Cover

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Title Page, copyright Page, Dedication, Quote

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Contents

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p. ix

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Preface

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pp. xi-xviii

Due to the complexity of organic matter sources in aquatic systems, the application of chemical biomarkers has become widespread in limnology and oceanography. We define biomarker molecules in this book as compounds that characterize certain biotic sources and selectively retain their source information, even after stages of decomposition and diagenesis (after Meyers, 2003). Hence, the term biomarker molecule should not be confused with the terms commonly used by ecotoxicologists or molecular biologists...

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Acknowledgments

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p. xix

Over the past two years it has taken to write this book, many people have helped along the way, and we are eternally grateful for their input. We thank our friends and colleagues for sharing new and unpublished work with us as well as their support during the writing and editing phases. Their positive comments and encouragement were a great help. In particular, E. Canuel would like to acknowledge the importance of the Gordon Research Conference on Organic Geochemistry for providing a stimulating, intellectual climate in which new ideas can be exchanged freely and warm friendships developed and nurtured. We would...

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1. Metabolic Synthesis

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pp. 22-39

In this chapter, we begin by providing a brief background on the classification of organisms. We then provide a general background on the synthesis of chemical biomarkers and their association with key metabolic pathways in organisms, as they relate to differences in cellular structure and function across the three systematic domains of life. We also discuss photosynthesis, the dominant pathway by which biomass is synthesized, and provide information about chemoautotrophic and microbial heterotrophic processes. This holistic view of biosynthetic pathways of chemical biomarkers provides a roadmap for other chapters in this...

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2. Chemical Biomarker Applications to Ecology and Paleoecology

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pp. 40-50

In this chapter, we provide a brief historical account of the successes and limitations of using chemical biomarkers in aquatic ecosystems. We also introduce the general concepts of chemical biomarkers as they relate to global biogeochemical cycling. The application of chemical biomarkers in modern and/or ancient ecosystems is largely a function of the inherent structure and stability of the molecule in question, as well as the physicochemical environment and depositional conditions of the study system. In some cases...

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3. Stable Isotopes and Radiocarbon

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pp. 51-69

Isotopes are widely used tools in the fields of ecology, geochemistry, limnology and oceanography, providing information about the sources and cycling of (1) bulk organic matter pools (dissolved, colloidal, particulate, and sedimentary), (2) biochemical classes, and (3) individual biomarker compounds. Stable isotope studies in aquatic geochemistry have incorporated the use of a variety of light, biogenic elements, including hydrogen, carbon, nitrogen, oxygen, and sulfur. The use of stable isotopes has contributed...

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4. Analytical Chemical Methods and Instrumentation

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pp. 70-99

Sampling and analytical tools are at the heart of the field of organic geochemistry, and technology has advanced the field throughout its history. This chapter reviews some of the primary analytical methods used by organic geochemists as well as new and evolving tools that show promise for their application to aquatic organic geochemistry. The ability to detect organic compounds in environmental samples at lower concentrations, as well as separate and characterize compounds of higher mass and complexity, has increased dramatically in recent decades. Overall, advances in our ability to characterize organic matter in environmental...

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5. Carbohydrates: Neutral and Minor Sugars

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pp. 100-118

Carbohydrates are important structural and storage molecules and are critical in the metabolism of terrestrial and aquatic organisms (Aspinall, 1970). The general chemical formula for carbohydrates is (CH2O)n. These compounds can be defined more specifically as polyhydroxyl aldehydes and ketones— or compounds that can be hydrolyzed to them.

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6. Proteins: Amino Acids and Amines

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pp. 119-147

Proteins make up approximately 50% of organic matter (Romankevich, 1984) and contain about 85% of the organic N in marine organisms (Billen, 1984). Peptides and proteins comprise an important fraction of the particulate organic carbon (POC) (13 to 37%) and nitrogen (PON) (30 to 81%) (Cowie et al., 1992; Nguyen and Harvey, 1994; Van Mooy et al., 2002), as well as dissolved organic nitrogen (DON) (5–20%) and carbon (DOC) (3–4%) in oceanic and coastal waters (Sharp, 1983). Other estimates show that acid-hydrolyzable, proteinaceous material accounts for as much as 50% of oceanic PON (Tanoue...

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7. Nucleic Acids and Molecular Tools

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pp. 148-164

In this chapter, we examine molecular tools based on nucleic acids, polymers of the nucleotides ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Topics include the biogeochemical significance of nucleic acids as a pool of organic nitrogen and phosphorus, as well as recent work characterizing the stable and radiocarbon isotopic signatures of nucleic acids to identify the sources and age of organic matter supporting heterotrophic bacteria. In addition to a discussion of nucleic acids as a class of biochemicals, we will...

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8. Lipids: Fatty Acids

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pp. 165-189

Lipids are operationally defined as all substances produced by organisms that are effectively insoluble in water but extractable by solvents (e.g., chloroform, hexane, toluene, and acetone). This broad definition includes a wide range of compounds, such as pigments, fats, waxes, steroids, and phospholipids. Alternatively, lipids may be more narrowly defined as fats, waxes, steroids, and phospholipids. This second definition relates specifically to their biochemical function in terms of energy storage rather than their hydrophobicity, which allows their extraction into organic solvents....

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9. Isoprenoid Lipids: Steroids, Hopanoids, and Triterpenoids

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pp. 190-205

Isoprenoids are a diverse class of naturally occurring organic compounds that are classified as lipids. This class of compounds has been the focus of studies in physiology, biochemistry, and natural products chemistry for 150 years (Patterson and Nes, 1991). Compounds within this class are derived from the five-carbon isoprene unit and many isoprenoids are multicyclic structures (fig. 9.1) that differ from one another both in their basic carbon skeletons as well as their functional group composition. Isoprenoids are classified according...

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10. Lipids: Hydrocarbons

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pp. 206-227

In this chapter we focus on naturally produced hydrocarbons, while hydrocarbons derived from anthropogenic activities are covered later in this book (see chapter 14). Hydrocarbons are one of the most widely used classes of biomarkers and have been applied to geochemical studies conducted over a range of timescales, from contemporary ecosystems to ancient sediments and rocks. In this chapter, we discuss traditional biomarkers such as aliphatic and cyclic hydrocarbons, which have been successfully used to distinguis...

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11. Lipids: Alkenones, Polar Lipids, and Ether Lipids

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pp. 228-241

Alkenones are long-chain (C35 to C40) di-, tri-, and tetra-unsaturated ketones (fig. 11.1). These compounds are produced by a restricted number of species of haptophyte algae (e.g., Emiliania huxleyi and Gephyrocapsa oceanica) that live over a wide temperature range (2–29◦C) in surface waters of the ocean. It is thought that these organisms are able to live under such a large temperature range because they are able to regulate the level to which their lipids are unsaturated, but the function of this class of lipids is...

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12. Photosynthetic Pigments: Chlorophylls, Carotenoids, and Phycobilins

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pp. 242-268

The primary photosynthetic pigments used in absorbing photosynthetically active radiation (PAR) are chlorophylls, carotenoids, and phycobilins—with chlorophyll representing the dominant photosynthetic pigment (Emerson and Arnold, 1932a,b; Clayton, 1971, 1980). Although a greater amount of chlorophyll is found on land, 75% of the global turnover (ca. 109 Mgyr−1) occurs in oceans, lakes, and rivers/estuaries (Brown et al., 1991; Jeffrey and Mantoura, 1997). All of the light-harvesting pigments...

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13. Lignins, Cutins, and Suberins

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pp. 269-287

Lignin has proven to be a useful chemical biomarker for tracing vascular-plant inputs to aquatic ecosystems (Gardner and Menzel, 1974; Hedges and Parker, 1976; Goñi and Hedges, 1992; Hedges et al., 1997; Bianchi et al., 1999b, 2002, 2007). Cellulose, hemicellulose, and lignin generally make up >75% of the biomass of woody plant materials (Sjöström, 1981). Lignins are a group of macromolecular heteropolymers (600–1000 kDa) found in the cell wall of vascular plants that are made up of hree-...

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14. Anthropogenic Markers

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pp. 288-307

This chapter will introduce readers to anthropogenic compounds representing a spectrum of sources, functional group compositions, physical behaviors, and environmental fates. We will draw from earlier sections of this book to discuss how the processes that control the behavior of naturally occurring organic compounds are similar to those influencing anthropogenic compounds and can aid in developing models to predict the behavior of contaminants in the environment. We will also introduce readers to the use of anthropogenic compounds as biomarkers (anthropogenic markers). Despite their often-deleterious consequences..

Appendix I. Atomic Weights of Elements

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pp. 308-311

Appendix II. Useful SI Units and Conversion Factors

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pp. 312-313

Appendix III. Physical and Chemical Constants

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pp. 314-315

Glossary

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pp. 316-329

Bibliography

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pp. 330-405

Index

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pp. 406-417