INTRODUCTION TO ORGANIC GEOCHEMISTRY

About this book

Organic geochemistry is the study of the transformation of organic matter of all types, whether of biological or man-made origin, in the Earth System.
These transformations range from those mediated by biological processes involved in the production of living tissue and the operation of food-chains,
to those controlled by temperature and pressure at depth in the crust, and by photochemical processes in the atmosphere and hydrosphere.
This book does not assume any particular specialist knowledge - explanatory boxes are used to provide essential information about topics and techniques.
Technical terms are highlighted and explained at their first appearance in the text.
SI units are presented in Appendix 1, prefixes used to denote exponents in Appendix 2 and a geological time scale in Appendix 3.
A comprehensive reference list, featuring articles in readily available journals, enables exploration of the original sources of concepts and case studies.
The text serves undergraduate and postgraduate courses in which organic geochemistry is an important component.
It may also be found a useful companion by experienced scientists from other disciplines encountering organic geochemistry for the first time.

We are pleased to make this text available for educational purposes – each chapter title is a link to a pdf of the text
A revised version with errata incorporated will appear in due course
Please advise authors of further errata at pangaea@macace.net
Copyright applies, so while use for personal private study is allowed, please apply to the authors for permission to reproduce material

Contents

1 Carbon, the Earth and life

  • 1.1 Carbon and the basic requirements of life
    • 1.1.1 Introduction
  • 1.2 Chemical elements, simple compounds and their origins
    • 1.2.1 Origin of elements
    • 1.2.2 The first organic compounds
  • 1.3 The origin of life
    • 1.3.1 The young Earth
    • 1.3.2 The raw material for life
    • 1.3.3 The common ancestor
  • 1.4 Evolution of life and the atmosphere
    • 1.4.1 Atmospheric oxygen and photosynthesis
    • 1.4.2 Geological record of oxygen levels
  • 1.5 Major contributors to sedimentary organic matter
    • 1.5.1 Major present-day contributors
    • 1.5.2 The fossil record of major contributors
    • 1.5.3 Evolution of marine life
    • 1.5.4 Evolution of terrestrial life
    • 1.5.5 Ecosystem variations

2 Chemical composition of organic matter

  • 2.1 Structure of natural products
    • 2.1.1 Introduction
    • 2.1.2 Bonding in organic compounds
    • 2.1.3 Stereoisomerism
  • 2.2 Carbohydrates
    • 2.2.1 Composition
    • 2.2.2 Occurrence and function
  • 2.3 Amino acids and proteins
    • 2.3.1 Composition
    • 2.3.2 Occurrence and function
  • 2.4 Lipids
    • 2.4.1 Glycerides
      • (a) Fats
      • (b) Phospholipids, glycolipids and ether lipids
    • 2.4.2 Waxes and related compounds
      • (a) Waxes
      • (b) Cutin, suberin and related polymers
    • 2.4.3 Terpenoids
      • (a) Monoterpenoids
      • (b) Sesquiterpenoids
      • (c) Diterpenoids
      • (d) Sesterterpenoids
      • (e) Triterpenoids
      • (f) Steroids
      • (g) Tetraterpenoids
      • (h) Polyterpenoids
    • 2.4.4 Tetrapyrrole pigments
  • 2.5 Lignins, tannins and related compounds
    • 2.5.1 Lignin
    • 2.5.2 Tannins and other hydroxy-aromatic pigments
  • 2.6 Nucleotides and nucleic acids
    • 2.6.1 Nucleotides
    • 2.6.2 Nucleic acids
  • 2.7 Geochemical implications of compositional variation
    • 2.7.1 Compositional variation of organisms
    • 2.7.2 Variations through geological time

3 Production, preservation and degradation oforganic matter

  • 3.1 How and why organic-rich deposits form
  • 3.2 Controls on primary production
      3.2.1 General controls on photosynthesis
    • 3.2.2 Stratification of the water column
      • (a) Oceanic stratification
      • (b) Lacustrine stratification
    • 3.2.3 Light
    • 3.2.4 Nutrients
      • (a) Low-latitude oceans
      • (b) Mid-latitude oceans
      • (c) High-latitude oceans
      • (d) Stratified lakes
    • 3.2.5 Spatial variation in marine primary production
    • 3.2.6 Variation in phytoplankton populations
    • 3.2.7 Biolimiting nutrient variations in the oceans
    • 3.2.8 Variations in higher-plant populations
    3.3 Preservation and degradation of organic matter
    • 3.3.1 Fate of primary production in the water column
      • (a) Dissolved organic matter
    • 3.3.2 Sedimentary fate of organic material
      • (a) Aerobic decomposition
      • (b) Anaerobic decomposition
    • 3.3.3 Degradation of biopolymers
      • (a) Proteins and amino acids
      • (b) Polysaccharides
      • (c) Lignin
    • 3.3.4 Factors affecting sedimentary preservation of organic matter
      • (a) Organic-rich sediments
      • (b) General controls on the organic content of marine sediments
      • (c) Feedbacks to atmospheric oxygen
  • 3.4 Depositional environments associated with accumulation of organic matter
    • 3.4.1 Lacustrine environments
      • (a) Open lakes
      • (b) Closed lakes
    • 3.4.2 Coal-forming mires
      • (a) Peat formation
      • (b) Mire types
    • 3.4.3 Marine environments
      • (a) Marine shelf deposits
      • (b) Enclosed and silled basins
      • (c) Production and preservation of organic matter in the Black Sea

4 Long-term fate of organic matter in thegeosphere

  • 4.1 Diagenesis
    • 4.1.1 Introduction
    • 4.1.2 Microbial degradation of organic matter during diagenesis
    • 4.1.3 Geopolymer formation
  • 4.2 Humic material
    • 4.2.1 Occurrence and classification
    • 4.2.2 Composition and structure
    • 4.2.3 Formation of humic substances
  • 4.3 Coal
    • 4.3.1 Classification and composition
      • (a) Classification
      • (b) Petrology
      • (c) Chemical composition
    • 4.3.2 Formation
      • (a) Peatification
      • (b) Biochemical stage of coalification
      • (c) Geochemical stage of coalification
  • 4.4 Kerogen
    • 4.4.1 Formation
      • (a) Geopolymer formation during diagenesis
      • (b) Biomarkers
      • (c) Sulphur incorporation
    • 4.4.2 Kerogen composition
    • 4.4.3 Kerogen classification
      • (a) Type I kerogen
      • (b) Type II kerogen
      • (c) Type III kerogen
      • (d) Type IV kerogen
      • (e) Improved kerogen typing
    • 4.4.4 Structural and compositional changes
      • (a) Structural changes
      • (b) Changes in chemical composition
  • 4.5 Catagenesis and metagenesis
    • 4.5.1 Petroleum generation
    • 4.5.2 Kerogen maturity and hydrocarbon composition
    • 4.5.3 Petroleum composition
      • (a) Major hydrocarbons in oils
      • (b) Biomarkers
    • 4.5.4 Reactions involved in hydrocarbon generation
      • (a) Isotopic fractionation
    • 4.5.5 Movement of hydrocarbons from kerogen and coal
      • (a) Mechanisms of expulsion
      • (b) Secondary migration
    • 4.5.6 Post-generation alteration of petroleum
      • (a) Migration
      • (b) De-asphalting
      • (c) Biodegradation
      • (d) Water washing
      • (e) Thermal alteration
      • (f) Thermochemical sulphate reduction
      • (g) Gas diffusion
      • (h) Evaporative fractionation
      • (i) Tertiary migration
      • (j) Carbon dioxide
  • 4.6 Temporal and geographical distribution of fossil organic carbon
    • 4.6.1 Coal and kerogen
    • 4.6.2 Oil and gas
      • (a) Methane hydrates

5 Chemical stratigraphic concepts and tools

  • 5.1 Biologically mediated transformations
    • 5.1.1 Introduction
    • 5.1.2 General differences between major groups of organisms
    • 5.1.3 Factors affecting the lipid composition of organisms
  • 5.2 Examples of source indicators in Recent sediments
    • 5.2.1 Fatty acids
      • (a) Monounsaturated fatty acids
      • (b) Polyunsaturated fatty acids
      • (c) Iso and anteiso methyl-branched fatty acids
      • (d) Internally branched and cycloalkyl fatty acids
      • (e) Hydroxy fatty acids
    • 5.2.2 Sterols
    • 5.2.3 Carbohydrates
    • 5.2.4 Lignins
  • 5.3 Diagenesis at the molecular level
    • 5.3.1 General diagenetic processes
      • (a) Carbohydrates and lignins
      • (b) Biomarkers
    • 5.3.2 Lipid diagenesis in the water column
      • (a) Sterols
      • (b) Chlorophylls
      • (c) Carotenoids
      • (d) Bacterial action
    • 5.3.3 Sedimentary diagenesis of lipids
      • (a) Fatty acids
      • (b) Tetrapyrrole pigments
      • (c) Carotenoids
      • (d) Reduction of regular steroids
      • (e) Rearrangement and aromatisation of regular steroids
      • (f) 4-Methyl steroids
      • (g) Mono-, sesqui- and diterpenoids
      • (h) Triterpenoid reduction and rearrangement
      • (i) Triterpenoid aromatisation
  • 5.4 Source and environmental indicators in ancient sediments and oil
    • 5.4.1 Introduction
    • 5.4.2 Source-related biomarkers
      • (a) Normal and methyl-branched alkanes
      • (b) Acyclic isoprenoids
      • (c) Microbial tricyclic and tetracyclic alkanes
      • (d) Steranes
      • (e) Hopanes
      • (f) Higher-plant diterpanes and triterpanes
    • 5.4.3 Indicators of depositional environment
      • (a) Freshwater and marine environments
      • (b) Argillaceous and carbonate sediments
      • (c) Hypersalinity
      • (d) Redox conditions and phytol diagenesis
  • 5.5 Thermal maturity and molecular transformations
    • 5.5.1 Configurational isomerisation
      • (a) Acyclic isoprenoidal alkanes
      • (b) Steranes
      • (c) Triterpanes
      • (d) Alternative explanations of apparent isomerisation
    • 5.5.2 Aromatisation
    • 5.5.3 Enrichment of short-chain hydrocarbons and cracking processes
      • (a) Steroids
      • (b) Porphyrins
    • 5.5.4 Methyl group migration in aromatic hydrocarbons
  • 5.6 Palaeotemperature and age measurement
    • 5.6.1 Introduction
    • 5.6.2 Amino acid epimerisation
    • 5.6.3 Degree of unsaturation in long-chain ketones
  • 5.7 Maturity of ancient sedimentary organic matter
    • 5.7.1 Bulk compositional indicators of maturity
    • 5.7.2 Molecular maturity parameters
      • (a) Light hydrocarbons
      • (b) Carbon preference index
      • (c) Biomarker transformations
      • (d) Methyl group isomerisation in aromatic hydrocarbons
    • 5.7.3 Modelling kerogen maturation
      • (a) Temperature and time
      • (b) Kerogen transformation kinetics
      • (c) Effect of geothermal gradient on molecular maturity parameters
  • 5.8 Isotopic palaeontology
    • 5.8.1 Isotopic fractionation
    • 5.8.2 Autotrophic pathways
    • 5.8.3 Biosynthetic pathways
    • 5.8.4 Heterotrophy
    • 5.8.5 Sedimentary isotopic record
    • 5.8.6 Isotopic distributions in petroleum
      • (a) Oils
      • (b) Gases

6 The carbon cycle and climate

  • 6.1 Global carbon cycle
    • 6.1.1 Carbon reservoirs and fluxes
    • 6.1.2 Biochemical subcycle
      • (a) Terrestrial component of the biochemical subcycle
      • (b) Marine component of the biochemical subcycle
    • 6.1.3 Geochemical subcycle
  • 6.2 Changes in carbon reservoirs over geological time
    • 6.2.1 Sedimentary preservation of organic carbon
    • 6.2.2 Atmospheric levels of carbon dioxide
  • 6.3 Palaeoclimatic variations
    • 6.3.1 Factors affecting climate
      • (a) Solar energy variations
      • (b) Lithospheric and hydrospheric processes
      • (c) Greenhouse gases and aerosols
      • (d) Dimethyl sulphide
      • (e) Methane
    • 6.3.2 Neoproterozoic glaciations
    • 6.3.3 Carboniferous-Permian icehouse
    • 6.3.4 Cretaceous hothouse
      • (a) Cretaceous anoxic events
    • 6.3.5 Quaternary ice ages
    • 6.3.6 The ultimate hothouse
  • 6.4 Isotopic excursions at period boundaries
    • 6.4.1 Cretaceous-Tertiary boundary event
    • 6.4.2 Paleocene-Eocene thermal maximum
    • 6.4.3 Permo-Triassic boundary event
  • 6.5 Human influence on the carbon cycle
    • 6.5.1 Deviation from the steady state system
    • 6.5.2 Greenhouse gas sources and fluxes
      • (a) Methane
      • (b) Carbon monoxide
    • 6.5.3 Atmospheric concentrations of carbon dioxide and methane
    • 6.5.4 Climatic change and greenhouse gases
    • 6.5.5 Eutrophication

7 Anthropogenic carbon and the environment

  • 7.1 Introduction
  • 7.2 Halocarbons
    • 7.2.1 Ozone depletion
    • 7.2.2 Greenhouse effect
  • 7.3 Hydrocarbon pollution in aquatic environments
    • 7.3.1 Fossil fuel combustion
      • (a) Polycyclic aromatic hydrocarbons in Recent sediments
      • (b) Polycyclic aromatic hydrocarbons in ancient sediments
    • 7.3.2 Oil spills
      • (a) Effects of oil pollution
      • (b) Oil pollution monitoring
  • 7.4 Endocrine-disrupting chemicals
    • 7.4.1 Endocrine activity
    • 7.4.2 Natural and synthetic oestrogens
  • 7.5 Environmental behaviour of selected xenobiotic compounds
    • 7.5.1 Physicochemical properties and bioaccumulation
    • 7.5.2 Tributyl tin
    • 7.5.3 Phthalates
    • 7.5.4 DDT and related compounds
    • 7.5.5 Polychlorinated biphenyls
      • (a) Aeolian transport
    • 7.5.6 Dioxins and related compounds
  • 7.6 Factors affecting the fate of anthropogenic components
    • 7.6.1 Environmental fate of chloroaromatics
    • 7.6.2 General considerations
    • 7.6.3 Bioavailability
    • 7.6.4 Mixtures and interactions
    • 7.6.5 Humic substances and pollutants
Apprendices & References
  • Appendix 1: SI units
  • Appendix 2: SI unit prefixes
  • Appendix 3: Geological time scale
  • References

Errata

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