergence of self-replicating systems, 323

17.6 The emergence of natural selection, 326

17.7 Three scenarios for the origins of life, 327

18. Mineralogical Co-evolution of the Geosphere and Biosphere, 333
Robert M. Hazen and Dominic Papineau

18.1 Introduction, 333

18.2 Prebiotic mineral evolution I – evidence from meteorites, 334

18.3 Prebiotic mineral evolution II – crust and mantle reworking, 335

18.4 The anoxic Archean biosphere, 336

18.5 The Great Oxidation Event, 340

18.6 A billion years of stasis, 341

18.7 The snowball Earth, 341

18.8 The rise of skeletal mineralization, 342

18.9 Summary, 343

19. Geobiology of the Archean Eon, 351
Roger Buick

19.1 Introduction, 351

19.2 Carbon cycle, 351

19.3 Sulfur cycle, 354

19.4 Iron cycle, 355

19.5 Oxygen cycle, 357

19.6 Nitrogen cycle, 359

19.7 Phosphorus cycle, 360

19.8 Bioaccretion of sediment, 360

19.9 Bioalteration, 365

19.10 Conclusions, 366

20. Geobiology of the Proterozoic Eon, 371
Timothy W. Lyons, Christopher T. Reinhard, Gordon D. Love and Shuhai Xiao

20.1 Introduction, 371

20.2 The Great Oxidation Event, 371

20.3 The early Proterozoic: Era geobiology in the wake of the GOE, 372

20.4 The mid-Proterozoic: a last gasp of iron formations, deep ocean anoxia, the 'boring' billion, and a mid-life crisis, 375

20.5 The history of Proterozoic life: biomarker records, 381

20.6 The history of Proterozoic life: mid-Proterozoic fossil record, 383

20.7 The late Proterozoic: a supercontinent, oxygen, ice, and the emergence of animals, 384

20.8 Summary, 392

21. Geobiology of the Phanerozoic, 403
Steven M. Stanley

21.1 The beginning of the Phanerozoic Eon, 403

21.2 Cambrian mass extinctions, 405

21.3 The terminal Ordovician mass extinction, 405

21.4 The impact of early land plants, 406

21.5 Silurian biotic crises, 406

21.6 Devonian mass extinctions, 406

21.7 Major changes of the global ecosystem in Carboniferous time, 406

21.8 Low-elevation glaciation near the equator, 407

21.9 Drying of climates, 408

21.10 A double mass extinction in the Permian, 408

21.11 The absence of recovery in the early Triassic, 409

21.12 The terminal Triassic crisis, 409

21.13 The rise of atmospheric oxygen since early in Triassic time, 410

21.14 The Toarcian anoxic event, 410

21.15 Phytoplankton, planktonic foraminifera, and the carbon cycle, 411

21.16 Diatoms and the silica cycle, 411

21.17 Cretaceous climates, 411

21.18 The sudden Paleocene–Eocene climatic shift, 414

21.19 The cause of the Eocene–Oligocene climatic shift, 415

21.20 The re-expansion of reefs during Oligocene time, 416

21.21 Drier climates and cascading evolutionary radiations on the land, 416

22. Geobiology of the Anthropocene, 425
Daniel P. Schrag

22.1 Introduction, 425

22.2 The Anthropocene, 425

22.3 When did the Anthropocene begin?, 426

22.4 Geobiology and human population, 427

22.5 Human appropriation of the Earth, 428

22.6 The carbon cycle and climate of the Anthropocene, 430

22.7 The future of geobiology, 433

Acknowledgements, 434

References, 435

Index, 437

Colour plate pages fall between pp. 228 and 229