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This chapter provides a brief historical account of the success and limitations of using chemical biomarkers in aquatic ecosystems. It also introduces 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, as well as the physicochemical environment of the system wherein it exists. In some cases, redox changes in sediments have allowed for greater preservation of biomarker compounds; in well-defined laminated sediments; for example, a strong case can be made for paleo-reconstruction of past organic matter composition sources. However, many of the labile chemical biomarkers may be lost or transformed within minutes to hours of being released from the cell from processes such as bacterial and/or metazoan grazing, cell lysis, and photochemical breakdown. The role of trophic effects versus large-scale physiochemical gradients in preserving or destroying the integrity of chemical biomarkers varies greatly across different ecosystems. These effects are discussed as they relate to aquatic systems such as lakes, estuaries, and oceans.

This chapter provides a general background on the synthesis of chemical biomarkers and their association with key metabolic pathways in organisms, as related to differences in cellular structure and function across the three domains of life. It discusses photosynthesis, the dominant pathway by which biomass is synthesized. It also presents information about chemoautotrophic and microbial heterotrophic processes. The holistic view of biosynthetic pathways of chemical biomarkers provides a roadmap for other chapters in the book, where more specific details on chemical pathways are presented for each of the respective biomarker groups. While other organic geochemistry books have generally introduced the concepts of chemical biomarkers in the context of physical and chemical gradients found in natural ecosystems (e.g., anaerobic, aerobic), this book begins by examining biosynthetic pathways at the cellular level of differentiation.

This chapter provides a background on the important role technology has played in the study of chemical biomarkers, and the many advances in the field that have resulted from the development of new analytical tools. It introduces some of the classic analytical tools used in organic geochemistry, including gas chromatography-mass spectrometry (GC-MS), pyrolysis GC-MS, direct temperature-resolved MS, compound-specific isotope analysis, high-performance liquid chromatography, and nuclear magnetic resonance (NMR) spectroscopy. Additionally, characterization of dissolved organic matter (DOM) and chromophoric DOM by fluorescence, use of pulsed amperometric detector (PAD) detectors in the analysis of sugars, and capillary electrophoresis are introduced. Recent advances in the following areas are also covered: (1) analysis of polar organic compounds utilizing liquid chromatography mass spectrometry, (2) multidimensional NMR, and (3) Fourier transform ion cyclotron resonance MS.