Hydrocarbons, Oils and Lipids: Diversity, Origin, Chemistry and Fate

Preface
Contents
About the Series Editor-in-Chief
About the Volume Editor
Contributors
Part I: Structures and Properties of Hydrocarbons and Lipids
	1 Hydrocarbons and Lipids: An Introduction to Structure, Physicochemical Properties, and Natural Occurrence
		1 Introduction
		2 Covalent Bonding
		3 Hydrocarbons
			3.1 Saturated Hydrocarbons
				3.1.1 n-Alkanes
				3.1.2 Branched Alkanes
				3.1.3 Cycloalkanes
			3.2 Unsaturated Hydrocarbons
			3.3 Aromatic Hydrocarbons
				3.3.1 Aromaticity
				3.3.2 Benzene Derivatives
				3.3.3 Polycyclic Aromatic Hydrocarbons
		4 Functionalized Organic Compounds and Lipids
			4.1 Oxygen- and Sulfur-containing Compounds
			4.2 Nitrogen-containing Compounds
			4.3 Halogenated Compounds
		5 Physical Properties
		6 Reactions
			6.1 Reactions of Saturated Hydrocarbons
			6.2 Reactions of Unsaturated Hydrocarbons
			6.3 Reactions of Aromatic Hydrocarbons
			6.4 Specific Reactions of Functionalized Organic Compounds
		References
	2 Introduction to Oil Chemistry and Properties Related to Oil Spills
		1 Introduction
		2 The Composition of Oil
			2.1 SARA
				2.1.1 Saturates
				2.1.2 Alkanes
				2.1.3 Cycloalkanes
				2.1.4 Alkenes or Olefins
				2.1.5 Aromatic Compounds
				2.1.6 Naphthenoaromatic Compounds
			2.2 Sulfur Compounds
			2.3 Oxygen Compounds
			2.4 Nitrogen Compounds
			2.5 Metals
			2.6 Resins
			2.7 Asphaltenes
		3 Properties of Oil
			3.1 Oils with High Densities Have Low API Gravities and Vice Versa
		4 Research Needs
		References
	3 Gas Hydrates: Formation, Structures, and Properties
		1 Introduction
		2 Structure and Composition
		3 Hydrate Formation Processes
			3.1 Hypothesis of the Nucleation at the Interface
			3.2 Labile Cluster Nucleation Hypothesis
			3.3 Local Structuring Nucleation Hypothesis
			3.4 Hydrate Growth
			3.5 Hydrate Formation in Nature: Effects of Sediments
		4 Thermodynamic Properties of Simple and Mixed Hydrates
		5 Research Needs
		References
Part II: Hydrocarbons and Lipids in the Biosphere
	4 Factors Controlling Carbon and Hydrogen Isotope Fractionation During Biosynthesis of Lipids by Phototrophic Organisms
		1 Introduction
		2 Controls on Isotopic Fractionation
		3 Algae
			3.1 Algal Lipids
			3.2 Carbon Isotopes in Algal Lipids
				3.2.1 External Controls
					δ13C of Carbon Source
					Concentration of CO2
				3.2.2 Internal Controls
					Fractionation During Carbon Uptake
					Lipid Type and Metabolic Pathways
			3.3 Hydrogen Isotopes in Algal Lipids
				3.3.1 External Controls on H Isotopes
					2H/1H of Source Water
					Salinity
					Temperature and Irradiance
				3.3.2 Internal Controls on H Isotopes
					Lipid Type and Metabolic Pathways
		4 Higher Plants
			4.1 Higher Plant Lipids
			4.2 Carbon Isotopes in Higher Plant Lipids
				4.2.1 External Controls on C Isotopes
					δ13C of Carbon Source
					Atmospheric Concentration of CO2
					Moisture Availability
					Irradiance
				4.2.2 Internal Controls on C Isotopes
					Biosynthetic Pathways
					Lipid Type and Metabolic Pathways
			4.3 Hydrogen Isotopes in Higher Plant Lipids
				4.3.1 External Controls on H Isotopes
					2H/1H of Source Water
					Relative Humidity and Transpiration
				4.3.2 Internal Controls on H Isotopes
					Biosynthetic Pathways
					Lipid Type and Metabolic Pathways
		5 Research Needs
		References
	5 Plant Cuticular Waxes: Composition, Function, and Interactions with Microorganisms
		1 Introduction
		2 Composition of Plant Cuticular Waxes
		3 Function of Plant Cuticular Waxes
		4 Interactions of Microorganisms with Plant Cuticular Waxes
		5 Research Needs
		References
	6 Biosynthesis of the Plant Cuticle
		1 Introduction
		2 Cutin Biosynthesis
			2.1 Cutin Monomer Synthesis
			2.2 Cutin Polymerization
		3 Pathways for Cuticular Wax Biosynthesis
			3.1 Fatty Acid Elongases Produce Very-Long-Chain Fatty Acids
			3.2 Alcohol-Forming Pathway
			3.3 Alkane-Forming Pathway
			3.4 Other Compounds
		4 Export of Cutin Monomers and Wax Compounds
		5 Research Needs
		References
	7 Lipids of Geochemical Interest in Microalgae
		1 Introduction
		2 Hydrocarbons
			2.1 n-Alkanes and n-Alkenes
			2.2 Isoprenoid Alkanes and Alkenes
			2.3 Highly Branched Isoprenoid (HBI) Alkenes in Diatoms
			2.4 Cyclic Hydrocarbons
		3 Fatty Acids
			3.1 Hydroxy Fatty Acids
		4 Fatty Alcohols
		5 Alkenones and Alkyl Alkenoates
		6 Alkyl Diols
		7 Algaenan
		8 Sterols
		9 Other Biochemical Constituents
		10 Research Needs
		References
	8 Abiotic Transformation of Unsaturated Lipids and Hydrocarbons in Senescent Phytoplanktonic Cells
		1 Introduction
		2 Photo- and Autoxidation during the Senescence of Phytoplankton
			2.1 Photosensitized Oxidation
			2.2 Free Radical Oxidation (Autoxidation)
		3 Photo- and Autoxidation of the Main Unsaturated Lipid Components of Algae
			3.1 Chlorophyll Phytyl Side-Chain
			3.2 Alkenes
			3.3 Alkenones
			3.4 Unsaturated Fatty Acids
			3.5 Delta5-Sterols
		4 Conclusion
		References
	9 Cuticular Hydrocarbons and Pheromones of Arthropods
		1 Introduction: Cuticular Hydrocarbons and Pheromones
		2 Insect Cuticular Hydrocarbons
		3 Insect Pheromones
			3.1 Lepidopteran Fatty Acid Derived (Type I Pheromones)
			3.2 Polyene Hydrocarbons (Type II) Pheromones
			3.3 Terpenoid Pheromones
			3.4 Other Pheromones
		4 Hydrocarbon Biosynthesis
		5 Pheromone Biosynthesis
			5.1 Alcohol, Aldehyde, and Acetate Ester Pheromones
			5.2 Polyene Hydrocarbons
			5.3 Terpenoid Pheromones
			5.4 Other Pheromones
		6 Research Needs
		References
			Relevant Website
	10 Lipidomic Analysis of Lower Organisms
		1 Introduction
		2 Fatty Acids
		3 Archaea
		4 Bacteria
			4.1 Plasmalogens
			4.2 Mycobacteria
		5 Yeast
		6 Cyanobacteria and Algae
			6.1 Cyanobacteria
			6.2 Algae
		7 Research Needs
		References
Part III: Hydrocabons and Lipids in the Geosphere
	11 Composition and Properties of Petroleum
		1 Introduction
		2 How to Define a Crude Oil?
		3 Characterization of Crude Oils
			3.1 Bulk Parameters
			3.2 Molecular Characteristics
				3.2.1 Sesquiterpanes
				3.2.2 Steranes
				3.2.3 Diamondoids
					C7 Compounds
				3.2.4 Aromatic Hydrocarbons
		4 Where Does the Oil Come From? Photosynthesis and How Things Change Over Time
		5 Productivity Versus Preservation
		6 What Are the Major Factors Involved in Determining the Composition of Crude Oils?
		7 What Is the Impact of Depositional Environment?
		8 What Is the Impact of Maturity?
		9 How Does the Molecular Composition of an Oil Change During and After Generation?
		10 Expulsion and Migration
		11 Biodegradation and Preservation
		12 Summary
		References
	12 Petroleomics
		1 What Is Petroleomics?
		2 Determining the Petroleome
			2.1 Gas Chromatography
			2.2 Liquid Chromatography
			2.3 Ultrahigh-Resolution Mass Spectrometry
			2.4 Modeling the Petroleome
		3 Applications of Petroleomics
		4 Limitations and Future Research
		References
	13 Stable Isotopes in Understanding Origin and Degradation Processes of Hydrocarbons and Petroleum
		1 Introduction
		2 Definitions
		3 Stable Isotope Applications in Petroleum Geochemistry
			3.1 Petroleum Formation in Sedimentary Basins
			3.2 Alteration Processes in Petroleum Reservoirs
		4 Research Needs
		References
	14 The Origin of Organic Sulphur Compounds and Their Impact on the Paleoenvironmental Record
		1 Introduction
		2 Nomenclature, Methods, and Instrumentation for the Characterization of Sedimentary Organic Sulphur Compounds
			2.1 Nomenclature and Chemical and Thermal Treatment for the Analysis of Organic S
			2.2 Instrumentation for the Analysis of Organic S
			2.3 Sulphur and Carbon Isotope Analysis
		3 The Marine Sulphur Cycle and Its Impact on Organic Matter
			3.1 The Link Between the Sulphur and Organic Carbon Cycles
				3.1.1 Isotopic Evidence for the Abiotic Sulphurization Pathway of Sedimentary Organic Matter
			3.2 Mechanism of Abiotic Sulphurization
			3.3 Timing of Abiotic Sulphurization
				3.3.1 Sulphur Isotope Considerations
			3.4 Sulphurization as OM Preservation Mechanism
			3.5 Other Possible Sources for Sedimentary Organic Sulphur
				3.5.1 Volatile Organic Sulphur Compounds (VOSC) as a Possible Source to Sedimentary Organic Sulphur
				3.5.2 Refractory Biotic Organic Sulphur Compounds in the Ocean Possible Abiotic Sulphurization of Dissolved and Particulate Or...
			3.6 The Formation and Structural Modifications of Sedimentary OSC During Catagenesis
		4 Application of Organic Sulphur Compounds in Paleoenvironmental Research
			4.1 n-Alkanes
			4.2 Long-Chain C37-C39 Alkenes and Alkenones
			4.3 Phytol-Derived and Phytol-Related Isoprenoids
			4.4 Highly Branched Isoprenoids (HBIs) and Their Sulphur-Containing Derivatives
			4.5 Steroids
			4.6 Hopanoids
			4.7 Carotenoids
			4.8 Porphyrins
			4.9 Polyprenoid Sulphides
			4.10 Carbohydrates
		5 Summary
			5.1 Future Directions
		References
	15 History of Life from the Hydrocarbon Fossil Record
		1 Introduction
		2 Evidence for the Earliest Life on Earth
		3 Methanogenic Archaea in the Archean
		4 Purple Sulfur Bacteria and the Oldest Syngenetic Biomarkers
		5 Cyanobacteria and the Great Oxidation Event
		6 Early Eukarya and Steranes
		7 The Diversification of Eukarya
		8 Rise of the Animals
		9 Gloeocapsomorpha prisca Dominates the Ordovician
		10 Higher Land Plants
		11 Biomarkers of the Great Dying
		12 Diatoms, 23,24-Dimethylcholestanes, and HBIs
		13 Glycerol Dialkyl Glycerol Tetraether (GDGTs)
		14 Phytoplankton Alkenones
		15 C30-C37 Botryococcene Derivatives
		16 Research Needs
		Appendix
		References
	16 Phospholipids as Life Markers in Geological Habitats
		1 Introduction
		2 The Life Marker Concept
		3 Methods
			3.1 Lipid Extraction
			3.2 Extract Column Fractionation
			3.3 Detection of Phospholipids Using HPLC-MS
			3.4 Detection of Phospholipid Fatty Acids (PLFAs) and Phospholipid Ethers (PLELs) Using GC-MS
			3.5 Determination of Phospholipid Fatty Acid Structures
		4 Applications of Phospholipid Biomarkers in Geoscience Research
			4.1 Presence and Abundance of Microbial Life in Natural Habitats
			4.2 Taxonomic Information from PLFAs
			4.3 Membrane Adaptation to Environmental Conditions
			4.4 Monitoring of Microbial Life Over Time and Space
		5 Research Needs
		References
	17 Formation of Organic-Rich Sediments and Sedimentary Rocks
		1 Introduction
		2 Depositional Settings
			2.1 The Sea
			2.2 Lakes
			2.3 Rivers and Peats
		3 Geochemical Transformations in Young Sediments
		4 Assessment of Organic Matter in Sedimentary Rocks
		5 Research Needs
		References
	18 Thermogenic Formation of Hydrocarbons in Sedimentary Basins
		1 Introduction
		2 Basic Mechanisms and Driving Forces for Thermogenic Petroleum Formation in Time and Space
		3 Classical and Novel Analytical Methods to Investigate Thermogenic Petroleum Formation
			3.1 Optical Microscopy
			3.2 Elemental Analysis
			3.3 Pyrolysis
				3.3.1 Open-System Pyrolysis
				3.3.2 Closed-System Pyrolysis
		4 Research Needs
		References
	19 Oil and Gas Shales
		1 Introduction
			1.1 What Is Shale Gas?
			1.2 What Is Shale Oil?
			1.3 The Organic Carbon Cycle
			1.4 Investigative Tools at Our Disposal
			1.5 Factors Governing Shale Prospectivity
		2 Original Organic Matter in Shales
			2.1 Depositional Environment
			2.2 Under the Microscope
			2.3 Building Blocks in Organic Macromolecules
			2.4 Generating Potentials
		3 Conversion
			3.1 Primary Cracking of Kerogen and Bitumen
			3.2 Secondary Cracking of Oil
			3.3 Role of Catalysis
			3.4 Radiolysis Effects
			3.5 Maturity Parameters
			3.6 Mass Balance Modelling
		4 Retention
			4.1 Shale Porosity and Kerogen Swelling
			4.2 Quantification of Precursors and Retained Products
		5 Production Characteristics
			5.1 Recognition of Sweet Spots Within Heterogeneous Sequences
			5.2 Rapid Insight into In-Situ Physical Properties of Fluids
			5.3 Fractionation During Production: Insights from PVT Modelling
		6 Research Needs for Unconventional Resource Assessments
		References
	20 Hydrothermal Petroleum
		1 Introduction
		2 Analytical Methods
		3 Geological Locales with Hydrothermal Petroleum
			3.1 Sediment-Covered Marine Systems
				3.1.1 Guaymas Basin, Gulf of California
				3.1.2 Northeastern Pacific (Escanaba Trough and Middle Valley)
				3.1.3 Other Sediment-Covered Systems
			3.2 Bare Rock Hydrothermal Systems
				3.2.1 East Pacific Rise (13N and 21N)
				3.2.2 Mid-Atlantic Ridge (TAG Area 26N)
			3.3 Continental Systems
		4 Nature and Alteration of Organic Matter in Hydrothermal Systems
			4.1 Organic Matter Alteration by Hydrothermal Processes
			4.2 Composition of Hydrothermal Petroleum
		5 Fluid Interactions
		6 Hydrothermal Petroleum Expulsion/Extraction/Migration
		7 Implications
			7.1 Petroleum Resources
			7.2 Mineral Deposits
			7.3 Hydrothermal Organic Synthesis
		8 Summary
		References
	21 Environmental and Economic Implications of the Biogeochemistry of Oil Sands Bitumen
		1 Introduction
		2 Biodegradation Systematics
		3 Extended Oil Sands Bitumen Compositional Analysis
			3.1 Compositional Continuum
			3.2 Asphaltenes
			3.3 Other Non-hydrocarbon Compounds in Bitumens
		4 Environmental Implications of Oil Sands Bitumen Biogeochemistry
		5 Research Needs
		References
	22 Secondary Microbial Gas
		1 Introduction
		2 Formation of Secondary Microbial Gas
		3 Recognition of Secondary Microbial Gas in Natural Environments
		4 Global Occurrences of Secondary Microbial Gas in Petroleum Accumulations
		5 Volumetric Significance of Secondary Microbial Gas
		6 Research Needs
		References
	23 Geological, Geochemical, and Microbial Factors Affecting Coalbed Methane
		1 Introduction
		2 Geology of Coal and CBM
			2.1 Characterization and Classification of Coal
			2.2 Coal as a CBM Reservoir
			2.3 Geochemical Factors of CBM: Stable Isotope Analysis
		3 Microbial Ecology of Coalbeds
			3.1 Overview of Anaerobic Degradation of Organic Matter
			3.2 Microbial Ecology of Deep Coalbeds
			3.3 Microbial Coal Bioconversion Pathways
		4 Field Trial Applications of Enhanced Biogenic CBM
		5 Future Research
		6 Cross-References
		References
	24 Gas Hydrates as an Unconventional Hydrocarbon Resource
		1 Introduction
		2 Methane Hydrate Formation in Marine Sediments
			2.1 Thermodynamic Controls on Gas Hydrate Stability
			2.2 Microbial Methane Formation
			2.3 Methane Hydrate Formation in Marine Sediments
		3 Gas Production from Hydrate-Bearing Sediments
		4 Research Needs
		References
Part IV: Hydrocarbons and Lipids in the Environment
	25 The Biogeochemical Methane Cycle
		1 Introduction
		2 Biogeochemical Process of Microbial Methane Formation
		3 Microbial Methane in Marine Environments
		4 Microbial Methane in Freshwater and Terrestrial Environments
		5 Microbial Methane in Special Environments
		6 Methane Oxidation
			6.1 Biological Methane Oxidation
			6.2 Aerobic Methane Oxidation
			6.3 Anaerobic Oxidation of Methane (AOM)
		7 Atmospheric Methane
		8 Summary
		References
	26 Marine Cold Seeps: Background and Recent Advances
		1 Introduction
		2 Seeps at Active Plate Margins
			2.1 Oceanic Plate: Continental Plate Convergence
			2.2 Oceanic Plate: Oceanic Plate Convergence
			2.3 Strike-Slip Faults, Transform Plate Margins, and Shear Zones
		3 Seeps at Passive Continental Margins
		4 Seep Footprints
			4.1 Imaging by Hydro- and Geo-acoustic Tools
			4.2 Hydrocarbon-Metazoan-Microbe-Mineral Association
				4.2.1 Biota Sustained by Anoxic Oxidation of Methane (AOM)
				4.2.2 AOM Stimulated by Metal Oxide Reduction
				4.2.3 Biomarkers
			4.3 Authigenic Carbonates
				4.3.1 Stable Isotopes and Mineralogy
				4.3.2 Age Determination
					Tales of Two Chimneys
			4.4 Fluid-Sediment Interaction
				4.4.1 Gas Hydrate Water
				4.4.2 Clay Dehydration
		5 Unique Seep Settings
			5.1 Gulf of Mexico
			5.2 Mediterranean Sea
			5.3 Black Sea
		6 Research Needs
			6.1 Budgets of Volatile Emissions from Seeps and Retention of Carbon as Authigenic Carbonates
			6.2 Fossilization of Microbial Structures Involved in AOM
			6.3 Elusive Carbonates from Serpentinization at Subducting Margins
		References
	27 Mud Volcano Biogeochemistry
		1 Introduction
		2 Hydrocarbon Emissions
		3 Geochemical Forcing
		4 Research Needs
		References
	28 Methane Carbon Cycling in the Past: Insights from Hydrocarbon and Lipid Biomarkers
		1 Introduction: Methane Sources and Sinks
			1.1 Methane Sources
				1.1.1 Methanogenesis
				1.1.2 Other Biologically Influenced Methane Sources
			1.2 Abiotic Methane Sources
		2 Methane Sinks
			2.1 Aerobic Oxidation of Methane
			2.2 Anaerobic Oxidation of Methane
			2.3 Major Abiotic Methane Sinks
		3 Lipid Biomarkers for the Aerobic Oxidation of Methane
			3.1 Biomarkers for Organisms Involved in Aerobic Methanotrophy
			3.2 Tracing Aerobic Methanotrophy in Ancient Environments
		4 Lipid Biomarkers for the Anaerobic Oxidation of Methane (AOM)
			4.1 Biomarkers for Organisms Involved in AOM
			4.2 Tracing AOM in Ancient Environments
		5 Research Needs
		References
	29 Chemistry of Volatile Organic Compounds in the Atmosphere
		1 Sources of VOCs in the Atmosphere
		2 Sinks of VOCs in the Atmosphere
			2.1 Degradation of Atmospheric Alkanes
			2.2 Degradation of Atmospheric Alkenes
			2.3 Degradation of Atmospheric Aromatic VOCs
			2.4 Degradation of Atmospheric OVOCs
		3 Research Needs
		References
			Further Reading
	30 Organic Matter in the Hydrosphere
		1 Introduction
		2 Terrestrial Surface Water Systems
			2.1 Transfer and Transport Processes Affecting the Residence of Organic Matter in Rivers and Lakes
			2.2 Natural Organic Substances
			2.3 Anthropogenic Organic Contamination
		3 Groundwater
			3.1 Influence of Redox Conditions on Organic Matter Quality in Groundwater
			3.2 Natural Organic Substances
			3.3 Anthropogenic Organic Contamination
		4 Marine Environment
			4.1 Occurrence and Fate of Organic Compounds in the Marine Environment
			4.2 Natural Organic Substances
			4.3 Anthropogenic Organic Contamination
		5 Research Needs
		References
	31 Lessons from the 2010 Deepwater Horizon Accident in the Gulf of Mexico
		1 Introduction
		2 Lesson 1. Marine Oil Biodegradation Like All Politics Is Local and DWH Had Many Unique Aspects
		3 Lesson 2. Oil in the Water Column and in Coastal Sediments Biodegraded Faster Than Expected
		4 Lesson 3. Long-Term Adaption to Natural Seeps Played an Important Role in DWH Oil Biodegradation
		5 Lesson 4. Jetting and Dispersants at the Well Head Increased Oil Biodegradation
		6 Lesson 5. Comparisons of DWH with Exxon Valdez Oil Spill for Oil Biodegradation Were Not Appropriate
		7 Lesson 6. Models for DWH Were Inappropriate at First
		8 Lesson 7. Cometabolic Oil Biodegradation May Be Important in Deep Marine Basins
		9 Lesson 8. Blooms of Oil Degraders in the Deep Led to a Temporal Succession of Other Bacterial Communities with Unknown Effec...
		10 Lesson 9. Molecular Techniques Led to a More Thorough Understanding of DWH Oil Biodegradation
		11 Lesson 10. Hydrostatic Pressure Had Little Effect on DWH Oil Biodegradation
		12 Research Needs
		References
Index