CHAPTER 2 • Marine Organic Geochemistry: A General Overview
49
is further oxidized to nitrate by Nitrobacter and other genera. This step also yields
energy (-17.5 kcal mor!). Energy yielded from oxidation of NH: by these chemosynthetic bacteria is used in reduction of CO2 to organic carbon.
Another sink of nitrate (besides uptake) is dissimilatory! reduction during respiration of organic matter. Nitrate is used as an electron acceptor by heterotrophic bacteria in a series of steps (Fig. 2.4). Nitrate is reduced to nitrite, nitric oxide (NO), and
then to the gases nitrous oxide (N20) and dinitrogen (N2). When the products of reduction of nitrate are gaseous, the process is called denitrification. Denitrification only
occurs at low concentrations of oxygen, mostly because the synthesis of enzymes is
repressed by the presence of O2 (Fenchel and Blackburn 1979). Denitrifying microbes
may reduce nitrate to ammonium with the intermediate production of hydroxylamine.
This pathway is thought to be minor compared with ammonium production by degradation of organic nitrogen (Valiela 1995).
2.2
Molecular Constituents of Organic Matter in the Ocean
For years, marine geochemists have attempted to infer the sources and behavior of organic
matter in the ocean on the basis of bulk parameters, such as organic carbon concentration, C/N ratios, stable carbon isotopic compositions, etc. While bulk parameters are informative, their use ignores the vast amount of information available at the molecular
level. Organisms biosynthesize organic compounds containing a wide range of organic
functional groups, many of which are specific to structural or metabolic functions
within the organisms. Many molecules have novel structures that provide organic
geochemists with a wealth of information related to the compounds' sources and, by
inference, the origin of bulk organic matter. Finally, organic chemical reactions affect
various functional groups in different ways that are diagnostic of how biogeochemical
reactions proceed. In the following section, we discuss aspects of the biogeochemistries of
important biochemical classes in the ocean, providing examples of how molecular-level
information can be used to characterize the sources and fates of organic matter as a whole.
2.2.1
Lipids
Lipids are operationally defined as substances that are practically insoluble in water
but extractable with non-polar organic solvents. After amino acids and carbohydrates,
lipids are the next most abundant biochemical in organisms. Plankton generally contain lipids equivalent to 10-60% of organic carbon (Parsons et al. 1984; Sargent and
Henderson 1986; Wakeham et al. 1997a,b), while in sediments 1% or less of OC is lipid
(e.g. Santos et al. 1994; Wakeham et al. 1997a,b). In organisms, lipids are involved in
energy storage and mobilization, membrane structure, and hormonal control of metabolic processes (Lehninger 1981). The wide variety of molecular structures of lipids
(Fig. 2.5) makes them valuable "biomarkers" for tracing sources of organic matter in
1 Dissimilatory processes do not involve cellular incorporation, only processes associated to energy
production.
49
is further oxidized to nitrate by Nitrobacter and other genera. This step also yields
energy (-17.5 kcal mor!). Energy yielded from oxidation of NH: by these chemosynthetic bacteria is used in reduction of CO2 to organic carbon.
Another sink of nitrate (besides uptake) is dissimilatory! reduction during respiration of organic matter. Nitrate is used as an electron acceptor by heterotrophic bacteria in a series of steps (Fig. 2.4). Nitrate is reduced to nitrite, nitric oxide (NO), and
then to the gases nitrous oxide (N20) and dinitrogen (N2). When the products of reduction of nitrate are gaseous, the process is called denitrification. Denitrification only
occurs at low concentrations of oxygen, mostly because the synthesis of enzymes is
repressed by the presence of O2 (Fenchel and Blackburn 1979). Denitrifying microbes
may reduce nitrate to ammonium with the intermediate production of hydroxylamine.
This pathway is thought to be minor compared with ammonium production by degradation of organic nitrogen (Valiela 1995).
2.2
Molecular Constituents of Organic Matter in the Ocean
For years, marine geochemists have attempted to infer the sources and behavior of organic
matter in the ocean on the basis of bulk parameters, such as organic carbon concentration, C/N ratios, stable carbon isotopic compositions, etc. While bulk parameters are informative, their use ignores the vast amount of information available at the molecular
level. Organisms biosynthesize organic compounds containing a wide range of organic
functional groups, many of which are specific to structural or metabolic functions
within the organisms. Many molecules have novel structures that provide organic
geochemists with a wealth of information related to the compounds' sources and, by
inference, the origin of bulk organic matter. Finally, organic chemical reactions affect
various functional groups in different ways that are diagnostic of how biogeochemical
reactions proceed. In the following section, we discuss aspects of the biogeochemistries of
important biochemical classes in the ocean, providing examples of how molecular-level
information can be used to characterize the sources and fates of organic matter as a whole.
2.2.1
Lipids
Lipids are operationally defined as substances that are practically insoluble in water
but extractable with non-polar organic solvents. After amino acids and carbohydrates,
lipids are the next most abundant biochemical in organisms. Plankton generally contain lipids equivalent to 10-60% of organic carbon (Parsons et al. 1984; Sargent and
Henderson 1986; Wakeham et al. 1997a,b), while in sediments 1% or less of OC is lipid
(e.g. Santos et al. 1994; Wakeham et al. 1997a,b). In organisms, lipids are involved in
energy storage and mobilization, membrane structure, and hormonal control of metabolic processes (Lehninger 1981). The wide variety of molecular structures of lipids
(Fig. 2.5) makes them valuable "biomarkers" for tracing sources of organic matter in
1 Dissimilatory processes do not involve cellular incorporation, only processes associated to energy
production.