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A comprehensive carbon budget was constructed to quantify carbon flows through the freshwater-marine continuum of a temperate, microtidal estuary. We performed coordinated measurements of dissolved inorganic carbon and total organic carbon fluxes to resolve spatial variability between and along the channel and shoals and diel variability across the entire estuary for 2 yr. Net ecosystem metabolism (NEM) was the most significant control on carbon flow within estuary regions. However, metabolic rates were spatially coupled such that counteracting fluxes across the channel-shoal gradient or along the river-ocean gradient resulted in system-wide NEM that was closely in balance (–3.0 ± 3.3 to 1.1 ± 4.4 molC m−2 yr−1). Similarly, large diel and seasonal variability in air–water CO2 fluxes were observed during 72 spatial surveys, but these short-term variations generally cancelled out when aggregated to annual budget terms. Although atmospheric exchanges were small (–0.2 ± 0.1 to 2.0 ± 0.4 molC m−2 yr−1), they were subject to large errors (± 4 molC m−2 yr−1) if diel variability was neglected. Internal mechanisms that maintained balanced carbon flows were strongly impacted by river discharge and were only apparent by separately quantifying channel and shoal fluxes. Notably, metabolic responses of the shoal to river forcing outweighed the responses of the channel, and the net impact was contrary to prior relationships derived from synthesis of lower-resolution carbon budgets. Our budget demonstrates that resolution of carbon fluxes at appropriate scales, including channel-shoal and diel variability, is critical to characterizing ecosystem function and the fate of carbon within the river-ocean continuum.

Physical-biological coupling helps structure aquatic communities, yet physical factors can vary widely across large, biogeographic scales. The eastern oyster (Crassostrea virginica) is an ecosystem engineer that creates intertidal reefs, filters water, promotes denitrification, stabilizes shorelines, and provides habitat throughout the inner waters of the U.S. South Atlantic Bight (SAB). We quantified physical variables (temperature, salinity, duration and depth of water inundation), oyster reef properties (slope, vertical relief), and oyster recruitment, density, and biomass over a 1500 km scale across the SAB for one year. All oyster-level and many reef-level variables exhibited unimodal patterns with latitude that peaked in Georgia and South Carolina estuaries. Of the physical variables, salinity and duration of water inundation over reefs were similar across all sites, and temperature declined linearly with increasing latitude, except during summer when it had no relationship with latitude. Depth of water inundation over reefs was the only physical variable with a prominent unimodal distribution that may explain the oyster’s biological responses. Similar durations of water inundation across all reefs coupled with higher water depths in the mid-latitude sites collectively indicate that these sites experience higher flow velocity, energy and net water volume delivery per unit time. The resultant higher accumulation of oyster biomass and heightened reef structure in areas of higher tidal energy emphasize that the physical forcing of the SAB (especially large cross-shelf gradients in tidal amplification) affects the biology of the eastern oyster, including its reef properties, with potential implications for community structure and ecosystem service delivery across a biogeographic scale.

We hypothesized that mats of a nonnative macroalga, Gracilaria vermiculophylla, which is often found incorporated several centimeters into intertidal mudflat sediments, would increase net denitrification rates relative to bare sediments. At moderate densities (, 40 g dry weight [dry wt] m22), net denitrification rates in June (182.37 6 16.87 mmol N-N2 m22 h21), July (213.19 6 16.30 mmol N-N2 m22 h21), and September (124.82 6 11.17 mmol N-N2 m22 h21) were higher than rates previously documented with macroalgal mats. Compared with rates from bare sediment in June (25.48 6 15.09 mmol N-N2 m22 h21) and September (46.47 6 15.79 mmol N-N2 m22 h21), net denitrification was significantly higher when G. vermiculophylla was present. Rates measured on bare sediment in July (254.81 6 19.86 mmol N-N2 m22 h21) were not significantly different from G. vermiculophylla counterparts, most likely because of highly reduced conditions in G. vermiculophylla cores, which could have limited nitrification. July incubations also demonstrate that at higher densities (, 120 g dry wt m22 G. vermiculophylla), denitrification rates can drop, suggesting a potential biomass threshold for macroalgal enhancement of denitrification.

Phytoplankton diagnostic photopigments in near-surface waters (≈0.5 m) were identified and quantified by high-performance liquid chromatography beginning in April 1994 in the Neuse River Estuary and in October 1999 in the Pamlico Sound, North Carolina. Photopigment concentrations were analyzed using ChemTax to determine the class-specific biomass of the dominant phytoplankton groups. Long-term annual and seasonal trends in phytoplankton biomass and composition were characterized along the river-estuarine continuum and compared to river flow rates, which were variable because of droughts, uncharacteristic seasonal rainfall patterns, and, since 1996, an increase in the frequency of tropical storms and hurricanes. We tested the hypothesis that temporal and spatial patterns of phytoplankton biomass and composition were largely controlled by changes in river flow rate through associated changes in salinity and residence time or through physical transport and advection of phytoplankton classes with river flow along the estuary. Significant interannual, seasonal, and spatial variability in phytoplankton biomass and composition was observed and coincided with variability in river flow rates. The five dominant phytoplankton classes (Chlorophyceae, Cryptophyceae, Cyanobacteria, Bacillariophyceae, and Dinophyceae) were physically displaced downstream during periods of elevated river flow. Dinoflagellates were reduced in abundance during high flow conditions, especially in the upper Neuse River Estuary. The abundance of cyanobacteria was also reduced throughout the system during elevated river flow conditions, although chlorophytes were more abundant. Changes in hydrology can be a useful indicator of seasonal phytoplankton distribution and higher level compositional changes along hydrologic gradients in these and similar systems.