Benthic fluxes in San Francisco Bay

Measurements of benthic fluxes have been made on four occasions between February 1980 and February 1981 at a channel station and a shoal station in South San Francisco Bay, using in situ flux chambers. On each occasion replicate measurements of easily measured substances such as radon, oxygen, ammonia, and silica showed a variability (±1) of 30% or more over distances of a few meters to tens of meters, presumably due to spatial heterogeneity in the benthic community. Fluxes of radon were greater at the shoal station than at the channel station because of greater macrofaunal irrigation at the former, but showed little seasonal variability at either station. At both stations fluxes of oxygen, carbon dioxide, ammonia, and silica were largest following the spring bloom. Fluxes measured during different seasons ranged over factors of 2–3, 3, 4–5, and 3–10 (respectively), due to variations in phytoplankton productivity and temperature. Fluxes of oxygen and carbon dioxide were greater at the shoal station than at the channel station because the net phytoplankton productivity is greater there and the organic matter produced must be rapidly incorporated in the sediment column. Fluxes of silica were greater at the shoal station, probably because of the greater irrigation rates there. N + N (nitrate + nitrite) fluxes were variable in magnitude and in sign. Phosphate fluxes were too small to measure accurately. Alkalinity fluxes were similar at the two stations and are attributed primarily to carbonate dissolution at the shoal station and to sulfate reduction at the channel station. The estimated average fluxes into South Bay, based on results from these two stations over the course of a year, are (in mmol m^–2 d^–1): O₂ = –27 ± 6; TCO₂ = 23 ± 6; Alkalinity = 9 ± 2; N + N = –0.3 ± 0.5; NH₃ = 1.4 ± 0.2; PO₄ = 0.1 ± 0.4; Si = 5.6 ± 1.1. These fluxes are comparable in magnitude to those in other temperate estuaries with similar productivity, although the seasonal variability is smaller, probably because the annual temperature range in San Francisco Bay is smaller.Budgets constructed for South San Francisco Bay show that large fractions of the net annual productivity of carbon (about 90%) and silica (about 65%) are recycled by the benthos. Substantial rates of simultaneous nitrification and denitrification must occur in shoal areas, apparently resulting in conversion to N₂ of 55% of the particulate nitrogen reaching the sediments. In shoal areas, benthic fluxes can replace the water column standing stocks of ammonia in 2–6 days and silica in 17–34 days, indicating the importance of benthic fluxes in the maintenance of productivity.Pore water profiles of nutrients and Rn-222 show that macrofaunal irrigation is extremely important in transport of silica, ammonia, and alkalinity. Calculations of benthic fluxes from these profiles are less accurate, but yield results consistent with chamber measurements and indicate that most of the NH₃, SiO₂, and alkalinity fluxes are sustained by reactions occurring throughout the upper 20–40 cm of the sediment column. In contrast, O₂, CO₂, and N + N fluxes must be dominated by reactions occurring within the upper one cm of the sediment-water interface. While most data support the statements made above, a few flux measurements are contradictory and demonstrate the complexity of benthic exchange.     

Gas exchange in San Francisco Bay

Gas exchange across the air-water interface is one of the most important processes controlling the concentrations of dissolved gases in estuarine systems. A brief review of principles and equations to predict gas exchange indicates that both current shear and wind shear are possible sources of turbulence for controlling gas exchange rates in estuaries. Rates of exchange determined by constructing a mass balance for radon-222 indicate that wind shear is dominant in San Francisco Bay. Because many estuaries have wind shear and current speeds comparable to this system, this conclusion may be true for other systems as well. A compilation of gas exchange rates measured in San Francisco Bay with those for other wind-dominated systems updates previous compilations and yields an equation for predicting gas exchange: K _l = 34.6 R _v (D_m20)^1/2 (U₁₀)^1.5 where R is the ratio of the kinematic viscosity of pure water at 20° C to the kinematic viscosity of water at the measured temperature and salinity, D_m20 is the molecular diffusivity of the gas of interest at 20°C in cm² s^–1, U₁₀ is the wind speed at 10 meters above the surface in m s^–1, and K_L is the liquid phase gas transfer coefficient in m d^–1. This relationship fits the available field data within 20% for wind speeds between 3 and 12 m s^–1. It is used to show that the residence time of dissolved oxygen in San Francisco Bay should range from 2 days during windy summer periods to as much as 15 days during calm winter periods. Because these times are short compared to time constants for other processes controlling oxygen distribution in this system, dissolved oxygen concentrations in San Francisco Bay are usually near atmospheric equilibrium. Other systems, such as Chesapeake Bay, may differ. There, despite ample air-water gas exchange rates, some bottom waters become anoxic during summer months due to slow vertical mixing.