Jon R. Burau

Measurements of Reynolds stress profiles in unstratified tidal flow

In this paper we present a method for measuring profiles of turbulence quantities using a broadband acoustic doppler current profiler (ADCP). The method follows previous work on the continental shelf and extends the analysis to develop estimates of the errors associated with the estimation methods. ADCP data was collected in an unstratified channel and the results of the analysis are compared to theory. This comparison shows that the method provides an estimate of the Reynolds stresses, which is unbiased by Doppler noise, and an estimate of the turbulent kinetic energy (TKE) which is biased by an amount proportional to the Doppler noise. The noise in each of these quantities as well as the bias in the TKE match well with the theoretical values produced by the error analysis. The quantification of profiles of Reynolds stresses simultaneous with the measurement of mean velocity profiles allows for extensive analysis of the turbulence of the flow. In this paper, we examine the relation between the turbulence and the mean flow through the calculation of u * , the friction velocity, and C d , the coefficient of drag. Finally, we calculate quantities of particular interest in turbulence modeling and analysis, the characteristic lengthscales, including a lengthscale which represents the stream-wise scale of the eddies which dominate the Reynolds stresses.

Structure and Flow-Induced Variability of the Subtidal Salinity Field in Northern San Francisco Bay

Abstract The structure of the salinity field in northern San Francisco Bay and how it is affected by freshwater flow are discussed. Two datasets are examined: the first is 23 years of daily salinity data taken by the U.S. Bureau of Reclamation along the axis of northern San Francisco Bay; the second is a set of salinity transects taken by the U.S. Geological Survey between 1988 and 1993. Central to this paper is a measure of salinity intrusion, X2: the distance from the Golden Gate Bridge to where the bottom salinity is 2 psu. Using X2 to scale distance, the authors find that for most flow conditions, the mean salinity distribution of the estuary is nearly self-similar with a salinity gradient in the center 70% of the region between the Golden Gate and X2 that is proportional to X−12. Analysis of covariability of Q and X2 showed a characteristic timescale of adjustment of the salinity field of approximately 2 weeks. The steady-state response deduced from the X2 time series implies that X2 is proportional ...

Observations of Turbulence in a Partially Stratified Estuary

The authors present a field study of estuarine turbulence in which profiles of Reynolds stresses were directly measured using an ADCP throughout a 25-h tidal day. The dataset that is discussed quantifies turbulent mixing for a water column in northern San Francisco Bay that experiences a sequence of states that includes a weak ebb and flood that are stratified, followed by a strong, and eventually unstratified, ebb and flood. These measurements show that energetic turbulence is confined to a bottom mixed layer by the overlying stratification. Examination of individual Reynolds stress profiles along with profiles of Richardson number and turbulent Froude number shows that the water column can be divided into regions based on the relative importance of buoyancy effects. Using the measured turbulence production rate P, the dissipation rate e is estimated. The observed turbulence had values of e/nN 2 . 20 all of the time and e/nN 2 . 200 most of the time, suggesting that the observed motions were buoyancy affected turbulence rather than internal waves. However, at times, turbulent Froude numbers in much of the upper-water column were less than one, indicating important stratification effects. Taken as a whole, the data show that stratification affects the turbulent velocity variance q2 most severely; that is, observed reductions in u9w9 are largely associated with small values of q2 rather than with a dramatic reduction in the efficiency with which turbulent motions produce momentum fluxes. Finally, the dataset is compared to predictions made using the popular Mellor‐Yamada level 2.5 closure. These comparisons show that the model tends to underestimate the turbulent kinetic energy in regions of strong stratification where the turbulence is strongly inhomogeneous and to overestimate the turbulent kinetic energy in weakly stratified regions. The length scale does not appear to compensate for these errors, and, as a result, similar errors are seen in the eddy viscosity predictions. It is hypothesized that the underestimation of q2 is due to an inaccurate parameterization of turbulence self-transport from the near-bed region to the overlying stratification.

Creation of residual flows in a partially stratified estuary

The creation of residual flows in estuaries is examined using acoustic Doppler current profiler data sets from northern San Francisco Bay. The data sets are analyzed using principal component analysis to examine the temporal variability of the flows which create the residual circulation. It is seen that in this periodically and partially stratified estuary the residual flows are created through a series of pulses with strong variability at the 24-hour timescale, through the interaction of shear, stratification and mixing. This interaction is captured through the use of a dimensionless number, the horizontal Richardson number (Rix), which is developed to examine the local balance between the stratifying and destratifying forces at the tidal timescale. It is seen that Rix is a valuable parameter in predicting the onset of the residual-creating events, with a threshold value of ≈3 on ebb tides. This critical value is argued to be a threshold, above which the stratification and shear flow create a feedback effect, each further intensifying the other. This feedback results in a highly variable exchange flow which creates the estuarine residual in intermittent pulses rather than as a steady flow. Although typically attributed to baroclinic forcing, an argument is made that these pulses of residual-creating exchange flow could be created by barotropic forcing in the presence of variable stratification which is asymmetric between flood and ebb tides. This result poses a great challenge for turbulence modeling, as the timing and magnitude of stratification and shear must be correctly simulated on the tidal timescale in order to reproduce the effects seen in the data sets presented.

Ecological Values of Shallow-Water Habitats: Implications for the Restoration of Disturbed Ecosystems

A presumed value of shallow-habitat enhanced pelagic productivity derives from the principle that in nutrient-rich aquatic systems phytoplankton growth rate is controlled by light availability, which varies inversely with habitat depth. We measured a set of biological indicators across the gradient of habitat depth within the Sacramento–San Joaquin River Delta (California) to test the hypothesis that plankton biomass, production, and pelagic energy flow also vary systematically with habitat depth. Results showed that phytoplankton biomass and production were only weakly related to phytoplankton growth rates whereas other processes (transport, consumption) were important controls. Distribution of the invasive clam Corbicula fluminea was patchy, and heavily colonized habitats all supported low phytoplankton biomass and production and functioned as food sinks. Surplus primary production in shallow, uncolonized habitats provided potential subsidies to neighboring recipient habitats. Zooplankton in deeper habitats, where grazing exceeded phytoplankton production, were likely supported by significant fluxes of phytoplankton biomass from connected donor habitats. Our results provide three important lessons for ecosystem science: (a) in the absence of process measurements, derived indices provide valuable information to improve our mechanistic understanding of ecosystem function and to benefit adaptive management strategies; (b) the benefits of some ecosystem functions are displaced by water movements, so the value of individual habitat types can only be revealed through a regional perspective that includes connectedness among habitats; and (c) invasive species can act as overriding controls of habitat function, adding to the uncertainty of management outcomes.

Persistence of tidally-oriented vertical migration by zooplankton in a temperate estuary

Tidal vertical migration by zooplankton is a common phenomenon in estuaries, usually associated with landward movement of meroplankton or position maintenance of holoplankton. Little is known about the persistence of this behavior, its spatial variability, or its response to changing environmental conditions. We extended a previous study of tidal movements of zooplankton in the low-salinity zone (LSZ) of the San Francisco estuary in 1994 to include data from two additional years with very different hydrology. Freshwater flow during sampling in 1995 was about 7-fold greater than in 1994; the LSZ was about 28 km further seaward, and gravitational circulation in the LSZ was strong. In 1996 freshwater flow and LSZ position were intermediate but, because the LSZ was in shallower water in 1996 than in 1995, gravitational circulation was uncommon. Behavior of copepods in both years was similar to that reported in 1994 with some tidal migration observed during most cruises. An exception was the introduced carnivorous copepodTortanus dextrilobatus, which did not migrate and maintained a position deep in the water column (1995 only). In 1996, mysids mainly stayed near the bottom with evidence for vertical migration from only 1 of 6 data sets, whereas amphipods migrated slightly on a diel schedule; these behaviors contrasted with the tidal migration observed in 1994. The bay shrimpCrangon franciscorum did not appear to migrate, but was more abundant in the water column during both ebb and flood, suggesting passive vertical dispersal. Zooplankton did not appear to maintain position by interactions with lateral circulation cells. The results for copepods suggest rigidity in behavior with little or no relaxation of the vertical movement in 1995 when strong gravitational circulation would have made upstream movement relatively easy. Mysids and amphipods altered their behavior depending on local conditions related to freshwater flow.

Intradaily Variability of Water Quality in a Shallow Tidal Lagoon: Mechanisms and Implications

Although surface water quality and its underlying processes vary over time scales ranging from seconds to decades, they have historically been studied at the lower (weekly to interannual) frequencies. The aim of this study was to investigate intradaily variability of three water quality parameters in a small freshwater tidal lagoon (Mildred Island, California). High frequency time series of specific conductivity, water temperature, and chlorophylla at two locations within the habitat were analyzed in conjunction with supporting hydrodynamic, meteorological, biological, and spatial mapping data. All three constituents exhibited large amplitude intradaily (e.g., semidiurnal tidal and diurnal) oscillations, and periodicity varied across constituents, space, and time. Like other tidal embayments, this habitat is influenced by several processes with distinct periodicities including physical controls, such as tides, solar radiation, and wind, and biological controls, such as photosynthesis, growth, and grazing. A scaling approach was developed to estimate individual process contributions to the observed variability. Scaling results were generally consistent with observations and together with detailed examination of time series and time derivatives, revealed specific mechanisms underlying the observed periodicities, including interactions between the tidal variability, heating, wind, and biology. The implications for monitoring were illustrated through subsampling of the data set. This exercise demonstrated how quantities needed by scientists and managers (e.g., mean or extreme concentrations) may be misrepresented by low frequency data and how short-duration high frequency measurements can aid in the design and interpretation of temporally coarser sampling programs. The dispersive export of chlorophylla from the habitat exhibited a fortnightly variability corresponding to the modulation of semidiurnal tidal currents with the diurnal cycle of phytoplankton variability, demonstrating how high frequency interactions can govern long-term trends. Process identification, as through the scaling analysis here, can help us anticipate changes in system behavior and adapt our own interactions with the system.

The Tidally Averaged Momentum Balance in a Partially and Periodically Stratified Estuary

Abstract Observations of turbulent stresses and mean velocities over an entire spring–neap cycle are used to evaluate the dynamics of tidally averaged flows in a partially stratified estuarine channel. In a depth-averaged sense, the net flow in this channel is up estuary due to interaction of tidal forcing with the geometry of the larger basin. The depth-variable tidally averaged flow has the form of an estuarine exchange flow (downstream at the surface, upstream at depth) and varies in response to the neap–spring transition. The weakening of the tidally averaged exchange during the spring tides appears to be a result of decreased stratification on the tidal time scale rather than changes in bed stress. The dynamics of the estuarine exchange flow are defined by a balance between the vertical divergence of the tidally averaged turbulent stress and the tidally averaged pressure gradient in the lower water column. In the upper water column, tidal stresses are important contributors, particularly during the n...

Sensitivity of survival to migration routes used by juvenile Chinook salmon to negotiate the Sacramento-San Joaquin River Delta

Populations of juvenile salmon emigrating from natal rivers to the ocean must often traverse different migratory pathways that may influence survival. In regulated rivers, migration routes may consist of a network of channels such as in the Sacramento-San Joaquin River Delta, or of different passage structures at hydroelectric dams (e.g., turbines or spillways). To increase overall survival, management actions in such systems often focus on altering the migration routing of fish to divert them away from low-survival routes and towards high-survival routes. Here, we use a 3-year data set of route-specific survival and movement of juvenile Chinook salmon in the Sacramento-San Joaquin Delta to quantify the sensitivity of survival to changes in migration routing at two major river junctions in the Sacramento River. Our analysis revealed that changes in overall survival in response to migration routing at one river junction depended not only differences in survival among alternative routes, but also on migration routing at the other river junction. Diverting fish away from a low-survival route at the downstream river junction increased population survival by less than expected, given the difference in survival among routes, because part of the population used an alternative migration route at the upstream river junction. We also show that management actions that influence only migration routing will likely increase survival by less than actions that alter both migration routing and route-specific survival. Our analysis provides an analytical framework to help fisheries managers quantify the suite of management actions likely to maximize increases in population level survival.

Riders on the storm: selective tidal movements facilitate the spawning migration of threatened delta smelt in the San Francisco Estuary

Migration strategies in estuarine fishes typically include behavioral adaptations for reducing energetic costs and mortality during travel to optimize reproductive success. The influence of tidal currents and water turbidity on individual movement behavior were investigated during the spawning migration of the threatened delta smelt, Hypomesus transpacificus, in the northern San Francisco Estuary, California, USA. Water current velocities and turbidity levels were measured concurrently with delta smelt occurrence at sites in the lower Sacramento River and San Joaquin River as turbidity increased due to first-flush winter rainstorms in January and December 2010. The presence/absence of fish at the shoal-channel interface and near the shoreline was quantified hourly over complete tidal cycles. Delta smelt were caught consistently at the shoal-channel interface during flood tides and near the shoreline during ebb tides in the turbid Sacramento River, but were rare in the clearer San Joaquin River. The apparent selective tidal movements by delta smelt would facilitate either maintaining position or moving upriver on flood tides, and minimizing advection down-estuary on ebb tides. These movements also may reflect responses to lateral gradients in water turbidity created by temporal lags in tidal velocities between the near-shore and mid-channel habitats. This migration strategy can minimize the energy spent swimming against strong river and tidal currents, as well as predation risks by remaining in turbid water. Selection pressure on individuals to remain in turbid water may underlie population-level observations suggesting that turbidity is a key habitat feature and cue initiating the delta smelt spawning migration.