A strain-induced freshwater pump in the Liverpool Bay ROFI

Liverpool Bay is a region of freshwater influence which receives significant freshwater loading from a number of major English and Welsh rivers. Strong tidal current flow interacts with a persistent freshwater-induced horizontal density gradient to produce strain-induced periodic stratification (SIPS). Recent work (Palmer in Ocean Dyn 60:219–226, 2010; Verspecht et al. in Geophys Res Lett 37:L18602, 2010) has identified significant modification to tidal ellipses in Liverpool Bay during stratification due to an associated reduction in pycnocline eddy viscosity. Palmer (Ocean Dyn 60:219–226, 2010) identified that this modification results in asymmetry in flow in the upper and lower layers capable of permanently transporting freshwater away from the Welsh coastline via a SIPS pumping mechanism. Observational data from a new set of observations from the Irish Sea Observatory site B confirm these results; the measured residual flow is 4.0 cm s⁻¹ to the north in the surface mixed layer and 2.4 cm s⁻¹ to the south in the bottom mixed layer. A realistically forced 3D hydrodynamic ocean model POLCOMS succeeds in reproducing many of the characteristics of flow and vertical density structure at site B and is used to estimate the transport of water through a transect WT that runs parallel with the Welsh coast. Model results show that SIPS is the dominant steady state, occurring for 78.2% of the time whilst enduring stratification exists only 21.0% of the year and enduring mixed periods, <1%. SIPS produces a persistent offshore flow of freshened surface water throughout the year. The estimated net flux of water in the surface mixed layer is 327 km³ year ⁻¹, of which 281 km³ year⁻¹ is attributable to SIPS periods. Whilst the freshwater component of this flux is small, the net flux of freshwater through WT during SIPS is significant, the model estimates 1.69 km³ year⁻¹ of freshwater to be transported away from the coast attributable to SIPS periods equivalent to 23% of annual average river flow from the four catchment areas feeding Liverpool Bay. The results show SIPS pumping to be an important process in determining the fate of freshwater and associated loads entering Liverpool Bay.     

The modification of current ellipses by stratification in the Liverpool Bay ROFI

Understanding the fate of freshwater runoff and corresponding nutrient and pollution loads is of critical importance for the development of accurate predictive models and coastal management tools. A key element of such studies is the identification and understanding of the interaction between stratification and current structure. This paper presents a new series of measurements made in the Liverpool Bay region of freshwater influence (ROFI) during spring 2004 where freshwater-maintained horizontal density gradients and strong tidal currents interact to produce strain-induced periodic stratification (SIPS). During stratification, tidal current profiles are significantly modified such that the tidal flow deviates from the otherwise rectilinear E–W axis generating counter rotating upper and lower mixed layers. This feature has often been reported for the Rhine ROFI but not previously identified in Liverpool Bay despite previous investigation at this site. Investigation of an ongoing long-term dataset collected nearby reveals this process to be a common feature throughout the year. Liverpool Bay is shown to maintain three different regimes, long term mixed, long term stratified, and a transitional state when SIPS occurs. The phase of SIPS relative to the tide results in a residual flow away from the Welsh coastline in the upper water column of 2.3–3.6 cm s⁻¹ with a counterflow in the lower layer of 2.8–3.1 cm s⁻¹ towards the coast.     

Enhanced turbulent mixing induced by strong wind on the South China Sea shelf

Integrated observations were made on the South China Sea shelf at 19°37’ N, 112°04’ E, under strong wind and heavy raining weather conditions in August 2005. Current data were obtained using a moored 150-kHz Acoustic Doppler Current Profiler, turbulent kinetic energy dissipation rate were measured with TurboMapII, and temperature was recorded by thermistor chains. Both the mixed layer thickness and the corresponding mean dissipation rate increased after the strong wind bursts. Average surface mixed layer thickness was 13.4 m pre-wind and 22.4 m post-wind, and the average turbulent dissipation rate in the mixed layer pre-wind and post-wind were 4.26 × 10^?7 and 1.09 × 10^?6 Wkg^?1, respectively. The post-wind dissipation rate was 2.5 times larger than the pre-wind dissipation rate in the interior layer and four times larger in the intermediate water column. Spectra and vertical mode analysis revealed that near-inertial motion post-wind, especially with high modes, was strengthened and propagated downward toward the intermediate layer. The downward group velocity of near-inertial current was about 8.1 × 10^?5 ms^?1 during the strong wind bursts. The mean percentage of wind work transmitted into the intermediate layer is about 4.2 %. The ratio of post-wind high-mode energy to total horizontal kinetic energy increased below the surface mixed layer, which would have caused instabilities and result in turbulent mixing. Based on these data, we discuss a previous parameterization that relates dissipation rate, stratification, and shear variance calculated from baroclinic currents with high modes (higher than mode 1) which concentrate a large fraction of energy.     

Excess bottom222Rn profiles and their implications in the northwestern Pacific Ocean

Vertical profiles of excess bottom²²²Rn and potential temperature were measured at 23 stations in the northwestern Pacific Ocean. The Rn profiles were classified into the following three types: quasi-exponential (type E), benthic boundary layer (type B), and horizontally disturbed (type H). The ratio among types E, B and H was approximately 2 : 3 : 1.An apparent vertical eddy diffusivity (K) was calculated by applying a one-dimensional diffusion model to the Rn profiles of types E and B. Type E had K values ranging from 15 to 180 cm² s^?1 (average: 70 cm² s^?1). As to type B, K values for the benthic boundary layer (4.5–260 cm² s^?1, average: 120 cm² s^?1) were always more than an order of magnitude larger than those for the upper layer (0.2–35 cm² s^?1, average: 7 cm² s^?1), indicating more active vertical mixing in the benthic boundary layer than in the upper layer.Rn profiles were measured in regions where the bottom topography is known. It was verified that the occurrence of type H related closely with local bottom topographic features accompanied by lateral transient supply of Rn-rich or Rn-poor water.A couple of Rn profiles at the same location, measured at time intervals of several years, were compared with each other for three locations. The general characteristics of Rn profiles were shown to remain unaltered with time, while the fine structure of Rn profiles may have short-term variations caused by local bottom topography and fluctuations of bottom current as indicated in type H.     

A test of the influence of tidal stream polarity on the structure of turbulent dissipation

Vertical mixing by the tides plays a key role in controlling water column structure over the seasonal cycle in shelf seas. The influence of tidal stirring is generally well represented as a competition between surface buoyancy input and the production of turbulent kinetic energy (TKE) by frictional stresses, a competition which is encapsulated in the Qh/u³ criterion. An alternative control mechanism arises from the limitation of the thickness of the bottom boundary layer due to the effects of rotation and the oscillation of the flow. Model studies indicate that, for conditions typical of the European shelf seas, the energy constraint exerts the dominant control but that for tidal streams with large positive polarisation (i.e. anti-clockwise rotation of velocity vector), some influence of rotation in limiting mixing should be detectable. We report here measurements of flow structure (with ADCPs) and turbulent dissipation (FLY Profiler) made at two similar locations in the Celtic Sea which differ principally in that the tidal currents rotate in opposite senses with approximately equal magnitude (polarity P=±0.6). A clear contrast was observed between the two sites in the vertical structure of the currents, the density profile and the rate of dissipation of TKE. At the positive polarity (PP) site (P≈+0.6), the bottom boundary layer in the tidal flow was limited to ∼20 mab (metre above the bed) and significant dissipation from bottom boundary friction was constrained within this layer. At the negative polarity (NP) site (P≈−0.6), the dominant clockwise rotary current component exhibited a velocity defect (i.e. reduction relative to the free stream) extending into the upper half of the water column while significant dissipation was observed to penetrate much further up the water column with dissipation levels ∼10^−4.5 W m⁻³ reaching to the base of the pycnocline at 70–80 mab. These contrasting features of the vertical distribution of dissipation are well reproduced by a 1-D model when run with windstress and tidal forcing and using the observed density profile. Model runs with reversed polarity at the two sites, support the conclusion that the observed contrast in the structure of tidal velocity, dissipation and stratification is due to the influence of tidal stream polarity. Increased positive polarity reduces the upward penetration of mixing which allows the development of stronger seasonal stratification, which, in turn, further inhibits vertical mixing.     

High-frequency vertical current observations in stratified seas

Although large-scale tidal and inertial motions dominate the kinetic energy and vertical current shear in shelf seas and ocean, short-scale internal waves at higher frequencies close to the local buoyancy frequency are of some interest for studying internal wave breaking and associated diapycnal mixing. Such waves near the upper limit of the inertio-gravity wave band are thought to have relatively short O (10²–10³ m) horizontal scales and to show mainly up- and downward motions, which contrasts with generally low aspect ratio large-scale ocean currents. Here, short-term vertical current (w) observations using moored acoustic Doppler current profiler (ADCP) are presented from a shelf sea, above a continental slope and from the open ocean. The observed w, with amplitudes between 0.015 and 0.05 m s⁻¹, all span a considerable part of the water column, which is not a small vertical scale O(water depth) or O (100–500 m, the maximum range of observations), with either 0 or π phase change. This implies that they actually represent internal waves of low vertical modes 1 or 2. Maximum amplitudes are found in layers of largest stratification, some in the main pycnocline bordering the frictional bottom boundary layer, suggesting a tidal source. These ‘pycnocline-w’ compose a regular train of (solitary) internal waves and linearly decrease to small values near surface and bottom.     

Turbulent mixing in fine-scale phytoplankton layers: Observations and inferences of layer dynamics

Turbulence measurements in fine-scale phytoplankton layers (∼1 to ∼10 m) in the Gulf of Aqaba (Red Sea) were used to evaluate mechanisms of layer formation, maintenance, and breakdown. Simultaneous profiles of chlorophyll a (Chl a) fluorescence and temperature microstructure were measured in the upper 40 m of a 430 m water column over a 16-d period, using a Self Contained Autonomous MicroProfiler (SCAMP). Layers of concentrated phytoplankton were identified in 95 of the 456 profiles. The layers were situated in density stratified regions between 15 and 38 m depth and were characterized by intensities of 0.1 to 0.35 μg Chl a L⁻¹ (as much as two times background concentrations) and an average thickness of 10 m. We show that turbulent mixing and isopycnal displacements associated with internal waves modulated the thickness of the layers. Variations in mixing rates within layers were connected to the vertical structure of the stratified turbulence and the stage of layer development. The breakdown of a persistent phytoplankton layer was tied to strong turbulent mixing at the base of the surface mixed layer, which encroached on the layer from above. Hydrographic observations and scaling analysis suggest that the layers most likely formed in horizontal intrusions from the adjacent coastal region. The cross-shore propagation of phytoplankton-rich intrusions may have important implications for the trophic state of offshore planktonic communities.     

Nutrient interleaving below the mixed layer of the Kuroshio Extension Front

Nitrate interleaving structures were observed below the mixed layer during a cruise to the Kuroshio Extension in October 2009. In this paper, we investigate the formation mechanisms for these vertical nitrate anomalies, which may be an important source of nitrate to the oligotrphoc surface waters south of the Kuroshio Extension Front. We found that nitrate concentrations below the main stream of the Kuroshio Extension were elevated compared to the ambient water of the same density (σ _?? = 23.5–25). This appears to be analogous to the “nutrient stream” below the mixed layer, associated with the Gulf Stream. Strong turbulence was observed above the vertical nitrate anomaly, and we found that this can drive a large vertical turbulent nitrate flux \(>\mathcal {O}\) (1 mmol N m^?2 day^?1). A realistic, high-resolution (2 km) numerical simulation reproduces the observed Kuroshio nutrient stream and nitrate interleaving structures, with similar lateral and vertical scales. The model results suggest that the nitrate interleaving structures are first generated at the western side of the meander crest on the south side of the Kuroshio Extension, where the southern tip of the mixed layer front is under frontogenesis. Lagrangian analyses reveal that the vertical shear of geostrophic and subinertial ageostrophic flow below the mixed layer tilts the existing along-isopycnal nitrate gradient of the Kuroshio nutrient stream to form nitrate interleaving structures. This study suggests that the multi-scale combination of (i) the lateral stirring of the Kuroshio nutrient stream by developed mixed layer fronts during fall to winter, (ii) the associated tilting of along-isopycnal nitrate gradient of the nutrient stream by subinertial shear, which forms vertical interleaving structures, and (iii) the strong turbulent diffusion above them, may provide a route to supply nutrients to oligotrophic surface waters on the south side of the Kuroshio Extension.     

Observed oceanic response to tropical cyclone Jal from a moored buoy in the south-western Bay of Bengal

Upper oceanographic and surface meteorological time-series observations from a moored buoy located at 9.98°N, 88°E in the south-western Bay of Bengal (BoB) were used to quantify variability in upper ocean, forced by a tropical cyclone (TC) Jal during November 2010. Before the passage of TC Jal, salinity and temperature profiles showed a typical BoB post-monsoon structure with relatively warm (30 °C) and low-saline (32.8 psu) waters in the upper 30- to 40-m layer, and relatively cooler and higher salinity (35 psu) waters below. After the passage of cyclone, an abrupt increase of 1 psu (decrease of 1 °C) in salinity (temperature) in the near-surface layers (up to 40-m depth) was observed from buoy measurements, which persisted up to 10–12 days during the relaxation stage of cyclone. Mixed layer heat budget analysis showed that vertical processes are the dominant contributors towards the observed cooling. The net surface heat flux and horizontal advection together contributed approximately 33 % of observed cooling, during TC Jal forced stage. Analysis showed the existence of strong inertial oscillation in the thermocline region and currents with periodicity of ～2.8 days. During the relaxation stage of the cyclone, upward movement of thermocline in near-inertial frequencies played significant role in mixed layer temperature and salinity variability, by much freer turbulent exchange between the mixed layer and thermocline.     

The effects of vertical shear and stratification on stationary rossby waves

Abstract

The generation of stationary Rossby waves by sources of potential vorticity in a westerly flow is examined here in the context of a two-layer, quasi-geostrophic, β-plane model. The response in each layer consists of a combination of a barotropic Rossby wave disturbance that extends far downstream of the source, and a baroclinic disturbance which is evanescent or wave-like in character, depending on the shear and degree of stratification. Contributions from each of these modes in each layer are strongly dependent on the basic flows in each layer; the degree of stratification; and the depths of the two layers. The lower layer response is dominated by an evanescent baroclinic mode when the upper layer westerlies are much larger than those in the lower layer. In this case, weak stationary Rossby waves of large wavelengths are confined to the upper layer and the disturbance in the lower layer is confined to the source region.

Increasing the upper layer flow (with the lower layer flow fixed) increases the Rossby wavelength and decreases the amplitude. Decreasing the lower layer flow (with the upper layer flow fixed) decreases the wavelength and increases the amplitude. Stratification increases the contribution from the barotropic wave-like mode and causes the response to be confined to the lower layer.

The finite amplitude response to westerly flow over two sources of potential vorticity is also considered. In this case stationary Rossby waves induced by both sources interact to reinforce or diminish the downstream wave pattern depending on the separation distance of the sources relative to the Rossby wavelength. For fixed separation distance, enhancement of the downstreatm Rossby waves will only occur for a narrow range of flow variables and stratification.     

Linear hydromagnetic stability of a differentially rotating non-uniformly stratified fluid layer

Summary Our discussion is concerned with the common effect of the non-uniformity of layer rotation and stratification. We have assumed a model of differential rotation with the upper part of the layer rotating more slowly, the bottom part more quickly. The upper part of the layer is stratified stably, the bottom part unstably.The thermal instabilities are preferred in the strong differential rotation case and they are the most easily excited by a strong magnetic field (10²–10³). The direction of its propagation is westward in the uniformly stratified layer and eastward in the non-uniformly stratified layer.     

Wind mixing of a stratified shear flow

The response of a shear flow to an imposed wind stress is studied both theoretically and by means of a numerical turbulence model. It is shown that for small initial gradient Richardson numbers (Ri₀ ≲ 4/3) a tail wind causes the slab velocity of the upper mixed layer to decrease. The theory is based on the assumption that during the wind-induced entrainment process the overall Richardson number will adjust to a quasi-constant value (Ri_u ≈ 2/3). The turbulence model is the so-called k-ɛ model. It is calibrated to five conditions by tuning only one constant. The details of the deepening process and the density and velocity distributions of the upper mixed layer during this anomalous behavior are thus made clear. The results imply that the common practice of estimating the total current velocity by vector addition of the original velocity and the wind-induced velocity (calculated from models based on an ocean at rest) may lead to an overestimation of the current speed.     

Longitudinal variations of phytoplankton compositions in lake-to-river systems

To test the hypothesis of longitudinal variations in phytoplankton compositions from a eutrophic lake to its river downstream and determine the length of the transition zone, we applied functional groups as well as taxonomical methods to this coupled aquatic system, which is composed of the Dianchi Lake upstream and the Tanglang River downstream, by sampling at 9 stations during Microcystis blooms in the Dianchi Lake in 2013. The longitudinal variations in phytoplankton compositions from lacustrine species to fluvial species were reflected by: (1) the shift from Microcystis to Chlorococcales green algae and centric diatoms; (2) the shift from the dominance of codon M to the coexistence of a variety of coda without one outstanding codon; and (3) except for codon M, the shift from lacustrine coda (H1, L_O, T) towards coda that are adapted to both lacustrine and fluvial circumstances (MP, X1, X2). The prominent difference of phytoplankton compositions between the Dianchi Lake and the lower reaches of the Tanglang River revealed that there was a transition zone in between. The upper and middle reaches of the Tanglang River with a length of approximately 26.4 km were considered the transition zone because: (1) the dominant lentic codon M in the Dianchi Lake disappeared at the lower reaches of the river; (2) the amount of codon P that is sensitive to stratification rose at the beginning of the river; and (3) the codon T, which is well adapted to the persistently mixed layer or epilimnia of lakes, lost a large number of biomass at the upper and middle reaches of the Tanglang River. In this study, we found that the eutrophic lake had a significant influence on the river downstream. In addition, we found that functional groups were sensitive to the changes of external aquatic conditions and helpful in determining the length of the transition zone.     

南方水库热分层消亡期混合层深度及缺氧区时空变化特征——以南宁市天雹水库为例

湖库热分层消亡引起的突发性水质恶化现象引起了广泛的关注,我国南方水库大多是暖单次混合型湖泊,每年混合一次,导致水库水质周期性下降,但目前对南方水库热分层消亡过程的高频监测研究较少。为探究我国南方水库热分层消亡期水体混合过程的时空变化规律及驱动因素,以广西南宁天雹水库为例,于冬季热分层消亡期(2019年11月—2020年2月)对水库多点位水体理化指标开展原位监测,并利用自建气象站获取气象水文数据。结果表明:(1)水库热分层消亡期间,过渡区水深较浅可在短期内达到完全混合状态且缺氧区同步消失;而湖泊区混合过程整体滞后于过渡区,混合层深度由6.85 m增加至13.65 m,缺氧区逐渐减小,缺氧指数(AI)由0.40减小至0.07,直至水体完全混合后缺氧区消失;水库过渡区较湖泊区提前约40 d达到完全混合状态。(2)气象因子是引起热分层结构变化的主要因素,气温(T)、辐射(R)与混合层深度(MLD)呈现显著负相关(R_T=0.927、R_R=0.925,P<0.01),风速(WS)与MLD呈现显著正相关(R_WS=0.728,P&...     

Vertical distributions of chlorophyll in deep, warm monomictic lakes

The factors affecting vertical distributions of chlorophyll fluorescence were examined in four temperate, warm monomictic lakes. Each of the lakes (maximum depth >80 m) was sampled over 2 years at intervals from monthly to seasonal. Profiles were taken of chlorophyll fluorescence (as a proxy for algal biomass), temperature and irradiance, as well as integrated samples from the surface mixed layer for chlorophyll a (chl a) and nutrient concentrations in each lake. Depth profiles of chlorophyll fluorescence were also made along transects of the longest axis of each lake. Chlorophyll fluorescence maxima occurred at depths closely correlated with euphotic depth (r ² = 0.67, P < 0.01), which varied with nutrient status of the lakes. While seasonal thermal density stratification is a prerequisite for the existence of a deep chlorophyll maximum (DCM), our study provides evidence that the depth of light penetration largely dictates the DCM depth during stratification. Reduction in water clarity through eutrophication can cause a shift in phytoplankton distributions from a DCM in spring or summer to a surface chlorophyll maximum within the surface mixed layer when the depth of the euphotic zone (z _eu) is consistently shallower than the depth of the surface mixed layer (z _SML). Trophic status has a key role in determining vertical distributions of chlorophyll in the four lakes, but does not appear to disrupt the annual cycle of maximum chlorophyll in winter.     

The deepening of the wind-Mixed layer

Abstract

A simple model is given that describes the response of the upper ocean to an imposed wind stress. The stress drives both mean and turbulent flow near the surface, which is taken to mix thoroughly a layer of depth h, and to erode the stably stratified fluid below. A marginal stability criterion based on a Froude number is used to close the problem, and it is suggested that the mean momentum has a strong role in the mixing process. The initial deepening is predicted to obey

where u. is the friction velocity of the imposed stress, N the ambient buoyancy frequency, and t the time.

After one-half inertial period the deepening is arrested by rotadeon at a depth h = 2^2/4 u.{(Nf)⁺

where f is the Coriolis frequency. The flow is then a “mixed Ekman” layer, with strong inertial oscillations superimposed on it. Three quarters of the mean energy of the deepening layer is found to be kinetic, and only one-quarter potential.

Heating and cooling are included in the model, but stress dominates for time-scales of a day or less. Non-uniform stratification and currents existing prior to the onset of the wind are easily included.

Agreement between the first formula above and laboratory experiments of Kato and Phillips is very satisfactory; the second formula is consistent with observations of Francis and Stommel, though a more thorough test is needed. Oceanic observations in general support the assumption of slab-like mean profiles and direct response of the fluid to local winds.     

Convective instabilities in a variable viscosity fluid cooled from above

Whether in the mantle or in magma chambers, convective flows are characterized by large variations of viscosity. We study the influence of the viscosity structure on the development of convective instabilities in a viscous fluid which is cooled from above. The upper and lower boundaries of the fluid are stress-free. A viscosity dependence with depth of the form ν₀ + ν₁ exp(?γ.z) is assumed. After the temperature of the top boundary is lowered, velocity and temperature perturbations are followed numerically until convective breakdown occurs. Viscosity contrasts of up to 10⁷ and Rayleigh numbers of up to 10⁸ are studied.For intermediate viscosity contrasts (around 10³), convective breakdown is characterized by the almost simultaneous appearance of two modes of instability. One involves the whole fluid layer, has a large horizontal wavelength (several times the layer depth) and exhibits plate-like behaviour. The other mode has a much smaller wavelength and develops below a rigid lid. The “whole layer” mode dominates for small viscosity contrasts but is suppressed by viscous dissipation at large viscosity contrasts.For the “rigid lid” mode, we emphasize that it is the form of the viscosity variation which determines the instability. For steep viscosity profiles, convective flow does not penetrate deeply in the viscous region and only weak convection develops. We propose a simple method to define the rigid lid thickness. We are thus able to compute the true depth extent and the effective driving temperature difference of convective flow. Because viscosity contrasts in the convecting region do not exceed 100, simple scaling arguments are sufficient to describe the instability. The critical wavelength is proportional to the thickness of the thermal boundary layer below the rigid lid. Convection occurs when a Rayleigh number defined locally exceeds a critical value of 160–200. Finally, we show that a local Rayleigh number can be computed at any depth in the fluid and that convection develops below depth z_r (the rigid lid thickness) such that this number is maximum.The simple similarity laws are applied to the upper mantle beneath oceans and yield estimates of 5 × 10¹⁵?5 × 10¹⁶ m² s^?1 for viscosity in the thermal boundary layer below the plate.     

Short-term variation in thermal stratification complicates estimation of lake metabolism

Previous studies have used sondes to measure diel changes in dissolved oxygen and thereby estimate gross primary production (GPP), ecosystem respiration (R), and net ecosystem production (NEP). Most of these studies estimate rates for the surface layer and require knowing the depth of the mixed layer (Z_mix), which is usually determined from discrete daily or weekly temperature profiles. However, Z_mix is dynamic, as the thermal structure of lakes may change at scales of minutes rather than days or weeks. We studied two thermally stratified lakes that exhibited intermittent microstratification in the mixed layer. We combined sonde-based estimates of metabolism with high-frequency measurements of stratification using thermistor chains to determine how the short-term dynamics of stratification affect metabolic rates. We calculated estimates of metabolism using time series of Z_mix measured at seasonal, weekly, daily, and 5-min intervals. Areal rates of GPP and R were up to 24 and 29% less, respectively, using the 5-min measurements of Z_mix rather than weekly Z_mix, while NEP was not significantly different. These reduced areal rates are mostly the consequence of the reduction in the depth of the mixed layer. Microstratification occurred frequently in both lakes and affected volumetric rates in one lake where R was significantly lower, NEP was significantly higher, and GPP was marginally lower compared to days without microstratification. Hence, microstratification not only affects the depth of the mixed layer, but also alters the processes that influence photosynthesis and respiration. Future studies should consider microstratification and possibly employ multiple sondes with thermistor chains that enable integrating metabolic rates to a specific depth, rather than assuming a stable upper mixed layer as the basis for calculations.     

Empirical model of Skeletonema costatum photosynthetic rate,with applications in the San Francisco Bay estuary

An empirical model of Skeletonema costatum photosynthetic rate is developed and fit to measurements of photosynthesis selected from the literature. Because the model acknowledges existence of: 1) a light-temperature interaction (by allowing optimum irradiance to vary with temperature), 2) light inhibition, 3) temperature inhibition, and 4) a salinity effect, it accurately estimates photosynthetic rates measured over a wide range of temperature, light intensity, and salinity. Integration of predicted instantaneous rate of photosynthesis with time and depth yields daily net carbon assimilation (pg C cell^?1 day^?1) in a mixed layer of specified depth, when salinity, temperature, daily irradiance and extinction coefficient are known. The assumption of constant carbon quota (pg C cell^?1) allows for prediction of mean specific growth rate (day^?1), which can be used in numerical models of Skeletonema costatum population dynamics.Application of the model to northern San Francisco Bay clearly demonstrates the limitation of growth by low light availability, and suggests that large population densities of S. costatum observed during summer months are not the result of active growth in the central deep channels (where growth rates are consistently predicted to be negative). But predicted growth rates in the lateral shallows are positive during summer and fall, thus offering a testable hypothesis that shoals are the only sites of active population growth by S. costatum (and perhaps other neritic diatoms) in the northern reach of San Francisco Bay.