Geology topics

Stephen G. Monismith

Publications and source records attributed to Stephen G. Monismith.

At least 19 recordsLinked to original sources

USGS2021

Characterization of the biological, physical, and chemical properties of a toxic thin layer in a temperate marine system

The distribution of plankton in the ocean is patchy across a wide range of spatial and temporal scales. One type of oceanographic feature that exemplifies this patchiness is a ‘thin layer’. Thin layers are subsurface aggregations of plankton that range in vertical thickness from centimeters to a few meters, which may extend horizontally for kilometers and persist for days. We undertook a field campaign to characterize the biological, physical, and chemical properties of thin layers in Monterey Bay, California (USA), an area where these features can be persistent. The particle aggregates (marine snow) sampled in the study had several quantifiable properties indicating how the layer was formed and how its structure was maintained. Particles were more elongated above the layer, and then changed orientation angle and increased in size within the layer, suggesting passive accumulation of particles along a physical gradient. The shift in particle aggregate orientation angle near the pycnocline suggests that shear may also have played a role in generating the thin layer. Pseudo-nitzschia spp. were the most abundant phytoplankton within the thin layer. Further, both dissolved and particulate domoic acid were highest within the thin layer. We suggest that phosphate stress is responsible for the formation of Pseudo-nitzschia spp. aggregates. This stress together with increased nitrogen in the layer may lead to increased bloom toxicity in the subsurface blooms of Pseudo-nitzschia spp. Several zooplankton groups were observed to aggregate above and below the layer. With the knowledge that harmful algal bloom events can occur in subsurface thin layers, modified sampling methods to monitor for these hidden incubators could greatly improve the efficacy of early-warning systems designed to detect harmful algal blooms in coastal waters.

Marine Ecology Progress Series (MEPS)↗

USGS2018

Three-dimensional modeling of ﬁne sediment transport by waves and currents in a shallow estuary

A suspended sediment transport model is implemented in the unstructured‐grid SUNTANS model and applied to study fine‐grained sediment transport in South San Francisco Bay. The model enables calculation of suspension of bottom sediment based on combined forcing of tidal currents and wind waves. We show that accurate results can be obtained by employing two‐size classes which are representative of microflocs and macroflocs in the Bay. A key finding of the paper is that the critical calibration parameter is the ratio of the erosion of the microflocs to macroflocs from the bed. Different values of this erosion ratio are needed on the shallow shoals and deeper channels because of the different nature of the sediment dynamics in these regions. Application of a spatially variable erosion ratio and critical shear stress for erosion is shown to accurately reproduce observed suspended sediment concentration at four‐field sites located along a cross‐channel transect. The results reveal a stark contrast between the behavior of the suspended sediment concentration on the shoals and in the deep channel. Waves are shown to resuspend sediments on the shoals, although tidal and wind‐generated currents are needed to mix the thin wave‐driven suspensions into the water column. The contribution to the suspended sediment concentration in the channel by transport from the shoals is similar in magnitude to that due to local resuspension. However, the local contribution is in phase with strong bottom currents which resuspend the sediments, while the contribution from the shoals peaks during low‐water slack tide.

San Francisco Bay↗

USGS2017

Behavior of a wave-driven buoyant surface jet on a coral reef

A wave-driven surface buoyant jet exiting a coral reef was studied in order to quantify the amount of water re-entrained over the reef crest. Both moored observations and Lagrangian drifters were used to study the fate of the buoyant jet. To investigate in detail the effects of buoyancy and along-shore flow variations, we developed an idealized numerical model of the system. Consistent with previous work, the ratio of along-shore velocity to jet-velocity and the jet internal Froude number were found to be important determinants of the fate of the jet. In the absence of buoyancy, the entrainment of fluid at the reef crest, creates a significant amount of retention, keeping 60% of water in the reef system. However, when the jet is lighter than the ambient ocean-water, the net effect of buoyancy is to enhance the separation of the jet from shore, leading to a greater export of reef water. Matching observations, our modeling predicts that buoyancy limits retention to 30% of the jet flow for conditions existing on the Moorea reef. Overall, the combination of observations and modeling we present here shows that reef-ocean temperature gradients can play an important role in reef-ocean exchanges.

Journal of Geophysical Research C: Oceans↗

USGS2016

Recent advances in understanding flow dynamics and transport of water-quality constituents in the Sacramento–San Joaquin River Delta

This paper, part of the collection of research comprising the State of Bay–Delta Science 2016, describes advances during the past decade in understanding flow dynamics and how water-quality constituents move within California’s Sacramento– San Joaquin River Delta (Delta). Water-quality constituents include salinity, heat, oxygen, nutrients, contaminants, organic particles, and inorganic particles. These constituents are affected by water diversions and other human manipulations of flow, and they greatly affect the quantity and quality of benthic, pelagic, and intertidal habitat in the Delta. The Pacific Ocean, the Central Valley watershed, human intervention, the atmosphere, and internal biogeochemical processes are all drivers of flow and transport in the Delta. These drivers provide a conceptual framework for presenting recent findings. The tremendous expansion of acoustic and optical instruments deployed in the Delta over the past decade has greatly improved our understanding of how tidal variability affects flow and transport. Sediment is increasingly viewed as a diminishing resource needed to sustain pelagic habitat and tidal marsh, especially as sea level rises. Connections among the watershed, Delta, and San Francisco Bay that have been quantified recently highlight that a landscape view of this system is needed, rather than consideration of each region in isolation. We discuss interactions of multiple drivers and information gaps.

California↗

USGS2013

Hydrodynamics of spur and groove formations on a coral reef

Spur and groove (SAG) formations are found on the fore reefs of many coral reefs worldwide. Although these formations are primarily present in wave‐dominated environments, their effect on wave‐driven hydrodynamics is not well understood. A two‐dimensional, depth‐averaged, phase‐resolving nonlinear Boussinesq model ( funwaveC ) was used to model hydrodynamics on a simplified SAG system. The modeling results show that the SAG formations together with shoaling waves induce a nearshore Lagrangian circulation pattern of counter‐rotating circulation cells. The mechanism driving the modeled flow is an alongshore imbalance between the pressure gradient (PG) and nonlinear wave (NLW) terms in the momentum balance. Variations in model parameters suggest the strongest factors affecting circulation include spur‐normal waves, increased wave height, weak alongshore currents, increased spur height, and decreased bottom drag. The modeled circulation is consistent with a simple scaling analysis based on the dynamical balance of NLW, PG, and bottom stress terms. Model results indicate that the SAG formations efficiently drive circulation cells when the alongshore SAG wavelength allows for the effects of diffraction to create alongshore differences in wave height without changing the mean wave angle.

Journal of Geophysical Research C: Oceans↗

USGS2010

The tidally averaged momentum balance in a partially and periodically stratified estuary

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 neap tides. The usefulness of an effective eddy viscosity in the tidally averaged momentum equation is explored, and it is seen that the effective eddy viscosity on the subtidal time scale would need to be negative to close the momentum balance. This is due to the dominant contribution of tidally varying turbulent momentum fluxes, which have no specific relation to the subtidal circulation. Using a water column model, the validity of an effective eddy viscosity is explored; for periodically stratified water columns, a negative effective viscosity is required.

Journal of Physical Oceanography↗

USGS2009

Hydrodynamic control of phytoplankton loss to the benthos in an estuarine environment

Field experiments were undertaken to measure the influence of hydrodynamics on the removal of phytoplankton by benthic grazers in Suisun Slough, North San Francisco Bay. Chlorophyll a concentration boundary layers were found over beds inhabited by the active suspension feeders Corbula amurensis and Corophium alienense and the passive suspension feeders Marenzellaria viridis and Laonome sp. Benthic losses of phytoplankton were estimated via both the control volume and the vertical flux approach, in which chlorophyll a concentration was used as a proxy for phytoplankton biomass. The rate of phytoplankton loss to the bed was positively correlated to the bed shear stress. The maximum rate of phytoplankton loss to the bed was five times larger than estimated by laboratory-derived pumping rates for the active suspension feeders. Reasons for this discrepancy are explored including a physical mechanism whereby phytoplankton is entrained in a near-bed fluff layer where aggregation is mediated by the presence of mucus produced by the infaunal community.

California↗

USGS2009

Shallow water processes govern system-wide phytoplankton bloom dynamics: A modeling study

A pseudo-two-dimensional numerical model of estuarine phytoplankton growth and consumption, vertical turbulent mixing, and idealized cross-estuary transport was developed and applied to South San Francisco Bay. This estuary has two bathymetrically distinct habitat types (deep channel, shallow shoal) and associated differences in local net rates of phytoplankton growth and consumption, as well as differences in the water column's tendency to stratify. Because many physical and biological time scales relevant to algal population dynamics decrease with decreasing depth, process rates can be especially fast in the shallow water. We used the model to explore the potential significance of hydrodynamic connectivity between a channel and shoal and whether lateral transport can allow physical or biological processes (e.g. stratification, benthic grazing, light attenuation) in one sub-region to control phytoplankton biomass and bloom development in the adjacent sub-region. Model results for South San Francisco Bay suggest that lateral transport from a productive shoal can result in phytoplankton biomass accumulation in an adjacent deep, unproductive channel. The model further suggests that turbidity and benthic grazing in the shoal can control the occurrence of a bloom system-wide; whereas, turbidity, benthic grazing, and vertical density stratification in the channel are likely to only control local bloom occurrence or modify system-wide bloom magnitude. Measurements from a related field program are generally consistent with model-derived conclusions.

Journal of Marine Systems↗

USGS2009

Turbulent stresses and secondary currents in a tidal-forced channel with significant curvature and asymmetric bed forms

Acoustic Doppler current profilers are deployed to measure both the mean flow and turbulent properties in a channel with significant curvature. Direct measurements of the Reynolds stress show a significant asymmetry over the tidal cycle where stresses are enhanced during the flood tide and less prominent over the ebb tide. This asymmetry is corroborated by logarithmic fits using 10 min "> 10 min 10min averaged velocity data. A smaller yet similar tendency asymmetry in drag coefficient is inferred by fitting the velocity and estimated large-scale pressure gradient to a one-dimensional along-channel momentum balance. This smaller asymmetry is consistent with recent modeling work simulating regional flows in the vicinity of the study site. The asymmetry in drag suggests the importance of previously reported bed forms for this channel and demonstrates spatial and temporarily variations in bed stress. Secondary circulation patterns observed in a relatively straight section of channel appear driven by local curvature rather than being remotely forced by the regions of significant curvature only a few hundred meters from the measurement site.

Journal of Hydraulic Engineering↗

USGS2008

Shallow water processes govern system-wide phytoplankton bloom dynamics: A field study

Prior studies of the phytoplankton dynamics in South San Francisco Bay, California, USA have hypothesized that bivalve filter-feeders are responsible for the limited phytoplankton blooms in the system. This study was designed to examine the effects of benthic grazing and light attenuation on this shallow, turbid, and nutrient replete system. We found that grazing by shallow water bivalves was important in determining phytoplankton bloom occurrence throughout the system and that above a shallow water bivalve grazing threshold, phytoplankton biomass did not exceed bloom levels. Wind speed, used as a proxy for light attenuation in the shallow water, was similarly important in determining bloom development in the shallow water. Environmental conditions and benthic grazing in the deep water channel had a less discernible effect on system-wide phytoplankton blooms although persistent water column stratification did increase bloom magnitude. The shallow water bivalves, believed to be preyed upon by birds and fish that migrate through the system in fall and winter, disappear each year prior to the spring phytoplankton bloom. Because growth of the phytoplankton depends so strongly on shallow water processes, any change in the shallow-water benthic filter-feeders or their predators has great potential to change the phytoplankton bloom dynamics in this system. ?? 2007 Elsevier B.V. All rights reserved.

Journal of Marine Systems↗

USGS2008

A note on the effect of wind waves on vertical mixing in Franks Tract, Sacramento-San Joaquin Delta, California, USA

A one-dimensional numerical model that simulates the effects of whitecapping waves was used to investigate the importance of whitecapping waves to vertical mixing at a 3-meter-deep site in Franks Tract in the Sacramento-San Joaquin Delta over an 11-day period. Locally-generated waves of mean period approximately 2 s were generated under strong wind conditions; significant wave heights ranged from 0 to 0.3 m. A surface turbulent kinetic energy flux was used to model whitecapping waves during periods when wind speeds > 5 m s-1 (62% of observations). The surface was modeled as a wind stress log-layer for the remaining 38% of the observations. The model results demonstrated that under moderate wind conditions (5–8 m s-1 at 10 m above water level), and hence moderate wave heights, whitecapping waves provided the dominant source of turbulent kinetic energy to only the top 10% of the water column. Under stronger wind (> 8 m s-1), and hence larger wave conditions, whitecapping waves provided the dominant source of turbulent kinetic energy over a larger portion of the water column; however, this region extended to the bottom half of the water column for only 7% of the observation period. The model results indicated that phytoplankton concentrations close to the bed were unlikely to be affected by the whitecapping of waves, and that the formation of concentration boundary layers due to benthic grazing was unlikely to be disrupted by whitecapping waves. Furthermore, vertical mixing of suspended sediment was unlikely to be affected by whitecapping waves under the conditions experienced during the 11-day experiment. Instead, the bed stress provided by tidal currents was the dominant source of turbulent kinetic energy over the bottom half of the water column for the majority of the 11-day period.

California↗

USGS2006

The importance of submarine groundwater discharge to the nearshore nutrient supply in the Gulf of Aqaba (Israel)

We used two short-lived radium isotopes (223Ra, 224Ra) and a mass balance approach applied to the radium activities to determine the nutrient contribution of saline submarine groundwater discharge to the coastal waters of the northern Gulf of Aqaba (Israel). Radium isotope activities were measured along transects during two seasons at a site that lacked any obvious surficial water input. An onshore well and an offshore end member were also sampled. For all samples, nutrients and salinity data were collected. Radium isotope activities generally decreased with distance offshore and exhibited significant tidal variability, which is consistent with a shore-derived tidally influenced source. Submarine groundwater contributes only 1-2% of the water along this coast, but this groundwater provides 8-46% of the nutrients. This saline groundwater is derived predominately from tidally pumped seawater percolating through the unconfined coastal aquifer and leaching radium and nutrients. This process represents a significant source of nutrients to the oligotrophic nearshore reef. ?? 2006, by the American Society of Limnology and Oceanography, Inc.

Limnology and Oceanography↗

USGS2005

Preliminary results from a shallow water benthic grazing study

The nutrient-rich, shallow waters of San Francisco Bay support high rates of primary production, limited not by nutrients but by light availability and benthic grazing (Alpine and others 1992; Cloern 1982). Phytoplankton blooms are an important food source for upper trophic levels. Consequently animal populations, such as fish, may suffer under conditions of high benthic bivalve grazing. It has been hypothesized that several species of fish are suffering as a result of severe decreases in available phytoplankton since the introduction of Potamocorbula amurensis into San Francisco Bay (Feyrer 2003). The extent of reduction in phytoplankton biomass by benthic bivalves is dependent on both physical and biological factors in addition to their spatial and temporal variability. Physical factors identified as important include: (1) vertical mixing rates, which are a function of wind velocity, currents, and bottom roughness; (2) suspended sediment concentrations; and (3) phytoplankton settling rates. The biological factors controlling the extent of phytoplankton grazing include animal density and organism size, pumping rate, food type and concentration, metabolic demands, assimilation efficiency, and behaviour (Wildish and Kristmanson 1997). Several laboratory studies involving model and live clams have shown that benthic grazers can deplete phytoplankton in the water column (for example, Cole and others 1992). Initially, these studies assumed that the water column remained well mixed above benthic suspension feeders; therefore, parameters measured in the bulk water column were believed to be representative of available particle concentration. For this reason many relationships describing the influence of the bulk flow and bulk seston concentration on benthic grazers physiological processes exist (for example, Levinton 1991). Laboratory measurements using live animals have shown that filtration rates vary with free stream velocity (for example, Levinton 1991). Increases in current speed lead to an increase in filtration rate; however, several studies have shown that filtration may cease at some critical current speed. It has been suggested that resuspension, occurring as a result of high current speeds, may be a factor that negatively affects uptake (Cloern 1987; Levinton 1991). Several mechanisms have been invoked to explain the effects of low speed on growth rates of active suspension feeders. These mechanisms include the formation of a concentration boundary layer and the limiting horizontal flux of seston. It is now accepted that a combination of these factors dictates the growth success of benthic grazers in a particular area. Several field studies have shown that concentration boundary layers can form over benthic ecosystems (for example, Frechette and others 1989, Dolmer 2000); however, many of these studies have failed to measure the hydrodynamics needed to calculate benthic grazing rates. Furthermore, calculating benthic grazing rates with vertical measurements at a single point is problematic due to lack of knowledge of the horizontal gradients in seston (Thompson and others, forthcoming). Despite great improvements in our knowledge on the effects of benthic grazers on seston concentrations in water columns, the effects of different hydrodynamic conditions on grazing rates has not been formulated. This makes it difficult to assess the system-wide effect of the benthic ecosystem on phytoplankton concentrations. Furthermore, it affects our ability to predict the potential success of a benthic species, such as the invasive clams Corbicula fluminea and Potamocorbula amurensis. This paper presents the preliminary results of a control volume approach to elucidate the effect of different hydrodynamic conditions on the grazing rates of Corbicula fluminea.

California↗

USGS2003

A study of model bivalve siphonal currents

We carried out experiments studying the hydrodynamics of bivalve siphonal currents in a laboratory flume. Rather than use living animals, we devised a simple, model siphon pair connected to a pump. Fluorescence-based flow visualization was used to characterize siphon-jet flows for several geometric configurations and flow speeds. These measurements show that the boundary-layer velocity profile, siphon height, siphon pair orientation, and size of siphon structure all affect the vertical distribution of the excurrent flow downstream of the siphon pair and the fraction of excurrent that is refiltered. The observed flows may effect both the clearance rate of an entire population of siphonate bivalves as well as the efficiency of feeding of any individual. Our results imply that field conditions are properly represented in laboratory flume studies of phytoplankton biomass losses to benthic bivalves when the shear velocity and bottom roughness are matched to values found in the field. Numerical models of feeding by a bivalve population should include an effective sink distribution which is created by the combined incurrent-excurrent flow field. Near-bed flows need to be accounted for to properly represent these benthic-pelagic exchanges. We also present velocity measurements made with a laser-Doppler anemometer (LDA) for a single configuration (siphons flush with bed, inlet downstream) that show that the siphonal currents have a significant local effect on the properties of a turbulent boundary layer.

Limnology and Oceanography↗

USGS2003

Interaction of lateral baroclinic forcing and turbulence in an estuary

Observations of density and velocity in a channel in northern San Francisco Bay show that the onset of vertical density stratification during flood tides is controlled by the balance between the cross-channel baroclinic pressure gradient and vertical mixing due to turbulence. Profiles of velocity, salinity, temperature, and suspended sediment concentration were measured in transects across Suisun Cutoff, in northern San Francisco Bay, on two days over the 12.5-hour tidal cycle. During flood tides an axial density front developed between fresher water flowing from the shallows of Grizzly Bay into the northern side of Suisun Cutoff and saltier water flowing up the channel. North of the front, transverse currents were driven by the lateral salinity gradient, with a top-to-bottom velocity difference greater than 30 cm/s. South of the front, the secondary circulation was weak, and along-channel velocities were greater than to the north. The gradient Richardson number shows that stratification was stable north of the front, while the water column was turbulently mixed south of the front. Time-series measurements of velocity and salinity demonstrate that the front develops during each tidal cycle. In estuaries, longitudinal dynamics predict less stratification during flood than ebb tides. These data show that stratification can develop during flood tides due to a lateral baroclinic pressure gradient in estuaries with complex bathymetry.

Journal of Geophysical Research C: Oceans↗

USGS2002

A comment on the use of flushing time, residence time, and age as transport time scales

Applications of transport time scales are pervasive in biological, hydrologic, and geochemical studies yet these times scales are not consistently defined and applied with rigor in the literature. We compare three transport time scales (flushing time, age, and residence time) commonly used to measure the retention of water or scalar quantities transported with water. We identify the underlying assumptions associated with each time scale, describe procedures for computing these time scales in idealized cases, and identify pitfalls when real-world systems deviate from these idealizations. We then apply the time scale definitions to a shallow 378 ha tidal lake to illustrate how deviations between real water bodies and the idealized examples can result from: (1) non-steady flow; (2) spatial variability in bathymetry, circulation, and transport time scales; and (3) tides that introduce complexities not accounted for in the idealized cases. These examples illustrate that no single transport time scale is valid for all time periods, locations, and constituents, and no one time scale describes all transport processes. We encourage aquatic scientists to rigorously define the transport time scale when it is applied, identify the underlying assumptions in the application of that concept, and ask if those assumptions are valid in the application of that approach for computing transport time scales in real systems.

Limnology and Oceanography↗

USGS2002

Tidal asymmetry and variability of bed shear stress and sediment bed flux at a site in San Francisco Bay, USA

The relationship between sediment bed flux and bed shear stress during a pair of field experiments in a partially stratified estuary is examined in this paper. Time series of flow velocity, vertical density profiles, and suspended sediment concentration were measured continuously throughout the water column and intensely within 1 meter of the bed. These time series were analyzed to determine bed shear stress, vertical turbulent sediment flux, and mass of sediment suspended in the water column. Resuspension, as inferred from near-bed measurements of vertical turbulent sediment flux, was flood dominant, in accordance with the flood-dominant bed shear stress. Bathymetry-induced residual flow, gravitational circulation, and ebb tide salinity stratification contributed to the flood dominance. In addition to this flow-induced asymmetry, the erodibility of the sediment appears to increase during the first 2 hours of flood tide. Tidal asymmetry in bed shear stress and erodibility help explain an estuarine turbidity maximum that is present during flood tide but absent during ebb tide. Because horizontal advection was insignificant during most of the observation periods, the change in bed mass can be estimated from changes in the total suspended sediment mass. The square wave shape of the bed mass time series indicates that suspended sediment rapidly deposited in an unconsolidated or concentrated benthic suspension layer at slack tides and instantly resuspended when the shear stress became sufficiently large during a subsequent tide. The variability of bed mass associated with the spring/neap cycle (about 60 mg/cm2) is similar to that associated with the semidiurnal tidal cycle.

California↗

USGS2002

Structure and flow-induced variability of the subtidal salinity field in northern San Francisco Bay

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, X 2 : the distance from the Golden Gate Bridge to where the bottom salinity is 2 psu. Using X 2 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 X 2 that is proportional to X −1 2 . Analysis of covariability of Q and X 2 showed a characteristic timescale of adjustment of the salinity field of approximately 2 weeks. The steady-state response deduced from the X 2 time series implies that X 2 is proportional to riverflow to the 1/7 power. This relation, which differs from the standard 1/3 power dependence that is derived theoretically assuming constant exchange coefficients, shows that the upstream salt flux associated with gravitational circulation is more sensitive to the longitudinal salinity gradient than theory supposes. This is attributed to the strengthening of stratification caused by the stronger longitudinal salinity gradient that accompanies larger river flows.

California↗