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Despite global investment in shellfish restoration activities, relatively little attention has been given to predicting optimal restoration sites and testing these expectations. We used a coupled biological-physical connectivity model as a guide to plant two distinct hatchery-spawned strains of the eastern oyster, Crassostrea virginica, in the Lafayette River, Virginia during the summer of 2013 at two locations corresponding to virtual spawning locations within the connectivity model. We utilized single nucleotide polymorphism markers to test the model predictions by genotyping oysters recruited after planting two hatchery-spawned strains and examining interannual recruitment variability for two successive years. Two spat were identified as hybrids of one of the planted strains and resident oyster genotypes. We also observed a genetic influence from an oyster strain used previously for restoration. Differences in environmental conditions between the two years of monitored recruitment likely affected larval dispersal and survival, contributing to observed interannual differences in the newly recruiting cohorts. Oyster spat from 2013 were genetically more similar to resident adults sampled in the Lafayette River, while the 2014 spat exhibited genotypic frequencies more similar to adults from surrounding rivers. The winds during the spawning seasons differed between years providing conditions for retention in 2013 and mixing of water masses in 2014. We recommend that the monitoring of restoration activities should consider relevant environmental conditions and observe multiple years of recruitment to assess the genetic impacts of restoration plantings and variable reproductive success. [ABSTRACT FROM AUTHOR]

Although both local processes (photosynthesis, respiration, grazing, and settling), and transport processes (advective transport and diffusive transport) significantly affect local phytoplankton dynamics, it is difficult to separate their contributions and to investigate the relative importance of each process to the local variability of phytoplankton biomass over different timescales. A method of using the transport rate is introduced to quantify the contribution of transport processes. By combining the time-varying transport rate and high-frequency observed chlorophyll a data, we can explicitly examine the impact of local and transport processes on phytoplankton biomass over a range of timescales from hourly to annually. For the Upper James River, results show that the relative importance of local and transport processes differs on different timescales. Local processes dominate phytoplankton variability on daily to weekly timescales, whereas the contribution of transport processes increases on seasonal to annual timescales and reaches equilibrium with local processes. With the use of the transport rate and high-frequency chlorophyll a data, a method similar to the open water oxygen method for metabolism is also presented to estimate phytoplankton primary production. [ABSTRACT FROM AUTHOR]

Massive blooms of the harmful alga Cochlodinium polykrikoides Margalef occurred in the lower Chesapeake Bay and its tributaries during the summers of 2007 and 2008. The Lafayette and Elizabeth Rivers appeared to act as initiation grounds for these blooms during both years. However, in 2008 there were also localized sites of initiation and growth of populations within the mesohaline portion of the James River. Bloom initiation appeared to be correlated with intense, highly localized rainfall events during neap tides. Subsequent spring tides increased tidal flushing and transport of C. polykrikoides from the Lafayette and Elizabeth Rivers into the lower James River where it was transported upriver by local estuarine circulation. Blooms dissipated in response to increased wind-driven mixing associated with frontal systems moving through the region. A combination of physical factors including, seasonal rainfall patterns, increased stratification, nutrient loading, spring-neap tidal modulation, and complex estuarine mixing and circulation allowed C. polykrikoides to spread and form massive blooms over large portions of the tidal James River and the lower Chesapeake Bay. [ABSTRACT FROM AUTHOR]

Abstract: Wind plays an important role in regulating mixing/stratification, estuarine circulation, and transport timescale in estuaries. A three-dimensional model was used to investigate the effect of wind on transport time by using the concept of water age (WA) in the tidal Rappahannock River, a western tributary of the Chesapeake Bay, USA. The model was calibrated for water level, current, and salinity. A series of experiments regarding the effects of wind on WA was conducted under various dynamic conditions. The effect of wind on transport timescale depends strongly on the competition between the wind and buoyancy forcings, and on the pre-status of the circulation. A down-estuary wind generally decreases WA along the estuary. An up-estuary wind increases WA substantially because it changes the vertical mixing and estuarine circulation more significantly. When the buoyancy forcing increases, the up-estuary wind effect decreases whereas the down-estuary wind effect increases. A 2-day period wind pulse with a maximum speed of 15ms−1 can alter WA for 3days; but the wind influence on WA lasts up to 40days in the simulation. Both local and non-local wind forcings alter WA distribution. The local wind enhances vertical mixing and changes the gravitational circulation in the downstream portion of the estuary whereas it enhances transport in the freshwater portion of the estuary. Consequently, the local wind has a significant impact on WA distribution. In contrast, the non-local wind does not change the gravitational circulation significantly by imposing setup (setdown) of water level at the open boundary, resulting in a lesser impact on WA distribution. [Copyright &y& Elsevier]

Abstract: Tropical Cyclone Isabel of 2003 generated large storm surge, strong waves, and subsequent river flooding in the York River Estuary, USA during its passage across the Chesapeake Bay region. A 3D model was used to investigate the changes of sediment concentration, sediment flux, and the recovery time of the York River Estuary to its naturally evolved condition without the storm. The results showed that two sediment concentration peaks appeared during the storm event. The first one was induced by the large upstream flow and waves during the storm surge rising period, and the later one was caused by the strong downstream flow during the descent of the storm surge. The advection, which was induced by the barotropic gradient, dominated the sediment flux during the storm event. The sediment fluxes increased by a factor of 100 during the rise and descent of the storm surge. A large amount of sediment that was transported into the estuary and eroded from the seabed during the rising of the storm surge was quickly transported out of the estuary during the descent of the storm surge. Waves played a key role in stirring the seabed and increasing the sediment concentration during the storm. Subsequent high freshwater inflow changed the sediment loading and hydrodynamics in the estuary, and thus, influenced the estuarine turbidity maximum (ETM) dynamics profoundly. The ETM moved downstream with the river flooding initially and returned upstream with the waning of river flooding and the re-establishment of gravitational circulation. The effect of river flooding on sediment concentration varied spatially and depended on the changes of ETM locations and vertical mixing. The model results suggest that a large amount of sediment was transported out of the estuary during the storm event and the subsequent river flooding had a larger impact on recovery time of the estuary. [Copyright &y& Elsevier]

Abstract: The Chesapeake Bay is vulnerable to severe flooding caused by hurricanes and strong Northeasters. A 3D storm surge model of the Chesapeake Bay is developed for studying the impact of model domain size, wind directions and Ekman transport on the storm surge in the Chesapeake Bay. The model encompasses the Chesapeake Bay and the US East Coast shelf to reduce the influence of model domain size on surge prediction inside the Chesapeake Bay and to account for both local and remote wind effects. This study used 3D model experiments, with respect to different wind directions, to diagnose the relative influences of the local and remote wind effects and Ekman transport on spatial surge distribution during storm events. The model results confirmed that spatial surge distribution can be well explained by the superposition of two distinct physically driven mechanisms during a storm event: incoming surge wave caused by remote effects and local wind forcings. A large model domain is a necessity for predicting storm surge accurately inside the Chesapeake Bay. The model results suggest that the interactions of the incoming surge propagating into the Bay and the local wind forcing from N and NE directions result in an enhanced setup in the lower to middle portions of the Bay, whereas the superposition of incoming surge and the local wind forcing from S and SE directions enhance the surge in the upper Bay region. A combined northwesterly wind over the middle to upper portions of the Bay and southwesterly wind over the lower Bay can cause a large setdown throughout the entire Bay. The Ekman setup along the coast contributes significantly to the water level variations during storm events. It enhances (reduces) surge inside the Bay under the wind forcings from N and NE (SW, S, and SE) directions. [Copyright &y& Elsevier]

The age concept is applied to an estuary to estimate time scales quantifying transport processes of dissolved substance for a spatially varying case. A real-time three-dimensional numerical model was applied to the tidal York River estuary, a western branch of the Chesapeake Bay, to calculate the age distribution for a substance released from the headwaters of tributaries of the estuary under different hydrological conditions. The mean age, residence time, and turnover time were computed through a series of numerical model experiments. Both mean age and residence time are functions of freshwater discharge. The model results show that substantial time is required for a substance discharged into the system at the headwaters of the tributaries to be transported to the downstream estuary. It takes about 2 months and 3 months for the substance discharged into the headwaters to be transported to the mouth of the estuary under high flow and mean flow conditions, respectively. The results provide useful information for understanding the transport processes in the estuary and can be used to estimate dissimilative capacity of the estuary for environmental assessment. [Copyright &y& Elsevier]

The impact of channel deepening and sea-level rise on the environmental integrity of an estuary is investigated using a three-dimensional hydrodynamic-eutrophication model. The model results show that dissolved oxygen (DO) only experienced minor changes, even when the deep channel was deepened by 3 m in the mesohaline and polyhaline regions of the James River. We found that vertical stratification decreased DO aeration while the estuarine gravitational circulation increased bottom DO exchange. The interactions between these two processes play an important role in modulating DO. The minor change in DO due to channel deepening indicates that the James River is unique as compared with other estuaries. To understand the impact of the hydrodynamic changes on DO, both vertical and horizontal transport timescales represented by water age were used to quantify the changes in hydrodynamic conditions and DO variation, in addition to traditional measures of stratification and circulation. The model results showed that channel deepening led to an increase in both gravitational circulation strength and vertical stratification. Saltwater age decreased and vertical exchange time increased with increases in channel depth. However, these two physical processes can compensate each other, resulting in minor changes in DO. A comparison of the impact of a sea-level rise of 1.0 m with channel deepening scenarios was conducted. As the sea level rises, the vertical transport time decreases slightly while the strength of gravitational circulation weakens due to an increase in mean water depth. Consequently, DO in the estuary experiences a moderate decrease. [ABSTRACT FROM AUTHOR]

Global sea level is rising, and the relative rate in the Chesapeake Bay region of the East Coast of the United States is greater than the worldwide rate. Sea-level rise can cause saline water to migrate upstream in estuaries and rivers, threatening freshwater habitat and drinking-water supplies. The effects of future sea-level rise on two tributaries of Chesapeake Bay, the James and Chickahominy (CHK) Rivers, were evaluated in order to quantify the salinity change with respect to the magnitude of sea-level rise. Such changes are critical to: 1) local floral and faunal habitats that have limited tolerance ranges to salinity; and 2) a drinking-water supply for the City of Newport News, Virginia. By using the three-dimensional Hydrodynamic-Eutrophication Model (HEM-3D), sea-level rise scenarios of 30, 50, and 100 cm, based on the U.S. Climate Change Science Program for the mid-Atlantic region for the 21st century, were evaluated. The model results indicate that salinity increases in the entire river as sea level rises and that the salinity increase in a dry year is greater than that in a typical year. In the James River, the salinity increase in the middle-to-upper river (from 25 to 50 km upstream of the mouth) is larger than that in the lower and upper parts of the river. The maximum mean salinity increase would be 2 and 4 ppt for a sea-level rise of 50 and 100 cm, respectively. The upstream movement of the 10 ppt isohaline is much larger than the 5 and 20 ppt isohalines. The volume of water with salinity between 10 and 20 ppt would increase greatly if sea level rises 100 cm. In the CHK River, with a sea-level rise of 100 cm, the mean salinity at the drinking-water intake 34 km upstream of the mouth would be about 3 ppt in a typical year and greater than 5 ppt in a dry year, both far in excess of the U.S. Environmental Protection Agency''s secondary standard for total dissolved solids for drinking water. At the drinking-water intake, the number of days of salinity greater than 0.1 ppt increases with increasing sea-level rise; during a dry year, 0.1 ppt would be exceeded for more than 100 days with as small a rise as 30 cm. [Copyright &y& Elsevier]

Abstract: The response of Chesapeake Bay to forcing from two hurricanes is investigated using an unstructured-grid three-dimensional hydrodynamic model SELFE. The model domain includes Chesapeake Bay, its tributaries, and the extended continental shelf in the mid-Atlantic Bight. The hurricanes chosen for the study are Hurricane Floyd (1999) and Hurricane Isabel (2003), both of which made landfall within 100km of the mouth of the Bay. The model results agree reasonably well with field observations of water level, velocity, and salinity. From the Bay’s water level response to the hurricanes, it was found that the storm surge in the Bay has two distinct stages: an initial stage set up by the remote winds and the second stage – a primary surge induced by the local winds. For the initial stage, the rising of the coastal sea level was setup by the remote wind of both hurricanes similarly, but for the second stage, the responses to the two hurricanes’ local winds are significantly different. Hurricane Floyd was followed by down-Bay winds that canceled the initial setup and caused a set-down from the upper Bay. Hurricane Isabel, on the other hand, was followed by up-Bay winds, which reinforced the initial setup and continued to rise up against the head of the Bay. From the perspective of volume and salt fluxes, it is evident that an oceanic saltwater influx is pushed into the Bay from the continental shelf by the remote wind fields in the initial stages of the storm surge for both Floyd and Isabel. In the second stage after the hurricane made landfall, the Bay’s local wind plays a key role in modulating the salinity and velocity fields through vertical mixing and longitudinal salt transport. Controlled numerical experiments are conducted in order to identify and differentiate the roles played by the local wind in stratified and destratified conditions. Down-estuary local wind stress (of Hurricane Floyd-type) tends to enhance stratification under moderate winds, but exhibits an increasing-then-decreasing stage when the wind stress increases. The up-estuary local wind stress (of Hurricane Isabel-type) tends to penetrate deeper into the water column, which reduces stratification by reversing gravitational circulation. To characterize mixing conditions in the estuary, a modified horizontal Richardson number that incorporates wind stress, wind direction, horizontal salinity gradient, and vertical eddy viscosity is used for both hurricanes. Finally, the direct precipitation of rainfall into the Bay during Hurricane Floyd appears to create not only a thin surface layer of low salinity but also a seaward barotropic pressure gradient that affects the subsequent redistribution of salinity after the storm. [Copyright &y& Elsevier]

Abstract: Understanding the dynamics of water exchange between Baltimore Harbor and the Chesapeake Bay is essential when evaluating transport and fate of dissolved substances in both of these systems. Conservative artificial tracers are used in this study to investigate transport processes through a three-dimensional hydrodynamic model (CH3D). The model well reproduced the three-layered circulation pattern in Baltimore Harbor. Several numerical experiments are performed to trace the water mass coming from different sources. The results indicate that both the upper and lower layers of the Harbor are the dominant pathways of transporting dissolved substances from Susquehanna River to the Harbor. Such inward transport is intensified (suppressed) during the high-discharge (low-discharge) period. The upper layer inflow transports water mass with high concentrations of dissolved substances while the inflow from the lower layer transports water mass with low concentrations of dissolved substances. The bottom layer is the dominant pathway for transporting dissolved substances from the lower Bay to the Harbor. Lower river discharge and stronger along-Bay pressure gradient (resulting in stronger landward residual flow in the bottom layer of the Bay) facilitate the bottom intrusion of dissolved substances from lower Bay to the Harbor. Once contaminants are transported into the Harbor, they usually stay for a longer time in the mid-depth of the Harbor than those in other layers due to the three-layer circulation in the Harbor. The time needed for the contaminants being transported out of the Harbor during a typical low-discharge period is about 1 month longer than that needed during a typical high-discharge period. The results, from the environmental perspective, provide new insights for quantitative evaluation on the transport processes of the dissolved biogeochemical substances between Baltimore Harbor and Chesapeake Bay. [Copyright &y& Elsevier]

Large uncertainty in the estimation of bacterial nonpoint sources often results in the poor simulation of bacteria concentration in estuaries using a deterministic model. To better quantify the uncertainty in bacterial modeling, a Bayesian approach was incorporated into a tidally averaged estuarine model for estimating bacterial loading using in-stream observations. This was accomplished by using Bayes' theorem to develop a joint probability distribution for nonpoint source loadings based on the bacteria observations in the estuary. To overcome the geometry variation along the estuary for a non-linear transport problem with no analytical solution, the approach was implemented on a finite difference model. The approach was applied to Holdens Creek, a tidal river of the Pocomoke Sound of the Chesapeake Bay, to explore the feasibility of estimating bacteria sources and to develop an allowable load for the Creek to attain water quality standards. Further experiments were conducted to investigate the convergence for loading estimation, and the errors and uncertainties associated with load estimation using different data sets with varied sample sizes. With the use of limited observations, the nonpoint source loads can be estimated within an acceptable error range by selecting appropriate prior loading distributions. Because of the high spatial correlations among observations in the estuary, the errors in loading estimation at adjacent watersheds compensated each other, resulting in a good estimation of loads for the entire watershed. The approach not only provides an efficient methodology to assess the nonpoint source contribution for watershed management, but also has the additional advantage of addressing the problems of the uncertainty and error associated with bacterial simulation in the estuary.

In this study, a linked model system including the Loading Simulation Program C++ (LSPC) and the tidal prism water quality model (TPWQM) was proposed as an alternative tool for total maximum daily load (TMDL) studies. The feasibility of the model system was tested by a case study in the Nassawadox Creek, a Virginia tidal water shellfish growing area. The watershed model, driven by hourly precipitation, simulates hydrology and fecal coliform accumulation and transport processes in the watershed. The simulated surface runoff and subsurface flow as well as fecal coliform loads from the watershed are discharged to the tidal creek. The tidal prism model simulates fecal coliform transport in the Creek. The model results demonstrate the effectiveness in simulating hydrology and fecal coliform concentration in the watershed and its embayment. A series of sensitivity runs was conducted to estimate the load reduction necessary for fecal coliform concentration to meet the water quality standards. The model application to the Nassawadox Creek indicates that the model system is useful in developing fecal coliform TMDLs for estuarine shellfish growing areas.