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Chemical Biomarkers in Aquatic Ecosystems

Chemical Biomarkers in Aquatic Ecosystems

Copyright Date: 2011
Pages: 392
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  • Book Info
    Chemical Biomarkers in Aquatic Ecosystems
    Book Description:

    This textbook provides a unique and thorough look at the application of chemical biomarkers to aquatic ecosystems. Defining a chemical biomarker as a compound that can be linked to particular sources of organic matter identified in the sediment record, the book indicates that the application of these biomarkers for an understanding of aquatic ecosystems consists of a biogeochemical approach that has been quite successful but underused. This book offers a wide-ranging guide to the broad diversity of these chemical biomarkers, is the first to be structured around the compounds themselves, and examines them in a connected and comprehensive way.

    This timely book is appropriate for advanced undergraduate and graduate students seeking training in this area; researchers in biochemistry, organic geochemistry, and biogeochemistry; researchers working on aspects of organic cycling in aquatic ecosystems; and paleoceanographers, petroleum geologists, and ecologists.

    Provides a guide to the broad diversity of chemical biomarkers in aquatic environmentsThe first textbook to be structured around the compounds themselvesDescribes the structure, biochemical synthesis, analysis, and reactivity of each class of biomarkersOffers a selection of relevant applications to aquatic systems, including lakes, rivers, estuaries, oceans, and paleoenvironmentsDemonstrates the utility of using organic molecules as tracers of processes occurring in aquatic ecosystems, both modern and ancient

    eISBN: 978-1-4008-3910-0
    Subjects: Ecology & Evolutionary Biology, Chemistry, Geology, Aquatic Sciences

Table of Contents

  1. Front Matter
    (pp. i-viii)
  2. Table of Contents
    (pp. ix-x)
  3. Preface
    (pp. xi-xviii)
  4. Acknowledgments
    (pp. xix-xx)
  5. 1. Metabolic Synthesis
    (pp. 1-18)

    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 book, where more specific details on chemical pathways are...

  6. 2. Chemical Biomarker Applications to Ecology and Paleoecology
    (pp. 19-29)

    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, where preservation of biomarker compounds is enhanced, such as laminated sediments or environments with decreased oxygen exposure times, a strong case can...

  7. 3. Stable Isotopes and Radiocarbon
    (pp. 30-48)

    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 novel insights about food web structure and organic matter sources over a variety of timescales, including contemporary, historical, and geological. Stable isotopes can also be used to assess the...

  8. 4. Analytical Chemical Methods and Instrumentation
    (pp. 49-78)

    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 samples have developed in three areas:...

  9. 5. Carbohydrates: Neutral and Minor Sugars
    (pp. 79-97)

    Carbohydratesare 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 andketones—or compounds that can be hydrolyzed to them. Carbohydrates can be further divided into monosaccharides (simple sugars), disaccharides (two covalently linked monosaccharides), oligosaccharides (a few, usually 3 to 10, covalently linked monosaccharides), and polysaccharides (polymers made up of chains of mono- and disaccharides). Based on the number of carbon atoms, monosaccharides (e.g., 3, 4, 5, and 6) are commonly termed...

  10. 6. Proteins: Amino Acids and Amines
    (pp. 98-126)

    Proteinsmake 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, 1992). In sediments, proteins...

  11. 7. Nucleic Acids and Molecular Tools
    (pp. 127-143)

    In this chapter, we examine molecular tools based onnucleic 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 discuss the application of molecular genetic information to organic geochemistry. The recent combination of biomarker information and molecular genetic data...

  12. 8. Lipids: Fatty Acids
    (pp. 144-168)

    Lipidsare 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 aspigments,fats,waxes,steroids, andphospholipids. 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 theirhydrophobicity, which allows their extraction into organic solvents.

    Fatty acidsare among the most versatile classes of lipidbiomarkercompounds and this class of biomarkers has been...

  13. 9. Isoprenoid Lipids: Steroids, Hopanoids, and Triterpenoids
    (pp. 169-184)

    Isoprenoidsare 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 to both the number of isoprene units and the number of cyclic structures they contain (table 9.1; fig. 9.1). Isoprene...

  14. 10. Lipids: Hydrocarbons
    (pp. 185-206)

    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 distinguish between algal, bacterial, and terrigenous vascular plant sources of carbon in aquatic systems. We also present several classes of isoprenoid hydrocarbon biomarkers, including highly...

  15. 11. Lipids: Alkenones, Polar Lipids, and Ether Lipids
    (pp. 207-220)

    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 huxleyiandGephyrocapsa oceanica) that live over a wide temperature range (2–29ºC) 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 largely unknown. Initially, it was thought that alkenones were membrane lipids and the increased...

  16. 12. Photosynthetic Pigments: Chlorophylls, Carotenoids, and Phycobilins
    (pp. 221-247)

    The primaryphotosynthetic pigmentsused in absorbing photosynthetically active radiation (PAR) arechlorophylls,carotenoids, andphycobilins—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 are bound to proteins, making up distinct carotenoid and chlorophyll–protein complexes. These pigment–protein complexes in algae and higher plants are located in thethylakoid membraneof chloroplasts (Cohen et al., 1995)....

  17. 13. Lignins, Cutins, and Suberins
    (pp. 248-266)

    Ligninhas 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-dimensional phenylpropanoid units held together by irregular carbon–carbon and diaryl–ether linkages (Sarkanen and Ludwig, 1971; De Leeuw and Largeau, 1993)....

  18. 14. Anthropogenic Markers
    (pp. 267-286)

    This chapter will introduce readers toanthropogeniccompounds 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 to aquatic environments and the organisms living within, contaminants can serve as useful proxies for...

  19. Appendix I. Atomic Weights of Elements
    (pp. 287-290)
  20. Appendix II. Useful SI Units and Conversion Factors
    (pp. 291-292)
  21. Appendix III. Physical and Chemical Constants
    (pp. 293-294)
  22. Glossary
    (pp. 295-308)
  23. Bibliography
    (pp. 309-384)
  24. Index
    (pp. 385-396)