Date Awarded


Document Type


Degree Name

Doctor of Philosophy (Ph.D.)


Virginia Institute of Marine Science


Elizabeth A. Canuel


Determining organic matter sources and their availability to higher organisms is essential to better understanding the link between organic matter (OM) dynamics and secondary production, particularly in highly-disturbed river-delta systems. The San Francisco Bay and its associated Delta, is one of the most modified aquatic systems, and is the focus of an ongoing restoration effort. Particulate organic matter (POM) and surficial sediments were collected in the Sacramento-San Joaquin River Delta, CA to document temporal and spatial variations in biochemical, (total protein, carbohydrate and lipid), lipid biomarker, and total hydrolysable amino acid (THAA) composition. Sources, composition and nutritional quality of OM was assessed at ten sites representing diverse sub-habitats including each of the two major rivers, rehabilitated shallow-water, open water and natural marsh habitats. Biochemical and biomarker results showed that terrigenous OM and phytoplankton were the primary sources of POM in the Sacramento and San Joaquin Rivers. On average, the Sacramento River exhibited lower quality POM than the San Joaquin River, due to lower contributions from phytoplankton. Winter periods were characterized by increased delivery of highly degraded, low-quality POM, resulting from higher freshwater flows. In contrast, low flow periods were characterized by phytoplankton blooms and higher-quality POM, particularly in the San Joaquin River during summer. Phytoplankton, submerged macrophytes and terrigenous OM were the dominant sources in SPM and sediments at all shallow-water sites, but to differing degrees. Between-site differences are likely due to variations in the frequency and size of phytoplankton and macrophyte blooms, hydrodynamics and grazing pressures. Shallow-water sites exhibited higher concentrations of biomarkers representing phytoplankton/algal sources than river sites, indicating POM of higher nutritional quality. THAA-based degradation indices (DI) were used to characterize habitats in terms of organic matter degradation state. DI indicated that shallow-water habitats were characterized by less degraded POM than river sites, corroborating lipid biomarker analyses. This study demonstrates the value of using a multiple biomarker approach in complex systems such as the Delta. This approach, incorporated into a larger study of the system's biology, hydrology and chemistry provides a useful strategy for addressing management issues in complex deltaic-estuarine systems.



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