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Research about San Francisco Bay

Source-linked reports with geographic coverage including San Francisco Bay.

At least 325 records · Page 18Linked to original sources
USGS1990

Remarkable invasion of San Francisco Bay (California, USA), by the Asian clam Potamocorbula amurensis. I. Introduction and dispersal

The euryhaline bivalve mollusc Potamocorbula amurensis (family Corbulidae), a native of China, Japan, and Korea, has recently appeared and become very abundant in San Francisco Bay. This clam appears to have been introduced as veliger larvae in the seawater ballast of cargo vessels. It was first collected in northern San Francisco Bay in late 1986. P, amurensis then spread throughout the estuary within 2 yr and reached densities at some sites exceeding 10 000 m -2 It lives primarily in the subtidal on all substrates (mud, sand, peat, and clay) and is found in the full range of bay salinities (< 1 to 33%). Its explosive increase in abundance and spread may result in major alterations of the San Francisco Bay estuary ecosystem. These could include changes in (1) trophic dynamics (through competition with other suspension-feeding and deposit-feeding infauna; changes in benthic community energy flow; availability of a new and abundant prey item for birds, fish, and crabs; and reduction - as a result of its filter feeding - of phytoplankton standmg stock) and (2) benthic dynamics (through inhibition and/or enhancement of infauna due to substrate destabilization; alteration of suspended sediment load of near-bottom water; and change of sediment surface redox balance). The early detection of the appearance and spread of P. amurensis in San Francisco Bay makes this one of the best documented invasions of any estuary in the world.

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USGS1989

Organic markers as source discriminants and sediment transport indicators in south San Francisco Bay, California

Sediment samples from nearshore sites in south San Francisco Bay and from streams flowing into that section of the Bay have been characterized in terms of their content of biogenic and anthropogenic molecular marker compounds. The distributions, input sources, and applicability of these compounds in determining sediment movement are discussed. By means of inspection and multivariate analysis, the compounds were grouped according to probable input sources and the sampling stations according to the relative importance of source contributions. A suite of polycyclic aromatic hydrocarbons (PAHs) dominated by pyrene, fluoranthene and phenanthrene, typical of estuarine environments worldwide, and suites of mature sterane and hopane biomarkers were found to be most suitable as background markers for the Bay. A homologous series of long-chain n-aldehydes (C12-C32) with a strong even-over-odd carbon number dominance in the higher molecular weight range and the ubiquitous n-alkanes (n-C24-C34) with a strong odd-over-even carbon number dominance were utilized as terrigenous markers. Several ratios of these terrigenous and Bay markers were calculated for each station. These ratios and the statistical indicators from the multivariate analysis point toward a strong terrigenous signal in the terminus of South Bay and indicate net directional movement of recently introduced sediment where nontidal currents had been considered to be minimal or nonexistent and tidal currents had been assumed to be dominant.

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USGS1989

Trace metal associations in the water column of South San Francisco Bay, California

Spatial distributions of copper (Cu), zinc (Zn) and cadmium (Cd) were followed along a longitudinal gradient of dissolved organic carbon (DOC) in South San Francisco Bay (herein referred to as the South Bay). Dissolved Cu, Zn and Cd concentrations ranged from 24 to 66 nM, from 20 to 107 nM and from 1·2 to 4·7 nM, respectively, in samples collected on five dates beginning with the spring phytoplankton bloom and continuing through summer,1985. Dissolved Cu and Zn concentrations varied indirectly with salinity and directly with DOC concentration which ranged from 2·1 to 4·1 mg l −1 . Available thermodynamic data strongly support the hypothesis that Cu speciation may be dominated by association with dissolved organic matter. Analogous control of Zn speciation by organic complexation was, however, not indicated in our computations. Computed free ion activity estimates for Cu, Zn and Cd were of the order of 10 −10 , 10 −8 and 10 −10 M, respectively. The availability of these metals may be among the factors regulating the growth of certain phytoplankton species within this region of the estuary. In contrast to dissolved Cu, dissolved Cd was directly related to the concentration of suspended particulate matter, suggesting a source of dissolved Cd coincident with elevated particle concentrations in the South Bay (e.g. runoff and solute desorption). Consistent with work in other estuaries, partitioning of all three trace metals onto suspended particulates was negatively correlated with salinity and positively correlated with increases in particulate organic carbon associated with the phytoplankton bloom. These results for the South Bay indicate that sorption processes influence dissolved concentrations of these trace metals, the degree of this influence varies among metals, and processes controlling metal distribution in this estuary appear to be more element-specific than spatially- or temporally-specific.

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USGS1989

Spatial and temporal variability in South San Francisco Bay (USA). I. Horizontal distributions of salinity, suspended sediments, and phytoplankton biomass and productivity

The horizontal pattern of mesoscale (1–4 km) variability in salinity was a poor predictor of mesoscale patterns in chlorophyll a , suspended particulate matter, and daily primary productivity in the South San Francisco Bay estuary during spring 1987. The tidally-averaged salinity distribution varied over weekly time scales, reflecting inputs of freshwater as well as transport processes. Spatial distributions of the other quantities also varied weekly, but not in concert with the salt field. Spatial patterns of phytoplankton biomass (chlorophyll a ) deviated from the salinity patterns, largely reflecting in situ production of phytoplankton biomass during the spring bloom. The tidally-averaged distribution of suspended particulate matter (SPM) was highly dynamic and responded to (1) the riverine input of suspended sediment during a freshet, (2) neap-spring variations in tidally-driven resuspension, and (3) resuspension in shallows following a period of wind mixing. Two-dimensional distributions of primary productivity P ′, derived from maps of biomass and turbidity (SPM), also varied weekly, but the spatial variability of P ′ was only about half that of SPM and chlorophyll. Since the magnitude and patterns of spatial variability differ among nonconservative quantities, at least in part because of local sources and sinks, we conclude that the spatial distributions of nonconservative quantities cannot be predicted from distributions of conservative tracers, such as salinity.

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USGS1989

Spatial and temporal variability in South San Francisco Bay (USA). II. Temporal changes in salinity, suspended sediments, and phytoplankton biomass and productivity over tidal time scales

Short-term variability of a conservative quantity (salinity) and two nonconservative quantities (chlorophyll a , suspended particulate matter) was measured across a sampling grid in the South San Francisco Bay estuary. Surface measurements were made every 2 h at each of 29 (or 38) sites, on four different dates representing a range of tidal current regimes over the neap-spring cycle. From the distribution of phytoplankton biomass (chlorophyll a ) and turbidity (SPM), we also estimated daily productivity and its variability at each site over the four tide cycles. As a general rule, both chlorophyll a and SPM concentrations varied about 50% from their tidal-means. However derived daily productivity varied less (about 15% from the mean) over a tidal cycle. Both chlorophyll a and SPM varied periodically with tidal stage (increasing on ebbing currents), suggesting that the short-term variability results simply from the tidal advection of spatial gradients. Calculation of the advective flux (current speed times spatial gradient) was used to test this hypothesis. For surface salinity, most (70–80%) of the observed intratidal variability was correlated with the tidal flux, both in the deep channel and over the lateral shoals. However the short-term variability of SPM concentration was only weakly correlated with the advective flux, indicating that local sources of SPM (resuspension) are important. Hourly changes in chlorophyll a were highly correlated with the advective flux in the deep channel (implying that phytoplankton biomass is conservative over short time scales there); however, chlorophyll a variability was only weakly correlated with the advective flux over the shoals, implying that local sources/sinks are important there. Hence, the magnitude and mechanisms of intratidal variability differ among constituents and among bathymetric regimes in this estuary.

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USGS1989

Potamocorbula amurensis discovered in San Francisco Bay

The small Asian clam, Potamocorbula amurensis , is now a major component of benthic communities in most areas of northern San Francisco Bay and some areas of South Bay. Because of its wide tolerance of salinity and other environmental variables and its high abundance in many areas, benthic ecologists believe this recent invasion may represent a major and permanent change in the bay system.

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USGS1988

Suspended sediment transport under estuarine tidal channel conditions

A modified version of the GEOPROBE tripod has been used to monitor flow conditions and suspended sediment distribution in the bottom boundary layer of a tidal channel within San Francisco Bay, California. Measurements were made every 15 minutes over three successive tidal cycles. They included mean velocity profiles from four electromagnetic current meters within 1 m of the seabed; mean suspended sediment concentration profiles from seven miniature nephelometers operated within 1 m of the seabed; near-bottom pressure fluctuations; vertical temperature gradient; and bottom photographs. Additionally, suspended sediment was sampled from four levels within 1 m of the seabed three times during each successive flood and ebb cycle. While the instrument was deployed, STD-nephelometer measurements were made throughout the water column, water samples were collected each 1–2 hours, and bottom sediment was sampled at the deployment site. From these measurements, estimates were made of particle settling velocity ( w s ) from size distributions of the suspended sediment, friction velocity (U * U &#x2217; "> ) from the velocity profiles, and reference concentration ( C a ) was measured at z = 20 cm. These parameters were used in the suspended sediment distribution equations to evaluate their ability to predict the observed suspended sediment profiles. Three suspended sediment particle conditions were evaluated: (1) individual particle size in the 4–11 φ (62.5-0.5 μm) range with the reference concentration C a at z = 20 cm ( C φ ), (2) individual particle size in the 4–6 φ size range, flocs representing the 7–11 φ size range with the reference concentration C a at z = 20 cm ( C f ), and (3) individual particle size in the 4–6 φ size range, flocs representing the 7–11 φ size range with the reference concentration predicted as a function of the bed sediment size distribution and the square of the excess shear stress. In addition, computations of particle flux were made in order to show vertical variations in horizontal mass flux for varying flow conditions.

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USGS1988

Plankton studies in San Francisco Bay; IX, Chlorophyll distributions and hydrographic properties of South San Francisco Bay, 1984-86

This report summarizes the distribution of phytoplankton biomass and selected hydrographic properties in South San Francisco Bay during 1984- 1986. There were a total of 67 cruises during the three-year period with the most frequent sampling occurring during the spring. Parameters measured were chlorophyll a, phaeopigments, in-vivo fluorescence, turbidity, salinity, and temperature.

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USGS1988

Phytoplankton growth rates in a light-limited environment, San Francisco Bay

Phytoplankton cells reside in a turbulent medium partitioned into an upper photic zone that sustains photosynthesis, and a lower aphotic zone that does not. In estuaries, vertical mixing rates between these 2 zones can be rapid (< 1 generation time) because of tidal stirring and because the mixing depth is generally shallow. Moreover, the photic depth is characteristically shallow in estuaries because of the high seston concentrations that typify these systems (e.g. Cloern 1987). Hence the mean light exposure of phytoplankton cells, and their rates of photosynthesis and growth in estuaries, should be related to the ratio of photic depth Z p to mixing Z m , (defined as either the water column depth, or the surface layer depth in a stratified estuary). Grobbelar (1985) has measured phytoplankton production in turbid waters and used the ratio Z p :Z m as a simple index to quantify the degree of light limitation. Harris and his colleagues have examined in detail the importance of the Z p :Z m ratio in lakes for influencing variability of phytoplankton production and photosynthetic parameters (Harris et al. 1980), and variability of species composition both temporally (Harris & Piccinin 1980) and spatially (Haffner et al. 1980). Phytoplankton growth rates have only rarely been measured in estuaries (Malone 1977, Furnas 1982, Harding et al. 1986) where cycling rates between the photic and aphotic zones can be much faster than in lakes or the open ocean. This study was motivated by the need for quantitative measures of phytoplankton population growth rate in an estuarine environment, and was designed around the presumption that growth rates can be related empirically to light exposure. We conducted the study in San Francisco Bay (California, USA), which has large horizontal gradients in light availability (Z p :Z m ) typical of many coastal plain estuaries, and nutrient concentrations that often exceed those presumed to limit phytoplankton growth (Cloern et al. 1985). We tested the hypothesis that light availability is the primary control of phytoplankton growth, and that previous estimates of growth rate based on the ratio of productivity to biomass (Cloern et al. 1985) are realistic. Specifically, we wanted to verify that growth rate varies spatially along horizontal gradients of light availability indexed as Z p :Z m , such that phytoplankton turnover rate is rapid in shallow clear areas (high Z p :Z m ) and slow in deep turbid areas (low Z p :Z m ). We used an in situ incubation technique which simulated vertical mixing, and measured both changes in cell number and carbon production as independent estimates of growth rate across a range of Z p :Z m ratios.

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USGS1987

The phytoplankton component of seston in San Francisco Bay

Phytoplankton biomass (as carbon) was estimated from chlorophyll a concentrations (Chl a ) and a mean value for the ratio of phytoplankton carbon to chlorophyll a in San Francisco Bay. The ratio was determined as the slope of a Model II regression of POC' against (Chl a ), where POC' is total particulate organic carbon minus sediment-associated non-phytoplankton carbon. Samples from 30 fixed sites in the channel and lateral shoals of San Francisco Bay were collected once or twice a month from April to November 1980, and at irregular intervals in South Bay during 1984 and 1985. For all data the calculated mean value of phytoplankton C:Chl a was 51 (95% confidence interval = 47–54). No significant differences were found in the C:Chl a ratio between shallow and deep sites (where light availability differs) or between northern and southern San Francisco Bay (where phytoplankton community composition differs). Using the mean C:Chl a ratio of 51, we calculated that phytoplankton biomass constitutes about one third of seston carbon under most circumstances, but this fraction ranges from about 95% during phytoplankton blooms to less than 20% during spring periods of low phytoplankton biomass and high suspended sediment concentration.

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USGS1987

Temporal variations in the benthic communities at four intertidal sites in San Francisco Bay, California, 1983-85

Benthic core samples were collected monthly from January 1983 through January 1985 at four intertidal sites in San Francisco Bay, California, two in the northern part of the bay (North Bay) and two in the southern part of the bay (South Bay). Considerable variation was observed in numbers of species and individuals at the four sites, and abundances within species varied widely. Temporal changes in species abundances appeared to be related to freshwater inflow patterns and resultant salinity variations in the estuary. The 1982-83 winter season was extremely wet, with heavy freshwater inflow to the bay from January through March, whereas the 1983-84 winter was closer to a normal pattern, with most rainfall occurring from November through January. Species were grouped into four categories depending on their patterns of abundance during the 2-yr period. Species that showed an abundance peak in the North Bay in 1983 only were Corophium sp.B and a Chironomidae larva, apparently responding to the extended period of lowered salinity throughout spring and early summer. Species with an abundance peak only in 1984 included Corophium Acherusicum, Eteone californica, Nereis succinea, and Grandidierella japonica, typical estuarine species that might have been suppressed during the extended freshwater inflows in 1983. Species with peaks in both years were Gemma gemma and Ampelisca abdita in the South Bay; both showed strong seasonal variations. A number of species in both North and South Bays, including dominant members of the intertidal community such as Macoma balthical and Streblospio benedicti, did not show any consistent seasonal or year-to-year trends. Results of this study suggest that the intensity and timing of freshwater inflow to San Francisco Bay, particularly higher-than-normal inflow during late spring and early summer, may be an important factor in determining the composition of the intertidal benthic communities. (Author 's abstract)

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USGS1987

A review of circulation and mixing studies of San Francisco Bay, California

A description of the major characteristics and remaining unknowns of circulation and mixing in San Francisco Bay has been constructed from a review of published studies. Description of net circulation and mixing over a few days to a few months illustrates best the interactions of major components. The discharge of the Sacramento-San Joaquin Delta into Suisun Bay is approximately 90% of the freshwater inflow to San Francisco Bay. Annual delta discharge is characterized by a winter season of high runoff and a summer season of low runoff. For the period 1956 to 1985 the mean of monthly discharges exceeded 1,000 cu m/s (35,000 cu ft/s) for the months of December through April, whereas for July through October, it was < 400 cu m/s (14,000 cu ft/s). The months of November, May, and June commonly were transition months between these seasons. Large year-to-year deviations from this annual pattern have occurred frequently. Much less is known about the ocean-bay exchange process. Net exchanges depend on net seaward flow in the bay, tidal amplitude , and longshore coastal currents, but exchanges have not yet been measured successfully. The bay is composed of a northern reach, which is strongly influenced by delta discharge, and South Bay, a tributary estuary which responds to conditions in Central Bay. In the northern reach net circulation is characterized by the river-induced seaward flow and a resulting gravitational circulation in the channels, and by a tide and wind-induced net horizontal circulation. During low delta discharges South Bay has nearly the same salinity as Central Bay and is characterized by tide and wind-induced net horizontal circulation. In the northern reach a nontidal current null zone moves rapidly seaward in response to increases in delta discharge, and after runoff events returns landward over a few months. During the low-discharge period the northern reach achieves an approximate salt balance in two to three months. When gravitational circulation penetrates these zones during high discharges, the mean residence time probably is reduced to less than a month. (Lantz-PTT)

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USGS1986

Suspended sediment transport in an estuarine tidal channel within San Francisco Bay, California

A recently developed instrumentation system has been used to monitor simultaneously flow conditions and suspended sediment distribution in the bottom boundary layer of a tidal channel within San Francisco Bay, California. Measurements were made every 15 min over six successive flood and ebb tidal cycles. They included mean velocity profiles from four electromagnetic current meters within 1 m of the seabed; mean suspended sediment concentration profiles from seven miniature nephelometers placed within 1 m of the seabed; near-bottom pressure fluctuations; vertical temperature gradient; and bottom photographs. Additionally, suspended sediment was sampled from four levels within 1 m of the seabed three times during the tidal cycle. The instrument system was retrieved during each slack water period to exchange suspended sediment sample bags. While the instrument was deployed STD-nephelometer measurements were made thoughout the water column and water samples were collected each 1-h and bottom sediment was sampled at the deployment site. Size distributions of the suspended sediment samples, estimates of particle settling velocity (??s), friction velocity (U*), and reference concentration (Ca) at z = 20 cm were used in the suspended sediment distribution equations to evaluate their ability to predict the observed suspended sediment profiles. Three suspended sediment particle conditions were evaluated: (1) individual particle sizes in the 4-11 ?? (62.5-0.5 ??m) size range with the reference concentration Ca at z = 20 cm (C??); (2) individual particle sizes in the 4-6 ?? size range, flocs representing the 7-11 ?? size range with the reference concentration Ca at z = 20 cm (Cf); and (3) individual particle sizes in the 4-6 ?? size range, flocs representing the 7-11 ?? size range with the reference concentration predicted as a function of the bed sediment size distribution and the square of the excess shear stress. An analysis was also carried out on the sensitivity of the suspended sediment distribution equation to deviations in the primary variables ??s, U*, and Ca. In addition, computations of mass flux were made in order to show vertical variations in mass flux for varying flow conditions. ?? 1986.

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USGS1986

The modification of an estuary

The San Francisco Bay estuary has been rapidly modified by human activity. Diking and filling of most of its wetlands have eliminated habitats for fish and waterfowl; the introduction of exotic species has transformed the composition of its aquatic communities; reduction of freshwater inflow by more than half has changed the dynamics of its plant and animal communities; and wastes have contaminated its sediments and organisms. Continued disposal of toxic wastes, the probable further reduction in freshwater inflow, and the possible synergy between the two provide the potential for further alteration of the estuary's water quality and biotic communities.

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USGS1986

Measurement of nitrous oxide reductase activity in aquatic sediments

Denitrification in aquatic sediments was measured by an N 2 O reductase assay. Sediments consumed small added quantities of N 2 O over short periods (a few hours). In experiments with sediment slurries, N 2 O reductase activity was inhibited by O 2 , C 2 H 2 , heat treatment, and by high levels of nitrate (1 mM) or sulfide (10 mM). However, ambient levels of nitrate (<100 &mu;M) did not influence activity, and moderate levels (about 150 &mu;M) induced only a short lag before reductase activity began. Moderate levels of sulfide (<1 mM) had no effect on N 2 O reductase activity. Nitrous oxide reductase displayed Michaelis-Menten kinetics in sediments from freshwater ( K m = 2.17 &mu;M), estuarine ( K m = 14.5 &mu;M), and alkaline-saline ( K m = 501 &mu;M) environments. An in situ assay was devised in which a solution of N 2 O was injected into sealed glass cores containing intact sediment. Two estimates of net rates of denitrification in San Francisco Bay under approximated in situ conditions were 0.009 and 0.041 mmol of N 2 O per m 2 per h. Addition of chlorate to inhibit denitrification in these intact-core experiments (to estimate gross rates of N 2 O consumption) resulted in approximately a 14% upward revision of estimates of net rates. These results were comparable to an in situ estimate of 0.022 mmol of N 2 O per m 2 per h made with the acetylene block assay.

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USGS1986

Formation of methane and carbon dioxide from dimethylselenide in anoxic sediments and by a methanogenic bacterium

Anaerobic San Francisco Bay salt marsh sediments rapidly metabolized [ 14 C]dimethylselenide (DMSe) to 14 CH 4 and 14 CO 2 . Addition of selective inhibitors (2-bromoethanesulfonic acid or molybdate) to these sediments indicated that both methanogenic and sulfate-respiring bacteria could degrade DMSe to gaseous products. However, sediments taken from the selenium-contaminated Kesterson Wildlife Refuge produced only 14 CO 2 from [ 14 C]DMSe, implying that methanogens were not important in the Kesterson samples. A pure culture of a dimethylsulfide (DMS)-grown methylotrophic methanogen converted [ 14 C]DMSe to 14 CH 4 and 14 CO 2 . However, the organism could not grow on DMSe. Addition of DMS to either sediments or the pure culture retarded the metabolism of DMSe. This effect appeared to be caused by competitive inhibition, thereby indicating a common enzyme system for DMS and DMSe metabolism. DMSe appears to be degraded as part of the DMS pool present in anoxic environments. These results suggest that methylotrophic methanogens may demethylate methylated forms of other metals and metalloids found in nature.

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