Rivers are the primary link between terrestrial and marine carbon reservoirs. Dissolved organic matter (DOM) contributes the majority of carbon flux between these environments. Understanding the influence of source, availability and transformations of dissolved organic carbon (DOC) in rivers and coastal ocean systems is important to determine the fate of DOM in the marine environment. Coupled microbial-photochemical incubations were used to analyze microbial and photochemical decomposition of plant leachates and to investigate DOM cycling in the Sacramento-San Joaquin River Delta/San Francisco Bay estuary. A wide range of chemical and optical parameters were tracked during coupled incubations including absorbance, fluorescence, enantiomeric amino acids, and neutral sugars measurements. Vascular plant leachates were characterized by high neutral sugar yields and low amino acid yields with variable THAA and THNS composition. Biomarkers that most accurately tracked vascular plant DOM and microbial DOM during coupled incubations were selected to apply to seasonal transects collected from the Sacramento-San Joaquin River Delta and San Francisco Bay, California. Enantiomeric amino acids and neutral sugars were used to investigate the composition and bioavailability of riverine DOM in this natural system. Biochemical trends in the Delta-Bay system were influenced by source inputs, wetlands, and environmental processes. Differences in DOM composition and concentration related to differences in regions, highlighting heterogenetic inputs, hydrology of the system, and in situ production of DOM. Furthermore, terrestrial DOM was already extensively degraded prior to entering the Delta and was largely refractory throughout the Bay. Neutral sugar yields in the transect were used to determine a median of ~10% terrestrial DOC labile fraction, and amino acid yields were used to determine a median of 5% in situ DOM labile fraction. Median total labile fraction in the Delta and Bay was 21% and was influenced by hydrological conditions in the estuary. Our study demonstrated the complexity of river delta and estuarine systems integrating complex varying sources and decomposition trends connected to seasons and flow regime. Bay systems were recognized as efficient filters of terrestrial DOM limiting its flux to the ocean and exerting a major control on air-sea CO2 fluxes, acidification and nutrient budgets in the estuary.
