Organic Geochemistry: Principles and Applications (Topics in Geobiology, 11)

As this is the first general textbook for the field published in over twenty years, the editors have taken great care to make sure coverage is comprehensive. Diagenesis of organic matter, kerogens, exploration for fossil fuels, and many other subjects are discussed in detail to provide faculty and students with a thorough introduction to organic geochemistry.

I • Introduction.- 1 • Biogeochemical Cycles: A Review of Fundamental Aspects of Organic Matter Formation, Preservation, and Composition.- 1. Introduction.- 2. Organic Matter as an Information Source.- 3. Classification of Living Organisms; the Importance and Diversity of Microbes.- 4. Biogeochemical Cycles and Inventories of Major Bioactive Elements.- 5. Biochemistry and Isotopic Consequences of Incorporation of Bioelements into Biomass; Diagnostic Isotopic Fossils.- 6. Diagnostic Molecular Structures Encoded in Fossil Organic Matter.- 7. Geological History of the Biogeochemical Cycles.- 8. Future Research Directions.- References.- 2 A Review of Macromolecular Organic Compounds That Comprise Living Organisms and Their Role in Kerogen, Coal, and Petroleum Formation.- 1. Introduction.- 2. Inventory of Macromolecular Substances, Their Ocurrence in Organisms, and Their Potential for Survival in Recent Sediments.- 3. Structural Relationships between Kerogen/Coal and Selectively Preserved Resistant Biopolymers.- 4. Consequences for Formation of Oil, Coal, and Gas.- References.- 3 • Isotope Fractionation during Primary Production.- 1. Introduction.- 2. Definition of Isotope Terms.- 3. Carbon Isotopes.- 4. Nitrogen Isotopes.- 5. Oxygen Isotopes.- 6. Hydrogen Isotopes.- 7. Sulfur Isotopes: Fractionation during Photosynthesis.- 8. Implications for Organic Geochemistry.- References.- II • Early Diagenesis of Organic Matter.- 4 • Early Diagenesis of Organic Matter: The Dynamics (Rates) of Cycling of Organic Compounds.- 1. Introduction.- 2. Methods of Measuring Decomposition and Transformation Rates during Early Diagenesis.- 3. Key Processes and Rates.- 4. Accuracy of Rate Measurements.- 5. Patterns of Variation in Rates of Early Diagenesis.- 6. Goals for the Future.- 7. Conclusions.- References.- 5 • The Early Diagenesis of Organic Matter: Bacterial Activity.- 1. Introduction to Bacteria as Primary Agents.- 2. Current Conceptual Models and Experimental Approaches.- 3. Bacterial Abundance and Global Distribution in Sediments.- 4. Constraints on Bacterial Activities in Sediments.- 5. Unique Catalytic Properties and Microbial Consortia.- 6. Concluding Remarks.- References.- 6 • Production, Transport, and Alteration of Particulate Organic Matter in the Marine Water Column.- 1. Introduction.- 2. Vertical Flux of Organic Matter Sinking through the Water Column.- 3. Influences on the Quality of Particulate Organic Matter Sinking through the Water Column.- 4. Concluding Remarks.- References.- 7 • Organic Matter at the Sediment-Water Interface.- 1. Introduction.- 2. Organic Material at the Mineral-Water Interface.- 3. Organic Matter at the Sediment-Water Interface.- 4. Synthesis and Future Directions.- References.- 8 • The Early Diagenesis of Organic Matter in Lacustrine Sediments.- 1. Sources and Sedimentation of Organic Matter in Lakes.- 2. Indicators of Early Diagenesis of Organic Matter in Lacustrine Sediments.- 3. Molecular Indicators of Early Diagenesis of Organic Matter.- 4. Summary and Conclusion.- References.- 9 • Early Diagenesis of Organic Matter in Sediments: Assessment of Mechanisms and Preservation by the Use of Isotopic Molecular Approaches.- 1. Introduction.- 2. Amino Acid Nitrogen in Sediments.- 3. Bulk Characterization of Sediments: C/N.- 4. Isotopes and Diagenetic Fractionation.- 5. Molecular-Level Isotope Analyses.- References.- 10 • Marine Invertebrate Feeding and the Sedimentary Lipid Record.- 1. Introduction.- 2. Fatty Acids.- 3. Phytol and Fatty Alcohols.- 4. Sterols.- 5. Hydrocarbons and Long-Chain Lipids.- 6. Conclusions.- References.- 11 • Early Diagenesis: Consequences for Applications of Molecular Biomarkers.- 1. Introduction.- 2. The Nature of Early Diagenesis.- 3. Compositional Trends in Degrading Organic Matter—a Simple Model.- 4. Effects of Early Diagenesis on Different Biomarker Applications.- 5. Conclusions.- References.- 12 • The Early Diagenesis of Organic Matter: Reaction at the Air-Sea Interface.- 1. Introduction.- 2. The Air-Sea Interface: Description and Composition.- 3. Transformation of Dissolved to Particulate Carbon in Surface Microlayers.- 4. Transformation from Low to High Molecular Weight.- 5. Photochemical Alterations.- 6. Summary and a Special Case.- References.- III • Kerogen and Related Materials.- 13 • Determination of Structural Components of Kerogens by the Use of Analytical Pyrolysis Methods.- 1. Introduction.- 2. Elucidation of Kerogen Composition by Pyrolysis.- 3. Pyrolysis as a Structural Tool.- 4. Analytical Pyrolysis and Implications for Kerogen Formation and Petroleum Generation.- 5. Summary.- References.- 14 • Chemical Methods for Assessing Kerogen and Protokerogen Types and Maturity.- 1. Introduction and Scope.- 2. Definitions and Isolation Procedures.- 3. Kerogen Type.- 4. Principal Kerogen Maturation Techniques Now in Use.- 5. Spectral Methods of Determining Kerogen Type and Maturation.- 6. Other Miscellaneous Methods of Kerogen Typing and Maturation.- References.- 15 • Organic Petrographic Approach to Kerogen Characterization.- 1. Introduction.- 2. Optical Methods of Kerogen Characterization.- 3. Optical Methods to Evaluate Thermal Maturity.- 4. Conclusions.- References.- IV • Thermal Alteration of Organic Matter and the Formation of Fossil Fuels.- 16 • The Thermal Alteration of Kerogen and the Formation of Oil.- 1. Introduction.- 2. Thermal Alteration of Kerogen.- 3. Quantitation of Hydrocarbon Generation.- 4. Composition of Crude Oils.- 5. Timing of Oil Generation.- 6. Conclusions.- References.- 17 • Hydrothermal Alteration of Organic Matter in Marine and Terrestrial Systems.- 1. Introduction.- 2. Geological Locales with Hydrothermal Petroleum.- 3. Interactions of Hydrothermal Activity with Organic Matter.- 4. Hydrothermal Petroleum Generation and Migration.- 5. Summary.- References.- 18 • Laboratory Simulation of Petroleum Formation: Hydrous Pyrolysis.- 1. Introduction.- 2. Definition of Hydrous Pyrolysis.- 3. Significance of Expelled Oil.- 4. Comparison of Pyrolysate Yields.- 5. Utility of Rock Samples.- 6. Effects of Reactor Wall Composition.- 7. Consideration of Experimental Artifacts.- 8. Conclusions.- References.- V • Applications of Organic Geochemical Research for Hydrocarbon Exploration.- 19 • Oil-Oil and Oil-Source Rock Correlations: Techniques.- 1. Introduction.- 2. Gas Chromatography and Mass Spectrometry.- 3. Direct Insertion Probe MS/MS (DIP-MS/MS).- 4. Pyrolysis.- 5. High-Pressure Liquid Chromatography and Mass Spectrometry.- 6. Supercritical Fluid Chromatography and Mass Spectrometry.- 7. Gas Chromatography and Carbon Deuterium and Isotopic Compositions.- 8. Summary.- References.- 20 • Organic Geochemistry of Estancia Vieja Oils, Rio Negro Norte Block: Correlation with Other Neuquen Basin, Argentina, Oils.- 1. Introduction.- 2. Results and Discussion.- 3. Conclusions.- References.- 21 • Oil to Source Rock Correlation: Concepts and Case Studies.- 1. Introduction.- 2. Oil-Source Rock Correlations—A Conceptual Framework.- 3. Case Studies.- 4. Future Directions.- References.- 22 • The Kinetics of Biomarker Reactions: Implications for the Assessment of the Thermal Maturity of Organic Matter in Sedimentary Basins.- 1. Introduction.- 2. Chemical Kinetics.- 3. Elucidation of the Activation Energy and Pre-Exponential Constant.- 4. Case Studies.- 5. The Effect of Mineral Matrix.- 6. Conclusions.- References.- 23 • Effect of Biodegradation and Water Washing on Crude Oil Composition.- 1. Introduction.- 2. Geologic Constraints and Physicochemical Conditions for Biodegradation and Water Washing.- 3. Effects of Biodegradation and Water Washing on Crude Oil Composition.- 4. Examples of Occurrences of Biodegradation and Water Washing.- 5. Summary.- References.- 24 • The Origin and Distribution of Gas Hydrates in Marine Sediments.- 1. Introduction.- 2. Structure and Stability.- 3. Bottom-Simulating Reflector.- 4. Geochemical Evidence and Hydrate Occurrence.- 5. The Significance of Gas Hydrates.- References.- VI • Organic Matter and Metalliferous Deposits.- 25 • The Role of Organic Matter in Ore Transport Processes.- 1. Introduction.- 2. Metals in Petroleum Liquids.- 3. Metals in Oil Field and Formation Waters.- 4. Discussion.- 5. Behavior of Metals in a Composite Petroleum-Brine System.- References.- 26 • Aspects of the Organic Geochemistry and Petrology of Metalliferous Ores.- 1. Introduction.- 2. Low-Temperature Deposits.- 3. High-Temperature Deposits: Optical Anisotropy.- 4. Hydrocarbon Phases.- 5. Thucholite.- 6. Petroleum Inclusions.- 7. Geological Controls.- 8. Conclusion.- References.- 27 • Metals in Black Shales.- 1. Introduction.- 2. Organic Matter in Shales.- 3. Metals in Shales.- 4. Metal Sources.- 5. Geochemistry of Metalliferous Black Shales.- 6. Carbon and Sulfur Relationships.- 7. Degree of Pyritization.- 8. Resources and Raw Materials.- 9. Summary.- References.- 28 • Trace and Minor Elements in Coal.- 1. Introduction.- 2. Source and Variation of Inorganic Constituents.- 3. Modes of Occurrence.- 4. Organic-Inorganic Interactions.- 5. Why Concern Ourselves with the Elements in Coal?.- 6. Conclusions.- References.- VII • The Precambrian.- 29 • Evolution of the Earth’s Atmosphere and Hydrosphere: Hadean to Recent.- 1. Formation of the Atmosphere and Ocean.- 2. Early Atmospheric Composition and Climate.- 3. Sulfur Gases and Ultraviolet Radiation.- 4. Ocean Composition and pH.- 5. The Faint Young Sun Problem and the Decline in Atmospheric CO2.- 6. The Rise of Oxygen and Ozone.- 7. Other Trace Gases.- 8. Summary.- References.- 30 • The Prebiotic Synthesis of Organic Compounds on the Early Earth.- 1. The Composition of the Primitive Atmosphere.- 2. Energy Sources.- 3. Prebiotic Synthesis of Amino Acids.- 4. Mildly Reducing and Nonreducing Atmospheres.- 5. Purine and Pyrimidine Synthesis.- 6. Sugars.- 7. Other Prebiotic Compounds.- 8. Compounds That Have Not Been Synthesized Prebiotically.- 9. Organic Compounds in Carbonaceous Chondrites.- 10. Interstellar Molecules.- 11. Production Rates and Concentrations of Hydrogen Cyanide, Formaldehyde, and Amino Acids in the Primitive Ocean.- 12. The Concentration of Amino Acids in the Primitive Ocean.- References.- 31 • The Initiation of Biological Processes on Earth: Summary of Empirical Evidence.- 1. Introduction.- 2. Origins of Life on Earth: Evidence and Constraints from the Geological Record.- 3. Summary and Conclusions.- References.- 32 • Organic Geochemistry of Precambrian Sedimentary Rocks.- 1. Introduction.- 2. The Precambrian: Geological and Paleontological Aspects.- 3. Organic Carbon.- 4. Kerogen Studies.- 5. Extract and Oil Studies.- 6. Economic Geology.- 7. Summary and Conclusions.- References.- 33 • The Organic Geochemistry of Carbonaceous Meteorites: Amino Acids and Stable Isotopes.- 1. Introduction.- 2. Distribution of Amino Acids in the Murchison Meteorite.- 3. Amino Acid Stereochemistry.- 4. Stable Isotopes.- 5. Implications for the Origin of Life on Earth.- 6. Conclusions.- References.- VIII • Applications of Organic Geochemistry for Quaternary Research.- 34 • Applications of Biomarkers for Delineating Marine Paleoclimatic Fluctuations during the Pleistocene.- 1. Introduction.- 2. Climatic Changes during the Pleistocene.- 3. Biomarkers as Climatic Indicators.- 4. Future Potential and Scope for Biomarkers in Paleoclimatic Assessment.- References.- 35 • The Diagenesis of Proteins and Amino Acids in Fossil Shells.- 1. Introduction.- 2. Diagenesis of Proteins and Amino Acids in Fossil Shells.- 3. Hydrolysis of Proteins and Peptides in Fossil Shells.- 4. Stereochemistry and Racemization of Amino Acids.- 5. Amino Acid Racemization in Fossil Shells.- 6. Rate and Extent of Isoleucine Epimerization in Peptides.- 7. A Model for Isoleucine Epimerization in Proteins.- 8. Summary.- References.- 36 • Applications of Organic Geochemistry for Quaternary Research: Aminostratigraphy and Aminochronology.- 1. Introduction.- 2. Foraminiferal Aminostratigraphy and Aminochronology: Examples of the Relationships among Enantiomeric Ratios, Statigraphic Position, and Taxonomy.- 3. Molluscan Aminostratigraphy: General Depositional Framework Models.- 4. Molluscan Aminostratigraphy: Examples of the Relationship between Enantiomeric Ratios, Stratigraphic Position, and Taxonomy.- 5. Molluscan Aminochronology: Examples of Calibrated Racemization Kinetics in Sequences of Coastal Deposits.- 6. Correlation.- 7. Geochemical Techniques for the Recognition of Anomalous Results.- 8. Summary and Conclusions.- References.- 37 • Sources and Cycling of Organic Matter within Modern and Prehistoric Food Webs.- 1. Introduction.- 2. Isotopic Variation among Primary Producers.- 3. Isotopic Composition of Consumers.- 4. Quantitative Analysis through Mixing Equations.- 5. Isotopic Compositions of Individual Compounds.- 6. Prehistoric Dietary Reconstruction.- 7. Conclusions.- References.- 38 • Macromolecules from Living and Fossil Biominerals: Implications for the Establishment of Molecular Phylogenies.- 1. Introduction.- 2. Fossil Proteins.- 3. Future Directions.- References.- 39 • Immunospecificity of Fossil Proteins: Implications for the Establishment of Evolutionary Trends.- 1. Introduction.- 2. Radioimmunoassay.- 3. Applications of RIA to Fossils.- 4. RIA Phylogenies, Biogeography, and Molecular Clocks.- 5. Future Prospects.- 6. Summary.- References.- IX • Summary.- 40 • Postscript.