Note: Intro -- Preface -- 1 Microbial properties and diversity -- 1.1 Classification of life -- 1.2 Physical properties of microorganisms -- 1.2.1 Prokaryotes -- 1.2.2 Eukaryotes -- 1.3 Requirements for growth -- 1.3.1 Physical requirements -- 1.3.2 Chemical requirements -- 1.3.3 Growth rates -- 1.4 Microbial diversity -- 1.5 Life in extreme environments -- 1.5.1 Hydrothermal systems -- 1.5.2 Polar environments viable population is available to seed the global -- 1.5.3 Acid environments -- 1.5.4 Hypersaline and alkaline environments -- 1.5.5 Deep-subsurface environments -- 1.5.6 Life on other planets -- 1.5.7 Panspermia -- 1.6 Summary -- 2 Microbial metabolism -- 2.1 Bioenergetics -- 2.1.1 Enzymes -- 2.1.2 Oxidation-reduction -- 2.1.3 ATP generation -- 2.1.4 Chemiosmosis -- 2.2 Photosynthesis -- 2.2.1 Pigments -- 2.2.2 The light reactions - anoxygenic photosynthesis -- 2.2.3 Classification of anoxygenic photosynthetic bacteria -- 2.2.4 The light reactions - oxygenic photosynthesis -- 2.2.5 The dark reactions -- 2.2.6 Nitrogen fixation -- 2.3 Catabolic processes -- 2.3.1 Glycolysis and fermentation -- 2.3.2 Respiration -- 2.4 Chemoheterotrophic pathways -- 2.4.1 Aerobic respiration -- 2.4.2 Dissimilatory nitrate reduction -- 2.4.3 Dissimilatory manganese reduction -- 2.4.4 Dissimilatory iron reduction -- 2.4.5 Trace metal and metalloid reductions -- 2.4.6 Dissimilatory sulfate reduction -- 2.4.7 Methanogenesis and homoacetogenesis -- 2.5 Chemolithoautotrophic pathways -- 2.5.1 Hydrogen oxidizers -- 2.5.2 Homoacetogens and methanogens -- 2.5.3 Methylotrophs -- 2.5.4 Sulfur oxidizers -- 2.5.5 Iron oxidizers -- 2.5.6 Manganese oxidizers -- 2.5.7 Nitrogen oxidizers -- 3 Cell surface reactivity and metal sorption -- 3.1 The cell envelope -- 3.1.1 Bacterial cell walls -- 3.1.2 Bacterial surface layers -- 3.1.3 Archaeal cell walls. , 3.1.4 Eukaryotic cell walls -- 3.2 Microbial surface charge -- 3.2.1 Acid-base chemistry of microbial surfaces -- 3.2.2 Electrophoretic mobility -- 3.2.3 Chemical equilibrium models -- 3.3 Passive metal adsorption -- 3.3.1 Metal adsorption to bacteria -- 3.3.2 Metal adsorption to eukaryotes -- 3.3.3 Metal cation partitioning -- 3.3.4 Competition with anions -- 3.4 Active metal adsorption -- 3.4.1 Surface stability requirements -- 3.4.2 Metal binding to microbial exudates -- 3.5 Bacterial metal sorption models -- 3.5.1 Kd coefficients -- 3.5.2 Freundlich isotherms -- 3.5.3 Langmuir isotherms -- 3.5.4 Surface complexation -- 3.5.5 Does a generalized sorption model exist? -- 3.6 The microbial role in contaminant mobility -- 3.6.1 Microbial sorption to solid surfaces -- 3.6.2 Microbial transport through porous media -- 3.7 Industrial applications based on microbial surface reactivity -- 3.7.1 Bioremediation -- 3.7.2 Biorecovery -- 3.8 Summary -- 4 Biomineralization -- 4.1 Biologically induced mineralization -- 4.1.1 Mineral nucleation and growth -- 4.1.2 Iron hydroxides -- 4.1.3 Magnetite -- 4.1.4 Manganese oxides -- 4.1.5 Clays -- 4.1.6 Amorphous silica -- 4.1.7 Carbonates -- 4.1.8 Phosphates -- 4.1.9 Sulfates -- 4.1.10 Sulfide minerals -- 4.2 Biologically controlled mineralization -- 4.2.1 Magnetite -- 4.2.2 Greigite -- 4.2.3 Amorphous silica -- 4.2.4 Calcite -- 4.3 Fossilization -- 4.3.1 Silicification -- 4.3.2 Other authigenic minerals -- 4.4 Summary -- 5 Microbial weathering -- 5.1 Mineral dissolution -- 5.1.1 Reactivity at mineral surfaces -- 5.1.2 Microbial colonization and organic reactions -- 5.1.3 Silicate weathering -- 5.1.4 Carbonate weathering -- 5.1.5 Soil formation -- 5.1.6 W eathering and global climate -- 5.2 Sulfide oxidation -- 5.2.1 Pyrite oxidation mechanisms -- 5.2.2 Biological role in pyrite oxidation -- 5.2.3 Bioleaching. , 5.2.4 Biooxidation of refractory gold -- 5.3 Microbial corrosion -- 5.3.1 Chemolithoautotrophs -- 5.3.2 Chemoheterotrophs -- 5.3.3 Fungi -- 5.4 Summary -- 6 Microbial zonation -- 6.1 Microbial mats -- 6.1.1 Mat development -- 6.1.2 Photosynthetic mats -- 6.1.3 Chemolithoautotrophic mats -- 6.1.4 Biosedimentary structures -- 6.2 Marine sediments -- 6.2.1 Organic sedimentation -- 6.2.2 An overview of sediment diagenesis -- 6.2.3 Oxic sediments -- 6.2.4 Suboxic sediments -- 6.2.5 Anoxic sediments -- 6.2.6 Preservation of organic carbon Preservation of organic carbon -- 6.2.7 Diagenetic mineralization -- 6.2.8 Sediment hydrogen concentrations -- 6.2.9 Problems with the biogeochemical zone scheme -- 6.3 Summary -- 7 Early microbial life -- 7.1 The prebiotic Earth -- 7.1.1 The Hadean environment -- 7.1.2 Origins of life -- 7.1.3 Mineral templates -- 7.2 The first cellular life forms -- 7.2.1 The chemolithoautotrophs -- 7.2.2 Deepest-branching Bacteria and Archaea -- 7.2.3 The fermenters and initial respirers -- 7.3 Evolution of photosynthesis -- 7.3.1 Early phototrophs -- 7.3.2 Photosynthetic expansion -- 7.3.3 The cyanobacteria -- 7.4 Metabolic diversification -- 7.4.1 Obligately anaerobic respirers -- 7.4.2 Continental platforms as habitats -- 7.4.3 Aerobic respiratory pathways -- 7.5 Earth's oxygenation -- 7.5.1 The changing Proterozoic environment -- 7.5.2 Eukaryote evolution -- 7.6 Summary -- References -- Index.

Note: Intro -- FUNDAMENTALS OF GEOBIOLOGY -- Contents -- Contributors -- 1. What is Geobiology? -- 1.1 Introduction -- 1.2 Life interacting with the Earth -- 1.3 Pattern and process in geobiology -- 1.4 New horizons in geobiology -- References -- 2. The Global Carbon Cycle: Biological Processes -- 2.1 Introduction -- 2.2 A brief primer on redox reactions -- 2.3 Carbon as a substrate for biological reactions -- 2.4 The evolution of photosynthesis -- 2.5 The evolution of oxygenic phototrophs -- 2.6 Net primary production -- 2.7 What limits NPP on land and in the ocean? -- 2.8 Is NPP in balance with respiration? -- 2.9 Conclusions and extensions -- References -- 3. The Global Carbon Cycle: Geological Processes -- 3.1 Introduction -- 3.2 Organic carbon cycling -- 3.3 Carbonate cycling -- 3.4 Mantle degassing -- 3.5 Metamorphism -- 3.6 Silicate weathering -- 3.7 Feedbacks -- 3.8 Balancing the geological carbon cycle -- 3.9 Evolution of the geological carbon cycle through Earth's history: proxies and models -- 3.10 The geological C cycle through time -- 3.11 Limitations and perspectives -- References -- 4. The Global Nitrogen Cycle -- 4.1 Introduction -- 4.2 Geological nitrogen cycle -- 4.3 Components of the global nitrogen cycle -- 4.4 Nitrogen redox chemistry -- 4.5 Biological reactions of the nitrogen cycle -- 4.6 Atmospheric nitrogen chemistry -- 4.7 Summary and areas for future research -- References -- 5. The Global Sulfur Cycle -- 5.1 Introduction -- 5.2 The global sulfur cycle from two perspectives -- 5.3 The evolution of S metabolisms -- 5.4 The interaction of S with other biogeochemical cycles -- 5.5 The evolution of the S cycle -- 5.6 Closing remarks -- Acknowledgements -- References -- 6. The Global Iron Cycle -- 6.1 Overview -- 6.2 The inorganic geochemistry of iron: redox and reservoirs -- 6.3 Iron in modern biology and biogeochemical cycles. , 6.4 Iron through time -- 6.5 Summary -- Acknowledgements -- References -- 7. The Global Oxygen Cycle -- 7.1 Introduction -- 7.2 The chemistry and biochemistry of oxygen -- 7.3 The concept of redox balance -- 7.4 The modern O2 cycle -- 7.5 Cycling of O2 and H2 on the early Earth -- 7.6 Synthesis: speculations about the timing and cause of the rise of atmospheric O2 -- References -- 8. Bacterial Biomineralization -- 8.1 Introduction -- 8.2 Mineral nucleation and growth -- 8.3 How bacteria facilitate biomineralization -- 8.4 Iron oxyhydroxides -- 8.5 Calcium carbonates -- Acknowledgements -- References -- 9. Mineral-Organic-Microbe Interfacial Chemistry -- 9.1 Introduction -- 9.2 The mineral surface (and mineral-bio interface) and techniques for its study -- 9.3 Mineral-organic-microbe interfacial processes: some key examples -- Acknowledgements -- References -- 10. Eukaryotic Skeletal Formation -- 10.1 Introduction -- 10.2 Mineralization by unicellular organisms -- 10.3 Mineralization by multicellular organisms -- 10.4 A brief history of skeletons -- 10.5 Summary -- Acknowledgements -- References -- 11. Plants and Animals as Geobiological Agents -- 11.1 Introduction -- 11.2 Land plants as geobiological agents -- 11.3 Animals as geobiological agents -- 11.4 Conclusions -- Acknowledgements -- References -- 12. A Geobiological View of Weathering and Erosion -- 12.1 Introduction -- 12.2 Effects of biota on weathering -- 12.3 Effects of organic molecules on weathering -- 12.4 Organomarkers in weathering solutions -- 12.5 Elemental profiles in regolith -- 12.6 Time evolution of profile development -- 12.7 Investigating chemical, physical, and biological weathering with simple models -- 12.8 Conclusions -- Acknowledgements -- References -- 13. Molecular Biology's Contributions to Geobiology -- 13.1 Introduction -- 13.2 Molecular approaches used in geobiology. , 13.3 Case study: anaerobic oxidation of methane -- 13.4 Challenges and opportunities for the next generation -- Acknowledgements -- References -- 14. Stable Isotope Geobiology -- 14.1 Introduction -- 14.2 Isotopic notation and the biogeochemical elements -- 14.3 Tracking fractionation in a system -- 14.4 Applications -- 14.5 Using isotopes to ask a geobiological question in deep time -- 14.6 Conclusions -- Acknowledgements -- References -- 15. Biomarkers: Informative Molecules for Studies in Geobiology -- 15.1 Introduction -- 15.2 Origins of biomarkers -- 15.3 Diagenesis -- 15.4 Isotopic compositions -- 15.5 Stereochemical considerations -- 15.6 Lipid biosynthetic pathways -- 15.7 Classification of lipids -- 15.8 Lipids diagnostic of Archaea -- 15.9 Lipids diagnostic of Bacteria -- 15.10 Lipids of Eukarya -- 15.11 Preservable cores -- 15.12 Outlook -- Acknowledgements -- References -- 16. The Fossil Record of Microbial Life -- 16.1 Introduction -- 16.2 The nature of Earth's early microbial record -- 16.3 Paleobiological inferences from microfossil morphology -- 16.4 Inferences from microfossil chemistry and ultrastructure (new technologies) -- 16.5 Inferences from microbialites -- 16.6 A brief history, with questions -- 16.7 Conclusions -- Acknowledgements -- References -- 17. Geochemical Origins of Life -- 17.1 Introduction -- 17.2 Emergence as a unifying concept in origins research -- 17.3 The emergence of biomolecules -- 17.4 The emergence of macromolecules -- 17.5 The emergence of self-replicating systems -- 17.6 The emergence of natural selection -- 17.7 Three scenarios for the origins of life -- Acknowledgements -- References -- 18. Mineralogical Co-evolution of the Geosphere and Biosphere -- 18.1 Introduction -- 18.2 Prebiotic mineral evolution I - evidence from meteorites -- 18.3 Prebiotic mineral evolution II - crust and mantle reworking. , 18.4 The anoxic Archean biosphere -- 18.5 The Great Oxidation Event -- 18.6 A billion years of stasis -- 18.7 The snowball Earth -- 18.8 The rise of skeletal mineralization -- 18.9 Summary -- Acknowledgements -- References -- 19. Geobiology of the Archean Eon -- 19.1 Introduction -- 19.2 Carbon cycle -- 19.3 Sulfur cycle -- 19.4 Iron cycle -- 19.5 Oxygen cycle -- 19.6 Nitrogen cycle -- 19.7 Phosphorus cycle -- 19.8 Bioaccretion of sediment -- 19.9 Bioalteration -- 19.10 Conclusions -- References -- 20. Geobiology of the Proterozoic Eon -- 20.1 Introduction -- 20.2 The Great Oxidation Event -- 20.3 The early Proterozoic: Era geobiology in the wake of the GOE -- 20.4 The mid-Proterozoic: a last gasp of iron formations, deep ocean anoxia, the 'boring' billion, and a mid-life crisis -- 20.5 The history of Proterozoic life: biomarker records -- 20.6 The history of Proterozoic life: mid-Proterozoic fossil record -- 20.7 The late Proterozoic: a supercontinent, oxygen, ice, and the emergence of animals -- 20.8 Summary -- Acknowledgements -- References -- 21. Geobiology of the Phanerozoic -- 21.1 The beginning of the Phanerozoic Eon -- 21.2 Cambrian mass extinctions -- 21.3 The terminal Ordovician mass extinction -- 21.4 The impact of early land plants -- 21.5 Silurian biotic crises -- 21.6 Devonian mass extinctions -- 21.7 Major changes of the global ecosystem in Carboniferous time -- 21.8 Low-elevation glaciation near the equator -- 21.9 Drying of climates -- 21.10 A double mass extinction in the Permian -- 21.11 The absence of recovery in the early Triassic -- 21.12 The terminal Triassic crisis -- 21.13 The rise of atmospheric oxygen since early in Triassic time -- 21.14 The Toarcian anoxic event -- 21.15 Phytoplankton, planktonic foraminifera, and the carbon cycle -- 21.16 Diatoms and the silica cycle -- 21.17 Cretaceous climates. , 21.18 The sudden Paleocene-Eocene climatic shift -- 21.19 The cause of the Eocene-Oligocene climatic shift -- 21.20 The re-expansion of reefs during Oligocene time -- 21.21 Drier climates and cascading evolutionary radiations on the land -- References -- 22. Geobiology of the Anthropocene -- 22.1 Introduction -- 22.2 The Anthropocene -- 22.3 When did the Anthropocene begin? -- 22.4 Geobiology and human population -- 22.5 Human appropriation of the Earth -- 22.6 The carbon cycle and climate of the Anthropocene -- 22.7 The future of geobiology -- Acknowledgements -- References -- Index -- Colour plates.