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Paulsen, ML, Andersson AJ, Aluwihare L, Cyronak T, D'Angelo S, Davidson C, Elwany H, Giddings SN, Page HN, Porrachia M, Schroeter S.  2018.  Temporal changes in seawater carbonate chemistry and carbon export from a Southern California estuary. Estuaries and Coasts. 41:1050-1068.   10.1007/s12237-017-0345-8   AbstractWebsite

Estuaries are important subcomponents of the coastal ocean, but knowledge about the temporal and spatial variability of their carbonate chemistry, as well as their contribution to coastal and global carbon fluxes, are limited. In the present study, we measured the temporal and spatial variability of biogeochemical parameters in a saltmarsh estuary in Southern California, the San Dieguito Lagoon (SDL). We also estimated the flux of dissolved inorganic carbon (DIC) and total organic carbon (TOC) to the adjacent coastal ocean over diel and seasonal timescales. The combined net flux of DIC and TOC (FDIC + TOC) to the ocean during outgoing tides ranged from - 1.8 +/- 0.5 x 10(3) to 9.5 +/- 0.7 x 10(3) mol C h(-1) during baseline conditions. Based on these fluxes, a rough estimate of the net annual export of DIC and TOC totaled 10 +/- 4 x 10(6) mol C year(-1). Following a major rain event (36 mm rain in 3 days), FDIC + TOC increased and reached values as high as 29.0 +/- 0.7 x 10(3) mol C h(-1). Assuming a hypothetical scenario of three similar storm events in a year, our annual net flux estimate more than doubled to 25 +/- 4 x 10(6) mol C year(-1). These findings highlight the importance of assessing coastal carbon fluxes on different timescales and incorporating event scale variations in these assessments. Furthermore, for most of the observations elevated levels of total alkalinity (TA) and pH were observed at the estuary mouth relative to the coastal ocean. This suggests that SDL partly buffers against acidification of adjacent coastal surface waters, although the spatial extent of this buffering is likely small.

Giddings, SN, MacCready P.  2017.  Reverse estuarine circulation due to local and remote wind forcing, enhanced by the presence of along-coast estuaries. Journal of Geophysical Research-Oceans. 122:10184-10205.   10.1002/2016jc012479   AbstractWebsite

Estuarine exchange flow governs the interaction between oceans and estuaries and thus plays a large role in their biogeochemical processes. This study investigates the variability in estuarine exchange flow due to offshore oceanic conditions including upwelling/downwelling, and the presence of a river plume offshore (from a neighboring estuary). We address these processes via numerical simulations at the mouth of the Salish Sea, a large estuarine system in the Northeast Pacific. An analysis of the Total Exchange Flow indicates that during the upwelling season, the exchange flow is fairly consistent in magnitude and oriented in a positive (into the estuary at depth and out at the surface) direction. However, during periods of downwelling favorable winds, the exchange flow shows significantly more variability including multiple reversals, consistent with observations, and surface intrusions of the Columbia River plume which originates 250 km to the south. Numerical along-strait momentum budgets show that the exchange flow is forced dominantly by the pressure gradients, particularly the baroclinic. The pressure gradient is modified by Coriolis and sometimes advection, highlighting the importance of geostrophy and local adjustments. In experiments conducted without the offshore river plume, reversals still occur but are weaker, and the baroclinic pressure gradient plays a reduced role. These results suggest that estuaries along strong upwelling coastlines should experience significant modulation in the exchange flow during upwelling versus downwelling conditions. Additionally, they highlight the importance of nearby estuaries impacting one-another, not only in terms of connectivity, but also altering the exchange flow. Plain Language Summary Estuarine systems provide extensive biological and ecological functions as well as contribute to human uses and economies. However, estuaries are susceptible to change and most estuaries have been significantly impacted, threatening their important functionality. Understanding estuarine dynamics is critical to understanding estuarine ecosystems. Hydrodynamic connectivity between estuaries and the coastal ocean is a key dynamical driver impacting critical biological and biogeochemical processes such as ocean/estuarine nutrient and phytoplankton exchange and regulation of estuarine residence time, dissolved oxygen, and acidification levels. Typically estuarine-ocean exchange brings oceanic water into the estuary at depth, mixes it upwards within the estuary, and returns an outflowing mixture of oceanic and riverine water at the surface to the ocean. This manuscript documents seasonal reversals to this typical circulation pattern and the hydrodynamic drivers of the reversals. It highlights the importance of offshore winds and connectivity with neighboring estuaries. Improved understanding of these mechanisms can help us predict how estuaries will respond to a changing climate.

Centurioni, LR, Hormann V, Talley LD, Arzeno I, Beal L, Caruso M, Conry P, Echols R, Fernando HJS, Giddings SN, Gordon A, Graber H, Harcourt RR, Jayne SR, Jensen TG, Lee CM, Lermusiaux PFJ, L'Hegaret P, Lucas AJ, Mahadevan A, McClean JL, Pawlak G, Rainville L, Riser SC, Seo H, Shcherbina AY, Skyllingstad E, Sprintall J, Subrahmanyam B, Terrill E, Todd RE, Trott C, Ulloa HN, Wang H.  2017.  Northern Arabian Sea Circulation Autonomous Research (NASCar): A research initiative based on autonomous sensors. Oceanography. 30:74-87.   10.5670/oceanog.2017.224   AbstractWebsite

The Arabian Sea circulation is forced by strong monsoonal winds and is characterized by vigorous seasonally reversing currents, extreme differences in sea surface salinity, localized substantial upwelling, and widespread submesoscale thermohaline structures. Its complicated sea surface temperature patterns are important for the onset and evolution of the Asian monsoon. This article describes a program that aims to elucidate the role of upper-ocean processes and atmospheric feedbacks in setting the sea surface temperature properties of the region. The wide range of spatial and temporal scales and the difficulty of accessing much of the region with ships due to piracy motivated a novel approach based on state-of-the-art autonomous ocean sensors and platforms. The extensive data set that is being collected, combined with numerical models and remote sensing data, confirms the role of planetary waves in the reversal of the Somali Current system. These data also document the fast response of the upper equatorial ocean to monsoon winds through changes in temperature and salinity and the connectivity of the surface currents across the northern Indian Ocean. New observations of thermohaline interleaving structures and mixing in setting the surface temperature properties of the northern Arabian Sea are also discussed.

MacCready, P, Giddings SN.  2016.  The Mechanical Energy Budget of a Regional Ocean Model. Journal of Physical Oceanography. 46:2719-2733.   10.1175/JPO-D-16-0086.1   Abstract

AbstractA method is presented for calculating a complete, numerically closed, mechanical energy budget in a realistic simulation of circulation in a coastal–estuarine domain. The budget is formulated in terms of the “local” available potential energy (APE; Holliday and McIntyre 1981). The APE may be split up into two parts based on whether a water parcel has been displaced up or down relative to its rest depth. This decomposition clearly shows the different APE signatures of coastal upwelling (particles displaced up by wind) and the estuary (particles displaced down by mixing). Because the definition of APE is local in almost the same sense that kinetic energy is, this study may form meaningful integrals of reservoir and budget terms even over regions that have open boundaries. However, the choice of volume to use for calculation of the rest state is not unique and may influence the results. Complete volume-integrated energy budgets over shelf and estuary volumes in a realistic model of the northeast Pacific and Salish Sea give a new way to quantify the state of these systems and the physical forces that influence that state. On the continental shelf, upwelling may be quantified using APE, which is found to have order-one seasonal variation with an increase due to winds and decrease due to mixing. In the Salish Sea estuarine system, the APE has much less seasonal variation, and the magnitude of the most important forcing terms would take over 7 months to fully drain this energy.

Siedlecki, SA, Banas NS, Davis KA, Giddings S, Hickey BM, MacCready P, Connolly T, Geier S.  2015.  Seasonal and interannual oxygen variability on the Washington and Oregon continental shelves. Journal of Geophysical Research: Oceans. 120:608-633.   10.1002/2014JC010254   Abstract

The coastal waters of the northern portion of the California Current System experience a seasonal decline in oxygen concentrations and hypoxia over the summer upwelling season that results in negative impacts on habitat for many organisms. Using a regional model extending from 43°N to 50°N, with an oxygen component developed in this study, drivers of seasonal and regional oxygen variability are identified. The model includes two pools of detritus, which was an essential addition in order to achieve good agreement with the observations. The model was validated using an extensive array of hydrographic and moored observations. The model captures the observed seasonal decline as well as spatial trends in bottom oxygen. Spatially, three regions of high respiration are identified as locations where hypoxia develops each modeled year. Two of the regions are previously identified recirculation regions. The third region is off of the Washington coast. Sediment oxygen demand causes the region on the Washington coast to be susceptible to hypoxia and is correlated to the broad area of shallow shelf (<60 m) in the region. Respiration and circulation-driven divergence contribute similar (60, 40%, respectively) amounts to the integrated oxygen budget on the Washington coast while respiration dominates the Oregon coast. Divergence, or circulation, contributes to the oxygen dynamics on the shelf in two ways: first, through the generation of retention features, and second, by determining variability.

Davis, KA, Banas NS, Giddings SN, Siedlecki SA, MacCready P, Lessard EJ, Kudela RM, Hickey BM.  2014.  Estuary-enhanced upwelling of marine nutrients fuels coastal productivity in the U.S. Pacific Northwest. Journal of Geophysical Research-Oceans. 119:8778-8799.   10.1002/2014jc010248   AbstractWebsite

The Pacific Northwest (PNW) shelf is the most biologically productive region in the California Current System. A coupled physical-biogeochemical model is used to investigate the influence of freshwater inputs on the productivity of PNW shelf waters using realistic hindcasts and model experiments that omit outflow from the Columbia River and Strait of Juan de Fuca (outlet for the Salish Sea estuary). Outflow from the Strait represents a critical source of nitrogen to the PNW shelf-accounting for almost half of the primary productivity on the Vancouver Island shelf, a third of productivity on the Washington shelf, and a fifth of productivity on the Oregon shelf during the upwelling season. The Columbia River has regional effects on the redistribution of phytoplankton, but does not affect PNW productivity as strongly as does the Salish Sea. A regional nutrient budget shows that nitrogen exiting the Strait is almost entirely (98%) of ocean-originupwelled into the Strait at depth, mixed into surface waters by tidal mixing, and returned to the coastal ocean. From the standpoint of nitrogen availability in the coastal euphotic zone, the estuarine circulation driven by freshwater inputs to the Salish Sea is more important than the supply of terrigenous nitrogen by rivers. Nitrogen-rich surface waters exiting the Strait follow two primary pathwaysto the northwest in the Vancouver Island Coastal Current and southward toward the Washington and Oregon shelves. Nitrogen flux from the Juan de Fuca Strait and Eddy Region to these shelves is comparable to flux from local wind-driven upwelling.

Giddings, SN, Monismith SG, Fong DA, Stacey MT.  2014.  Using Depth-Normalized Coordinates to Examine Mass Transport Residual Circulation in Estuaries with Large Tidal Amplitude Relative to the Mean Depth. Journal of Physical Oceanography. 44(1):128-148.: American Meteorological Society   10.1175/JPO-D-12-0201.1   AbstractWebsite

Residual (subtidal) circulation profiles in estuaries with a large tidal amplitude-to-depth ratio often are quite complex and do not resemble the traditional estuarine gravitational circulation profile. This paper describes how a depth-normalized σ-coordinate system allows for a more physical interpretation of residual circulation profiles than does a fixed vertical coordinate system in an estuary with a tidal amplitude comparable to the mean depth. Depth-normalized coordinates permit the approximation of Lagrangian residuals, performance of empirical orthogonal function (EOF) analysis, estimation of terms in the along-stream momentum equations throughout depth, and computation of a tidally averaged momentum balance. The residual mass transport velocity has an enhanced two-layer exchange flow relative to an Eulerian mean because of the Stokes wave transport velocity directed upstream at all depths. While the observed σ-coordinate profiles resemble gravitational circulation, and pressure and friction are the dominant terms in the tidally varying and tidally averaged momentum equations, the two-layer shear velocity from an EOF analysis does not correlate with the along-stream density gradient. To directly compare to theoretical profiles, an extension of a pressure–friction balance in σ coordinates is solved. While the barotropic riverine residual matches theory, the mean longitudinal density gradient and mean vertical mixing cannot explain the magnitude of the observed two-layer shear residual. In addition, residual shear circulation in this system is strongly driven by asymmetries during the tidal cycle, particularly straining and advection of the salinity field, creating intratidal variation in stratification, vertical mixing, and shear.

Giddings, SN, MacCready P, Hickey BM, Banas NS, Davis KA, Siedlecki SA, Trainer VL, Kudela RM, Pelland NA, Connolly TP.  2014.  Hindcasts of potential harmful algal bloom transport pathways on the Pacific Northwest coast. Journal of Geophysical Research: Oceans. 119:2439–2461.   10.1002/2013JC009622   AbstractWebsite

Harmful algal blooms (HABs) pose a significant threat to human and marine organism health, and negatively impact coastal economies around the world. An improved understanding of HAB formation and transport is required to improve forecasting skill. A realistic numerical simulation of the US Pacific Northwest region is used to investigate transport pathways from known HAB formation hot spots, specifically for Pseudo-nitzschia (Pn), to the coast. We show that transport pathways are seasonal, with transport to the Washington (WA) coast from a northern source (the Juan de Fuca Eddy) during the summer/fall upwelling season and from a southern source (Heceta Bank) during the winter/early spring due to the predominant wind-driven currents. Interannual variability in transport from the northern source is related to the degree of wind intermittency with more transport during years with more frequent relaxation/downwelling events. The Columbia River plume acts to mitigate transport to the coast as the plume front blocks onshore transport. The plume's influence on alongshore transport is variable although critical in aiding transport from the southern source to the WA coast via plume entrainment. Overall transport from our simulations captures most observed Pn HAB beach events from 2004 to 2007 (characterized by Pseudo-nitzschia cell abundance); however, numerous false positives occur. We show that incorporating phytoplankton biomass results from a coupled biogeochemical model reduces the number of false positives significantly and thus improves our Pn HAB predictions.

Giddings, SN, Fong DA, Monismith SG, Chickadel CC, Edwards KA, Plant WJ, Wang B, Fringer OB, Horner-Devine AR, Jessup AT.  2012.  Frontogenesis and Frontal Progression of a Trapping-Generated Estuarine Convergence Front and Its Influence on Mixing and Stratification. Estuaries and Coasts. 35(2):665-681.: Springer-Verlag   10.1007/s12237-011-9453-z   AbstractWebsite

Estuarine fronts are well known to influence transport of waterborne constituents such as phytoplankton and sediment, yet due to their ephemeral nature, capturing the physical driving mechanisms and their influence on stratification and mixing is difficult. We investigate a repetitive estuarine frontal feature in the Snohomish River Estuary that results from complex bathymetric shoal/channel interactions. In particular, we highlight a trapping mechanism by which mid-density water trapped over intertidal mudflats converges with dense water in the main channel forming a sharp front. The frontal density interface is maintained via convergent transverse circulation driven by the competition of lateral baroclinic and centrifugal forcing. The frontal presence and propagation give rise to spatial and temporal variations in stratification and vertical mixing. Importantly, this front leads to enhanced stratification and suppressed vertical mixing at the end of the large flood tide, in contrast to what is found in many estuarine systems. The observed mechanism fits within the broader context of frontogenesis mechanisms in which varying bathymetry drives lateral convergence and baroclinic forcing. We expect similar trapping-generated fronts may occur in a wide variety of estuaries with shoal/channel morphology and/or braided channels and will similarly influence stratification, mixing, and transport.

Wang, B, Giddings SN, Fringer OB, Gross ES, Fong DA, Monismith SG.  2011.  Modeling and understanding turbulent mixing in a macrotidal salt wedge estuary. Journal of Geophysical Research. 116(C02036):1-23.   10.1029/2010JC006135   AbstractWebsite

A high-resolution three-dimensional numerical simulation is performed with the parallel, unstructured grid SUNTANS model to study the spatiotemporal dynamics of turbulent mixing in a shallow, macrotidal salt wedge estuary that experiences periodic mixing and strong stratification. Unresolved vertical mixing is parameterized with the k − kl closure scheme with the Canuto-A stability functions based on a careful comparison of multiple two-equation closure schemes and stability functions via the generic length scale approach. The predictions of velocity, salinity, Richardson number, and Reynolds stress are in good agreement with field observations, and the top and bottom salinity predictions achieve skill scores of 0.86 and 0.91, respectively. The model shows that the salt wedge starts to strengthen upstream at the beginning of weak ebb and gradually expands downstream during the weak tide. Mixing is most active along a density interface during the weak ebb, while it is most active in a bottom mixed layer during weak flood, consistent with the findings inferred from the observations. Stratification decays during the strong ebb in a mixing event along the horizontal extent of the salt wedge while it is also being advected offshore. Local mixing is shown to account for roughly half of the decay rate of the stratification in this process. Numerical experiments are performed to investigate the response of stratification and mixing to changes in the magnitude of the buoyancy. High sensitivity is shown under intermediate levels of stratification that occur in the real system, which becomes considerably weaker under more extreme conditions.

Giddings, SN, Fong DA, Monismith SG.  2011.  Role of straining and advection in the intratidal evolution of stratification, vertical mixing, and longitudinal dispersion of a shallow, macrotidal, salt wedge estuary. 116:C03003.: AGU   10.1029/2010JC006482   AbstractWebsite

A month of flow observations in the Snohomish River Estuary reveals the complex intratidal and fortnightly stratification, mixing, and dispersion dynamics in this macrotidal, shallow, salt wedge estuary system. Both salt wedge propagation and concomitant straining of the density field dominate temporal and spatial variations in stratification leading to intratidal variability of shear and mixing that differs in important ways from observations in partially mixed estuaries. Bottom-generated turbulent kinetic energy production is enhanced during spring tides and acts in concert with straining to counteract advection and minimize vertical stratification during the spring flood tides. This bottom-generated mixing contributes to a buoyancy flux near the top of a well-mixed layer during strong flood tides. During strong ebb tides, interfacial shear production and buoyancy flux occur along the sharp straining-enhanced interface just before the system becomes well mixed. Longitudinal dispersion is less sensitive to the spring/neap cycle yet exhibits strong intratidal variability. Reduced longitudinal dispersion is observed during the large floods relative to the rest of the tidal cycle, behavior we attribute to a lack of vertical shear. Overall, ebb tide advection and straining enhance stratification and longitudinal dispersion and allow for interfacial mixing. Intratidal variability, which varies on the spring/neap scale, is a dominant feature of this estuary, suggesting the importance of intratidal processes and tidally varying mixing coefficients in similar strongly stratified, strongly forced estuaries.

Wang, B, Fringer OB, Giddings SN, Fong DA.  2009.  High-resolution simulations of a macrotidal estuary using SUNTANS. Ocean Modelling. 26(1-2):60-85., Oxford, U.K.   10.1016/j.ocemod.2008.08.006   AbstractWebsite

The parallel, finite-volume, unstructured-grid SUNTANS model has been employed to study the interaction of the tides with complex bathymetry in the macrotidal Snohomish River estuary. The unstructured grid resolves the large-scale, O(10 km) tidal dynamics of the estuary while employing 8 m grid-resolution at a specific region of interest in the vicinity of a confluence of two channels and extensive intertidal mudflats to understand detailed local intratidal flow processes. After calibrating tidal forcing parameters to enforce a match between free surface and depth-averaged velocities at several locations throughout the domain, we analyze the complex dynamics of the confluence and show that the exposure of the intertidal mudflats during low tide induces a complex flow reversal. When coupled with the longitudinal salinity gradient, this flow reversal results in a highly variable salinity field, which has profound implications for local mixing, stratification and the occurrence of fine-scale flow structures. This complex flow is then used as a testbed from which to describe several challenges associated with high resolution modeling of macrotidal estuaries, including specification of high resolution bathymetry, specification of the bottom stress, computation of the nonhydrostatic pressure, accurate advection of momentum, and the influence of the freshwater inflow. The results indicate that with high resolution comes the added difficulty of requiring more accurate specification of boundary conditions. In particular, the bottom bathymetry plays the most important role in achieving accurate predictions when high resolution is employed.

Plant, WJ, Branch R, Chatham G, Chickadel CC, Hayes K, Hayworth B, Horner-Devine AR, Jessup AT, Fong DA, Fringer OB, Giddings SN, Monismith SG, Wang B.  2009.  Remotely sensed river surface features compared with modeling and in situ measurements. Journal of Geophysical Research. 114:C11002.   10.1029/2009JC005440   AbstractWebsite

Images of river surface features that reflect the bathymetry and flow in the river have been obtained using remote sensing at microwave, visible, and infrared frequencies. The experiments were conducted at Jetty Island near the mouth of the Snohomish River at Everett, Washington, where complex tidal flow occurs over a varied bathymetry, which was measured as part of these experiments. An X band (9.36 GHz) Doppler radar was operated from the river bank and produced images of normalized radar cross sections and radial surface velocities every 20 min over many tidal cycles. The visible and infrared instruments were flown in an airplane. All of these techniques showed surface evidence of frontal features, flow over a sill, and flow conditioned by a deep hole. These features were modeled numerically, and the model results correspond well to the remote observations. In situ measurements made near the hole showed that changes in measured velocities correlate well with the occurrence of the features in the images. In addition to tidal phase, the occurrence of these features in the imagery depends on tidal range. The surface roughness observed in the imagery appears to be generated by the bathymetry and flow themselves rather than by the modulation of wind waves.

Harley, RA, Marr LC, Lehner JK, Giddings SN.  2005.  Changes in Motor Vehicle Emissions on Diurnal to Decadal Time Scales and Effects on Atmospheric Composition. Environmental science &amp; technology. 39(14):5356-5362.: American Chemical Society   10.1021/es048172+   AbstractWebsite

Emissions from gasoline and diesel engines vary on time scales including diurnal, weekly, and decadal. Temporal patterns differ for these two engine types that are used predominantly for passenger travel and goods movement, respectively. Rapid growth in diesel fuel use and decreasing NOx emission rates from gasoline engines have led to altered emission profiles. During the 1990s, on-road use of diesel fuel grew 3 times faster than gasoline. Over the same time period, the NOx emission rate from gasoline engines in California was reduced by a factor of ?2, while the NOx emission rate from diesel engines decreased only slightly. Diesel engines therefore grew in both relative and absolute terms as a source of NOx, accounting for about half of all on-road NOx emissions as of 2000. Diesel truck emissions decrease by 60?80% on weekends. Counterintuitive responses to these emission changes are seen in measured concentrations of ozone. In contrast, elemental carbon (EC) concentrations decrease on weekends as expected. Weekly and diurnal patterns in diesel truck activity contribute to variability in the ratio of organic carbon (OC) to EC in primary source emissions, and this could be a source of bias in assessments of the importance of secondary organic aerosol.; Emissions from gasoline and diesel engines vary on time scales including diurnal, weekly, and decadal. Temporal patterns differ for these two engine types that are used predominantly for passenger travel and goods movement, respectively. Rapid growth in diesel fuel use and decreasing NOx emission rates from gasoline engines have led to altered emission profiles. During the 1990s, on-road use of diesel fuel grew 3 times faster than gasoline. Over the same time period, the NOx emission rate from gasoline engines in California was reduced by a factor of ?2, while the NOx emission rate from diesel engines decreased only slightly. Diesel engines therefore grew in both relative and absolute terms as a source of NOx, accounting for about half of all on-road NOx emissions as of 2000. Diesel truck emissions decrease by 60?80% on weekends. Counterintuitive responses to these emission changes are seen in measured concentrations of ozone. In contrast, elemental carbon (EC) concentrations decrease on weekends as expected. Weekly and diurnal patterns in diesel truck activity contribute to variability in the ratio of organic carbon (OC) to EC in primary source emissions, and this could be a source of bias in assessments of the importance of secondary organic aerosol.