CiNii Books - Fundamentals of geobiology

2012 PROSE Award, Earth Science: Honorable Mention For more than fifty years scientists have been concerned with the interrelationships of Earth and life. Over the past decade, however, geobiology, the name given to this interdisciplinary endeavour, has emerged as an exciting and rapidly expanding field, fuelled by advances in molecular phylogeny, a new microbial ecology made possible by the molecular revolution, increasingly sophisticated new techniques for imaging and determining chemical compositions of solids on nanometer scales, the development of non-traditional stable isotope analyses, Earth systems science and Earth system history, and accelerating exploration of other planets within and beyond our solar system. Geobiology has many faces: there is the microbial weathering of minerals, bacterial and skeletal biomineralization, the roles of autotrophic and heterotrophic metabolisms in elemental cycling, the redox history in the oceans and its relationship to evolution and the origin of life itself. This book is the first to set out a coherent set of principles that underpin geobiology, and will act as a foundational text that will speed the dissemination of those principles. The chapters have been carefully chosen to provide intellectually rich but concise summaries of key topics, and each has been written by one or more of the leading scientists in that field. Fundamentals of Geobiology is aimed at advanced undergraduates and graduates in the Earth and biological sciences, and to the growing number of scientists worldwide who have an interest in this burgeoning new discipline. Additional resources for this book can be found at: http://www.wiley.com/go/knoll/geobiology.

Table of Contents

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

Volume: : pbk ISBN 9781405187527

Description

2012 PROSE Award, Earth Science: Honorable Mention For more than fifty years scientists have been concerned with the interrelationships of Earth and life. Over the past decade, however, geobiology, the name given to this interdisciplinary endeavour, has emerged as an exciting and rapidly expanding field, fuelled by advances in molecular phylogeny, a new microbial ecology made possible by the molecular revolution, increasingly sophisticated new techniques for imaging and determining chemical compositions of solids on nanometer scales, the development of non-traditional stable isotope analyses, Earth systems science and Earth system history, and accelerating exploration of other planets within and beyond our solar system. Geobiology has many faces: there is the microbial weathering of minerals, bacterial and skeletal biomineralization, the roles of autotrophic and heterotrophic metabolisms in elemental cycling, the redox history in the oceans and its relationship to evolution and the origin of life itself.. This book is the first to set out a coherent set of principles that underpin geobiology, and will act as a foundational text that will speed the dissemination of those principles. The chapters have been carefully chosen to provide intellectually rich but concise summaries of key topics, and each has been written by one or more of the leading scientists in that field.. Fundamentals of Geobiology is aimed at advanced undergraduates and graduates in the Earth and biological sciences, and to the growing number of scientists worldwide who have an interest in this burgeoning new discipline. Additional resources for this book can be found at: http://www.wiley.com/go/knoll/geobiology.

Table of Contents

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

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