Environmental setting of San Francisco Bay

San Francisco Bay, the largest bay on the California coast, is a broad, shallow, turbid estuary comprising two geographically and hydrologically distinct subestuaries: the northern reach lying between the connection to the Pacific Ocean at the Golden Gate and the confluence of the Sacramento-San Joaquin River system, and the southern reach (herein called South Bay) between the Golden Gate and the southern terminus of the bay. The northern reach is a partially mixed estuary dominated by seasonally varying river inflow, and the South Bay is a tidally oscillating lagoon-type estuary. Freshwater inflows, highest during winter, generate strong estuarine circulation and largely determine water residence times. They also bring large volumes of dissolved and particulate materials to the estuary. Tidal currents, generated by mixed semidiurnal and diurnal tides, mix the water column and, together with river inflow and basin geometry, determine circulation patterns. Winds, which are strongest during summer and during winter storms, exert stress on the bay's water surface, thereby creating large waves that resuspend sediment from the shallow bay bottom and, together with the tidal currents, contribute markedly to the transport of water masses throughout the shallow estuary.     

Intratidal fluctuations in stratification within a mangrove estuary

The dependence of salinity stratification on the vertical structure of the longitudinal salinity gradient is investigated by solving the equations of longitudinal momentum and salt conservation. The results are used to interpret measurements made throughout 31 tidal cycles in the Merbok Estuary, Malaysia, as part of an ecological study of a tropical mangrove estuary. The solutions show that a substantial part of the salinity stratification was caused by vertical shear in the currents coupled with advection of the longitudinal salinity gradient. This mechanism led to maximum stratification around low water and minimum stratification around high water. Observed intratidal variations in stratification at neap tides greatly exceeded modelled values when a depth-independent, longitudinal salinity gradient was assumed. Simulations made using a longitudinal salinity gradient of simple depth-dependent, power-law form implied that this difference arose mainly because the near-surface, longitudinal salinity gradient in the field was significantly larger than that near the bed during neap tides and at times of high run-off. The longitudinal, dispersive transport of salt, fresh water and solutes due to vertical shear is shown to be important during periods of stratification at neap tides and during high run-off. The relevance of stratification to mangrove estuaries is discussed.     

Temporal dynamics of estuarine phytoplankton: A case study of San Francisco Bay

Detailed surveys throughout San Francisco Bay over an annual cycle (1980) show that seasonal variations of phytoplankton biomass, community composition, and productivity can differ markedly among estuarine habitat types. For example, in the river-dominated northern reach (Suisun Bay) phytoplankton seasonality is characterized by a prolonged summer bloom of netplanktonic diatoms that results from the accumulation of suspended particulates at the convergence of nontidal currents (i.e. where residence time is long). Here turbidity is persistently high such that phytoplankton growth and productivity are severely limited by light availability, the phytoplankton population turns over slowly, and biological processes appear to be less important mechanisms of temporal change than physical processes associated with freshwater inflow and turbulent mixing. The South Bay, in contrast, is a lagoon-type estuary less directly coupled to the influence of river discharge. Residence time is long (months) in this estuary, turbidity is lower and estimated rates of population growth are high (up to 1–2 doublings d^–1), but the rapid production of phytoplankton biomass is presumably balanced by grazing losses to benthic herbivores. Exceptions occur for brief intervals (days to weeks) during spring when the water column stratifies so that algae retained in the surface layer are uncoupled from benthic grazing, and phytoplankton blooms develop. The degree of stratification varies over the neap-spring tidal cycle, so the South Bay represents an estuary where (1) biological processes (growth, grazing) and a physical process (vertical mixing) interact to cause temporal variability of phytoplankton biomass, and (2) temporal variability is highly dynamic because of the short-term variability of tides. Other mechanisms of temporal variability in estuarine phytoplankton include: zooplankton grazing, exchanges of microalgae between the sediment and water column, and horizontal dispersion which transports phytoplankton from regions of high productivity (shallows) to regions of low productivity (deep channels).Multi-year records of phytoplankton biomass show that large deviations from the typical annual cycles observed in 1980 can occur, and that interannual variability is driven by variability of annual precipitation and river discharge. Here, too, the nature of this variability differs among estuary types. Blooms occur only in the northern reach when river discharge falls within a narrow range, and the summer biomass increase was absent during years of extreme drought (1977) or years of exceptionally high discharge (1982). In South Bay, however, there is a direct relationship between phytoplankton biomass and river discharge. As discharge increases so does the buoyancy input required for density stratification, and wet years are characterized by persistent and intense spring blooms.     

Feeding rhythms of the green-lipped mussel, Perna viridis (Linnaeus, 1758) (Bivalvia: Mytilidae) during spring and neap tidal cycles

Food availability and feeding responses of the green mussel Perna viridis were investigated for two complete tidal cycles during both spring and neap tides. Temporal changes in total particulate matter (TPM), particulate inorganic matter (PIM) and particulate organic matter (POM), were smaller during neap than spring tides. Seston characteristics at different times of a tidal cycle were compared for both spring and neap tides. Only during spring tides were TPM and PIM significantly higher at high tides while POM remained relatively constant (P>0.05). The clearance rate of the mussels underwent temporal variations with tides, and was a negative power function of TPM and a positive linear function of f (organic content), during both spring and neap tides. f was the key factor influencing filtration rate, organic ingestion rate, absorption rate and absorption efficiency. All feeding rates increased linearly with increases in organic content. Pseudofaeces were produced only during spring but not neap tides. Feeding rates and absorption efficiency were highest at low and lowest at high tides (P<0.01). There was no significant temporal change in the wet weight and protein content of the crystalline style with the tidal regime. For the digestive gland, alpha-amylase activity was higher at spring than at neap tides, and higher during high tides in a tidal cycle. The digestive gland cellulase activity did not change significantly with the tides. For the crystalline style, both the activity of cellulase and alpha-amylase were not significantly different (P>0.05) between spring and neap tides. Tidal rhythms in feeding and digestion in this species were likely controlled by temporal variations in food availability in the seawater. By adjusting feeding rates and enzymatic activities, absorption in Perna viridis remained constant, irrespective of the changes in food availability.     

Modulation of dissolved oxygen levels in a hypertidal estuary by sediment resuspension

Hyperconcentrated benthic layers, which form during neap tides, recruit much of the fine sediment population of the turbidity maximum of a hypertidal estuary. Measurements of tidal amplitude and suspended solids concentration reveal that resuspension of the hyperconcentrated layers occurs between three and eight tides after neap tides rather than during spring tides (12 to 15 tides after neaps). During these resuspension events, dissolved oxygen levels are reduced but recover by spring tides. Peak solids concentrations and critically depressed dissolved oxygen levels are out of phase with tidal current amplitude. Thus observations close to neap and spring tides do not necessaraly capture the extremes of the envelope of water quality conditions.     

Seasonal Variability and Transport of Suspended Microfungi in a Southeastern Salt Marsh

Tidally induced fluctuations and transports of microfungi were investigated. Samples were collected at three depths from three stations positioned at a transect in a large salt marsh creek. Samples were taken every 1.5 h for 50 consecutive h during neap tides and 50 consecutive h during the corresponding spring tides. In each season, microfungi concentrations fluctuated out of phase with the tides during both neap and spring tides. Mean concentrations of suspended microfungi did not vary appreciably throughout the year. Fungi were exported from the marsh during the majority of the tidal cycles studied. The results suggest that microfungi may serve as indicators of water mass movements.     

Time scales and mechanisms of estuarine variability,a synthesis from studies of San Francisco Bay

This review of the preceding papers suggests that temporal variability in San Francisco Bay can be characterized by four time scales (hours, days-weeks, months, years) and associated with at least four mechanisms (variations in freshwater inflow, tides, wind, and exchange with coastal waters). The best understood component of temporal variability is the annual cycle, which is most obviously influenced by seasonal variations in freshwater inflow. The winter season of high river discharge is characterized by: large-scale redistribution of the salinity field (e.g. the upper estuary becomes a riverine system); enhanced density stratification and gravitational circulation with shortened residence times in the bay; decreased tissue concentrations of some contaminants (e.g. copper) in resident bivalves; increased estuarine inputs of river-borne materials such as dissolved inorganic nutrients (N, P, Si), suspended sediments, and humic materials; radical redistributions of pelagic organisms such as copepods and fish; low phutoplankton biomass and primary productivity in the upper estuary; and elimination of freshwater-intolerant species of macroalgae and benthic infauna from the upper estuary. Other mechanisms modulate this river-driven annual cycle: (1) wind speed is highly seasonal (strongest in summer) and causes seasonal variations in atmosphere-water column exchange of dissolved gases, resuspension, and the texture of surficial sediments; (2) seasonal variations in the coastal ocean (e.g. the spring-summer upwelling season) influence species composition of plankton and nutrient concentrations that are advected into the bay; and (3) the annual temperature cycle influences a few selected features (e.g. production and hatching of copepod resting eggs). Much of the interannual variability in San Francisco Bay is also correlated with freshwater inflow: wet years with persistently high river discharge are characterized by persistent winter-type conditions.Mechanisms of short-term variability are not as well understood, although some responses to storm events (pulses in residual currents from wind forcing, erosion of surficial sediments by wind waves, redistribution of fish populations) and the neap-spring tidal cycle (enhanced salinity stratification, gravitational circulation, and phytoplankton biomass during neap tides) have been quantified. In addition to these somewhat predictable features of variability are (1) largely unexplained episodic events (e.g. anomalous blooms of drift macroalgae), and (2) long-term trends directly attributable to human activities (e.g. introduction of exotic species that become permanent members of the biota).     

A model study on variations in larval supply: are populations of the polychaete <Emphasis Type="Italic">Owenia fusiformis</Emphasis> in the English Channel open or closed?

The polychaete Owenia fusiformis is one of the most ecologically important species in the muddy fine sand sediments in the English Channel where it is distributed in geographically separated populations. A vertically averaged Lagrangian hydrodynamic model integrating tidal residual currents and wind-induced currents was used to drive an advection–diffusion model for investigating the variability of larval transport in order to assess the self-seeding capabilities and the degree of connectivity between local populations. Three different types of environmental forcing (i.e. tidal forcing alone, tidal forcing coupled with either NE winds or SW winds) were applied to 19 distinct populations. Without wind influence, self-seeding is the principal mechanism involved in the renewal of most populations. However, larval retention ranged from under 1% up to 81% in relation to the adult habitat size and the mean velocity of tidal residual currents. Wind forcing had a strong influence on larval dispersal patterns by modifying the origin and densities of settlers as well as the degree of connectivity between populations. As a consequence, larval supply from distant populations generally exceeded local supply and the inter-annual variability of wind forcing induced large year-to-year variations in larval settlement rates. Larval exchanges occurred mainly between neighbouring populations and three groups of interconnected local populations were thereby identified. Within each group, settlement patterns were related to inter-annual variations in the direction and magnitude of larval exchanges. Electronic Publication     

Rhythmic swimming behaviour of the New Zealand sand beach isopod Pseudaega punctata Thomson

The swimming rhythm of Pseudaega punctata Thomson is shown to have dual circadian and tidal components. The rhythm is endogenous, persisting for ten days under constant conditions in the laboratory and has a free-running period of greater than tidal frequency. The swimming activity has a basic semi-lunar rhythm even in the absence of marked differences between the heights of spring and neap tides. The rhythm is phased by exogenous factors such as light and tides but is flexible enough to deal with seasonal variations in day length and the shifting tidal cycle. Chilling weakly-rhythmic isopods re-inforces the rhythm. Control is thought to be neurosecretory, depletion of a neurosecretory product accumulated during a quiescent phase terminating swimming activity. The work is compared with similar studies on the related Eurydice pulchra which fills the same ecological niche in the northern hemisphere.     

Tidal asymmetry in creeks surrounded by saltflats and mangroves with small swamp slopes

Most mangrove swamp/salt flat systems have tidal currents that are ebb dominated, however, some systems show only slight ebb dominance despite having a very large swamp volume relative to the creek volume. Cocoa Ck in northern Australia is such a system. Results are presented from a simple analytical model for flow in Cocoa creek together with detailed water level observations in the swamps. It was found that the primary factor reducing the ebb dominance of this system was the very low slope of the swamp surface. During rising tides, water floods as sheet flow; however, on ebb tides, the surface water slope in the swamp becomes greater than the swamp surface slope, with the result that areas of swamp closest to the main feeder creek (Cocoa Ck) dry before areas furthest from the creek. Thus, about an hour after ebb tide commences, there is a large quantity of water perched on the salt flats/mangroves, tens of centimetres higher than the water in the creek. This water cannot leave the swamp via sheet flow, but must leave through a very small and shallow creek which is also highly constricted by vegetation. This effectively increases the friction on ebb tides and results in a delay in water leaving the swamps and salt flats, reducing any tendency towards ebb dominance.     

Methodology for studying exchanges between salt marshes and coastal marine waters

The salt marshes of the Mont St. Michel bay represent a complex system in continuous change, mostly due to the frequent exchanges with the coastal waters through tidal processes. In such ecosystems, water is an important element insofar as it represents the common vector of flows between and among several ecosystem compartments. The purpose of the approach discussed here is to estimate the volume of water coming in and out and to determine the variations of the water quality according to time and nutrients concentrations. The estimation of the water fluxes is dependent on the channel calibration downstream of the watershed. Among the different methods examined, the continuous integrals calibration appears as the best one because the water level changes very quickly.Up to now, estimations of nutrients exchanges in wetlands have been based on rigorously regular field sampling, in consideration of the fact that exchanges occurred mainly during annual spring tides or during spring tides of each cycle of the year. According to our results, it seems that every tide, and portion of a tide, of a monthly and seasonal cycle has some importance and variability, which suggests that all parts of a tide should be considered in estimations of exchanges between wetlands and coastal waters.Corresponding Editor: W. Mitsch     

Tower construction by the manicure crab <Emphasis Type="Italic">Cleistostoma dilatatum</Emphasis> during dry periods on an intertidal mudflat

Animals living on upper intertidal mudflats experience habitat desiccation during neap tides when water does not flood the habitat. Individuals of the manicure crab Cleistostoma dilatatum construct cone-shaped towers at the entrance of their burrows, in which they remain during neap tides. These towers are the tallest known structures compared to body size built by crabs living on intertidal flats. The frequency of tower construction followed semilunar tidal cycles with most building done prior to neap tides when few crabs were active on the mudflat surface. Bigger crabs tended to make taller and wider towers with a wider pinhole on the top. These towers may regulate the microclimate in burrows.     

The influence of tidal forcing on groundwater flow and nutrient exchange in a salt marsh-dominated estuary

Data from salt marshes in the U.S. Southeast show that long-term variations in mean water level (MWL) correlate strongly with salt marsh productivity and porewater salinity. Here we used numerical models of tidally-driven groundwater flow to assess the effect of variations in tidal amplitude and MWL on porewater exchange between salt marshes and tidal creeks. We modeled homogeneous and layered stratigraphy and compared flat and sloped topography for the marsh surface. Results are consistent with field observations and showed that increases in tidal amplitude increased groundwater flushing, particularly when increasing the tidal amplitude caused the marsh platform to be inundated at high tide. Increases in MWL caused groundwater flushing to increase if that rise caused greater areas of the marsh to be inundated at high tide. Once the marsh was fully inundated at high tide, further increases in MWL caused groundwater flushing to decrease. Results suggest that small increases in MWL associated with sea level rise could increase nutrient export significantly in marshes with elevations that are equilibrated near mean high water, but rising sea level could decrease the export of nutrients to, and thus fertility in, estuaries adjacent to marshes that are equilibrated lower in the tidal frame. Likewise, macrotidal estuaries are predicted to be subject to much larger groundwater and nutrient exchange than similar microtidal estuaries. We speculate that the early stages of rising relative sea level may significantly impact water quality in estuaries that are not river-dominated by raising the discharge of nutrients from coastal wetlands.     

Wave and tidal flushing in a near-equatorial mesotidal atoll

Most of the atolls found worldwide are under microtidal regimes, and their circulation mechanisms are widely documented and well known. Here, we describe the flushing mechanisms of a small-sized mesotidal atoll, based on water-level, wave and current data obtained during two different periods (total of 60 d). Rocas is the only atoll in the South Atlantic Ocean and is built primarily of coralline algae. Two reef passages connect the atoll lagoon to the ocean. Synchronous current profilers were deployed at the two reef passages, one inside and one outside the atoll, to characterize the influence of tides and waves on the circulation. Results showed that wind waves drove a setup on the exposed side of the atoll and that currents were predominately downwind, causing outflow at both reef passages. Waves breaking on the windward side supplied water to the atoll causing the lagoon water level to rise above ocean water level, driving the outflow. However, unlike microtidal atolls, at Rocas Atoll the water level drops significantly below the reef rim during low tides. This causes the reef rim to act as a barrier to water pumping into the lagoon by waves, resulting in periodic activation of the wave pumping mechanism throughout a tidal cycle. As result, inflow occurs in the wider passage during 27% of each tidal cycle, starting at low tides and reversing direction during mid-flood tide when the water level exceeded approximately 1.6 m (while overtopping the atoll’s rim). Our findings show that tides play a direct role in driving circulation on a mesotidal atoll, not only by modulating wave setup but also by determining the duration of wave pumping into the lagoon.

     

Neap-spring tidal effects on dissolved oxygen in two Malaysian estuaries

The longitudinal distributions of dissolved oxygen change dramatically during neap-spring tidal cycles in the lower Selangor and Klang Rivers. An oxygen deficit develops in both estuaries when the tidal range is high. The Selangor River inflow is nearly saturated with D.O., but during spring tides D.O. falls to as little as 15% of saturation in the middle reaches of the estuary. The Klang River has low D.O. freshwater input, an oxygen minimum develops during neap tides, and anoxic conditions are produced by spring tides. These oxygen minima are attributed to the high oxygen demand of sediment that rests on the bottom during neap tides and is resuspended during spring tides. The ecological effects of tidal cycling patterns of dissolved oxygen in these Malaysian estuaries need further study, within the context of land use patterns and other human activities.     

Fortnightly periodicity in the abundance of diatom and dinoflagellate taxa at a coastal study site

From 3 July to 15 September 2000, plankton samples were collected roughly every 2 days at three stations within 1.5 km from shore at Sunset Bay, OR. In these samples we enumerated Coscinodiscus-like diatoms, Protoperidinium spp., and the potentially toxic phytoplankter, Pseudo-nitzschia spp. Using time series analysis, the abundance of these phytoplankters was compared to wind stress, tidal range, and sea surface temperature (SST). SST was significantly cross-correlated with wind stress (lower SST occurred during upwelling favorable winds) and maximum daily tidal range (cold and warm anomalies in SST occurred around the neap and spring tides, respectively). We found no significant cross-correlations between wind stress (upwelling vs. downwelling winds) and the abundance of any of the taxa. Significant cross-correlations were found between phytoplankton abundances and the maximum daily tidal range (peak concentrations occurred between the neap and spring tides) and SST (peak concentrations occurred during periods of warmer SST). We hypothesize that this pattern of abundance may be caused by shoreward transport of offshore phytoplankton populations by internal tidal waves.     

Effects of Natural and Anthropogenic Change on Habitat Use and Movement of Endangered Salt Marsh Harvest Mice

The northern salt marsh harvest mouse (Reithrodontomys raviventris halicoetes) is an endangered species endemic to the San Francisco Bay Estuary. Using a conservation behavior perspective, we examined how salt marsh harvest mice cope with both natural (daily tidal fluctuations) and anthropogenic (modification of tidal regime) changes in natural tidal wetlands and human-created diked wetlands, and investigated the role of behavioral flexibility in utilizing a human-created environment in the Suisun Marsh. We used radio telemetry to determine refuge use at high tide, space use, and movement rates to investigate possible differences in movement behavior in tidal versus diked wetlands. We found that the vast majority of the time salt marsh harvest mice remain in vegetation above the water during high tides. We also found no difference in space used by mice during high tide as compared to before or after high tide in either tidal or diked wetlands. We found no detectable difference in diurnal or nocturnal movement rates in tidal wetlands. However, we did find that diurnal movement rates for mice in diked wetlands were lower than nocturnal movement rates, especially during the new moon. This change in movement behavior in a relatively novel human-created habitat indicates that behavioral flexibility may facilitate the use of human-created environments by salt marsh harvest mice.     

Diel and tidal changes in the distribution and feeding habits of Japanese temperate bass Lateolabrax japonicus juveniles in the surf zone of Ariake Bay

Japanese temperate bass Lateolabrax japonicus juveniles recruit to the surf zone and grow by feeding on commonly occurring coastal copepods. However, little is known about diel and tidal patterns in their migration and feeding habits. We sampled wild juveniles during the neap and spring tides, over periods of 24 h, with small seine nets in the sand flat of the eastern part of Ariake Bay, Kyushu, western Japan. In both the neap and spring tides, abundance of juveniles significantly increased during the daytime, being highest around the time of high tide. The relative gut fullness indices of juveniles drastically increased in the morning (0700–0900) and during the flood tide in the daytime, while major prey copepod (Paracalanus spp.) density in the ambient water was relatively constant. We summarized that L. japonicus juveniles would migrate to the surf zone after sunrise to feed on copepods, and then emigrate from the surf zone after sunset. The migratory behavior of L. japonicus juveniles would be influenced by light (daytime) and feeding activity influenced by both light (morning) and tidal condition (flood tide). The intertidal region of the tidal flat was recognized to be one of the important habitats for L. japonicus during their early life history.     

Transport of microbial biomass through the North Inlet ecosystem

Tidal fluctuations and transports of total microbial biomass (measured as adenosine triphosphate [ATP]) were investigated at three marsh creeks comprising the major transfer points between the North Inlet marsh and the adjoining aquatic ecosystems. Two creeks, Town Creek and North Jones Creek, form the inlet mouth and are the only marsh-ocean exchange points. The third creek, South Jones Creek, connects to a brackish water embayment. The creeks were simultaneously sampled every 1.5 hours for 50 consecutive hours during neap tides (four tidal cycles) and 50 consecutive hours during spring tides of each season. At the inlet, ATP concentration fluctuated in phase with the tide during winter and fall and out of phase with the tide during the spring. Fluctuation patterns at South Jones Creek were irregular. The highest ATP concentrations were during the spring (mean=2.17 mg of ATP per m³) and the lowest concentrations were during the winter (mean=0.65 mg of ATP per m³). Net transports of ATP varied from tidal cycle to tidal cycle with regard to direction of transport (import or export) and magnitude. Net transports were small compared to large instantaneous transports and only 4 of 22 determinations of net transport were different from zero transport.     

The distribution and abundance of planktonic penaeid larvae in Tudor creek,Mombasa, Kenya

The temporal distribution and abundance of penaeid prawn larvae in surface waters of Tudor creek were studied. Only late mysis and early post mysis stages of development were encountered in the creek waters with a descending gradient from the mouth station (station 1) to the innermost station 5. Larval encounter incidence (% incidence) was highest in plankton tows taken during night spring tides (59%) followed by night neap tides (45.4%), day spring tides (34.9%) and day neap tides (21.4%). This encounter incidence was more skewed towards the seaward stations (1 and 2) during the neap tides than during spring tides. Likewise, larval density (mean catch/standard 5 min. tow) decreased less steeply up the creek during spring tides than it did during neap tides. Higher catch rates were in general obtained in night samples than in day samples at each station and in each neap/spring phase. The diel cycle had a greater effect on both incidence and abundance of larvae than did the tidal cycle.Intensified larval incursion into the creek was observed between March and June.