Abstract Analytical solutions were derived for linear barotropic instabilities of the mean along-channel, tidally driven current flowing through inlets with variable geometry and idealized cross-inlet structure. Analytic solutions converge to previous solutions for surfzone alongshore currents and are consistent with solutions for shelf currents at the continental slope. The cubic polynomial dispersion equation depends on the wavenumber, maximum current magnitude, horizontal shear of the current, cross-inlet geometry and bathymetry, and a linear friction coefficient. For bounded tidal currents with inviscid flow, the characteristic wavelengths are O (10 2 ) m, periods are O (10 2 –10 3 ) s, and growth rates of the fastest-growing unstable modes are O (10 −3 –10 −2 ) s −1 with phase speeds approximately one-third of the maximum velocity, similar to prior nearshore findings. Bottom friction suppresses the unstable motions leading to slower growth rates and a reduced range of unstable wavenumbers. Faster-growing modes with a larger range of unstable wavenumbers and stronger horizontal mixing of momentum (represented by the cross-inlet Reynolds shear stress) occur under stronger shear conditions and wide, flat cross-inlet bathymetry. The Reynolds stress is inversely proportional to the strength of the background potential vorticity, which is dependent on the cross-channel shear of the along-channel flows. At the location of maximum flow, horizontal mixing acts to smooth the initial velocity cross-channel structure. Predicted dispersion curves are consistent with field observations of instabilities in a New Hampshire tidal inlet and discussed in the companion paper. Significance Statement Tidal currents flowing through a narrow inlet bounded by land or manufactured structures can have strong horizontal, cross-channel gradients in the along-channel flow. A small disturbance in the velocity gradient can cause the mean flow to become unstable, leading to a meandering of the mean along-channel current and potentially the spinoff of large eddies. This instability and the resulting high-frequency variability of the currents and vorticities may affect small vessel navigation and the transport of organic and inorganic matter and cause lateral mixing of momentum across the inlet. The dispersion of the linear instabilities was solved analytically for a given range of wavenumbers under various channel geometries and simple bathymetry.

Abstract Strong cross-channel shear of tidal currents through a bounded channel can lead to instabilities in the flow, causing a meandering of the mean along-channel current and potentially the spinoff of large eddies. To estimate the wavenumbers of shear instabilities within the Hampton-Seabrook Estuary, New Hampshire, a spatially lagged array consisting of seven sensors measuring bidirectional horizontal currents and pressure was deployed for 1 week during the spring tide in May 2021. Using iterative maximum likelihood estimators, wavenumber–frequency spectra are estimated during 3–4-h periods with approximately steady currents on both the flood and ebb tides. Dominant wavenumbers (±0.002–0.02 m −1 ) of the low-frequency motions (0.0006–0.01 s −1 ) are resolved and consistent with motions determined from barotropic linear stability analysis described in the companion paper. The instabilities propagate into the inlet on flood tides and out of the inlet on the ebbs, consistent with the expected propagation of unstable modes. The normalized velocity-to-pressure variance ratio at each station shows that the infragravity band is dominated by rigid-lid-like motions characteristic of instabilities. The lack of breaking wave group modulations within the inlet and the presence of the seaward propagating instabilities on the ebb flow indicate that the presence of the instabilities can be attributed to the shear of the tidal current. Significance Statement Horizontal instabilities of tidal currents flowing through bounded channels can lead to a meandering of the mean along-channel current and potentially the spinoff of large eddies. The resulting high-frequency variability of the currents and vorticities may affect navigation and the transport of organic and inorganic matter and cause lateral mixing of momentum across the inlet. Instabilities of the mean current are observed in a tidal inlet on both the ebb and flood tides propagating in the direction of the mean current, and the dominant wavelengths and periods are estimated and compared with theoretical linear stability predictions. The forcing is from the strong gradient in velocity and is not tied to breaking incident gravity wave groups that are absent in the inlet.

The decline of important reef building corals has motivated the development of habitat suitability models used to identify optimal locations for coral restoration. In the Florida Keys habitat suitability models incorporate coarse spatial data sampled over large areas, resulting in recommended outplant sites at distant locations, making it logistically difficult and expensive to access and regularly monitor. Restoration efforts to date show that outplanting success can vary widely within a limited space, necessitating improved predictive abilities of coral outplant success at high spatial resolutions within a restoration site. With the advent of Structure-from-Motion image reconstruction, fine-scale, site specific, digital terrain models can be created to support habitat suitability model development. In this study, generalized linear mixed models used extracted seafloor terrain attributes and environmental variables to identify within site locations of high Acropora cervicornis growth and healthy coral cover of long-term outplants. Percent healthy coral cover significantly decreased after two years of outplantation. The submodel of corals exclusively less than two years old was unable to identify environmental conditions associated with higher healthy cover. For all corals, outplant recommendations for higher healthy cover are in deeper waters, away from the coast, in less rough terrain, and closer to the reef edge. Model results for growth support these recommended outplant sites, in addition to concave locations near high slope relief. Finally, our results also indicate that marine heat waves, but especially marine cold waves negatively correspond with coral growth, and high wind events positively correspond with coral growth. These model results provide a basis for further endeavors in modeling endangered organismal success, which are vulnerable to minute differences in local environmental conditions. ### Competing Interest Statement The authors have declared no competing interest.

We developed a particle tracking model for the transport and dispersion of American lobster (Homarus americanus) larvae for the Gulf of Maine (GoM) that considers both passively drifting larval stages and their swimming ability during the postlarval (pre-settlement) stage. The model takes into account two characteristics of the postlarval stage: directional swimming toward shallower regions and diel fluctuations of their swimming speed. Diffusivity (lateral mixing), based on surface GPS drifter observations, was also considered and used to validate this model. Numerical experiments, using the hydrodynamics predicted by the Gulf of Maine Operational Forecasting System (GoMOFS) model, were conducted to test the potential impact of postlarval swimming ability on successful settlement on suitable habitat (defined as regions shallower than 20 m). The results of this experiment showed that elevated swimming ability (18 cm/s) in postlarvae significantly improves settlement success compared to trials modeling postlarvae with a diminished swimming ability (7 cm/s), or no swimming ability (control) at all. In contrast, diel swimming behavior in postlarvae slightly decreased successful settlement. In addition, ocean drifter observations and numerical simulations consistently revealed that successful settlement decreases the further the initial release point of larvae is from the coast. Combined, these experiments indicate that both the swimming ability of postlarvae and the distance they are from shore when they hatch are critical factors that influence their potential to reach viable settlement locations in the GoM. These data also suggest that if the GoM continues to warm, and females move further offshore to avoid warmer inshore waters, the settlement success of their larvae may be compromised.

AbstractTo predict ecosystem change in the Arctic Ocean, understanding Arctic phytoplankton phenology is essential. We develop a marine ecosystem model focusing on phytoplankton dynamics and the competition for multiple resources based on knowledge from in situ data obtained in the Chukchi Sea. The model is designed to include the unique ecological characteristics of the Arctic Ocean. To the best of our knowledge, this is the first model successfully simulating the current paradigm for Arctic phytoplankton phenology, including both under‐ice blooms and succession of phytoplankton groups. Sensitivity experiments show that the dominance of diatoms can be sustained by lateral transport of a high‐silicate water mass (Pacific Winter Water). Experiments for future scenarios show that sea ice retreat drives a decrease in large diatoms and an increase in the other relatively small non‐diatom groups. These results suggest that dominant phytoplankton groups can be shifted from diatoms to non‐diatoms under ongoing Arctic Ocean sea ice retreat.

Many ecosystem models have chronic issues that result in unrealistic oligotrophic conditions in the shallow coastal regions. This problem is attributed to the poorly resolved bottom boundary condition for ecological tracers; detritus reaching the bottom boundary in shallow water escapes the model domain resulting in continuously decreasing total nitrogen levels. The scaling for the problem is determined by a vertical length scale w d /delta , where w d is detritus sinking speed and delta is remineralization rate. For shallow water depths h << w d /delta corresponding to shallow marginal coastal ocean regions where loss of nitrogen is significant, ecosystem models predict unrealistic oligotrophic water masses. To alleviate the problem, the classical Nutrient-PhytoplanktonZooplankton-Detritus (NPZD) model is expanded here to consider denitrification and nitrogen fixation. Internal dynamics of the expanded model are examined through steady-state solutions. The intensity of denitrification, scaled as the ratio between w d /delta and water depth, plays an important role sustaining nitrogen fixers by regulating phosphorus competition with normal phytoplankton. The theoretical equilibriums of the expanded model well represent characteristics of coastal and pelagic ecosystems. The expanded ecosystem model is then fully coupled with a numerical hydrodynamics model and compared with the classical NPZD model. It is shown that unrealistic oligotrophic conditions along the coast predicted by the classical NPZD model are not present when denitrification and nitrogen fixation processes are considered because strong denitrification (loss of nitrogen) in the shallow region enhances nitrogen fixation that compensates the loss.

This study investigates the geotechnical characteristics of a soft tidal mudflat in the Great Bay Estuary, New Hampshire. Laboratory testing of surficial sediment samples of the upper 10 cm and field observations from a portable free-fall penetrometer (PFFP) were used to characterize soil strength properties (coefficient of consolidation and undrained shear strength). Pore pressure measurements from the PFFP were analyzed using a square-root of time method to estimate t50 and empirical correlations from the literature to estimate the coefficient of consolidation. Undrained shear strengths were estimated from the PFFP deceleration using cone factors of 10-12 and a strain rate correction factor of 0, resulting in undrained shear strengths of 0.5-1.1 kPa. Laboratory testing using miniature vane shear testing found the undrained shear strength to be 0.6-1.8 kPa. Both techniques indicate soft soils. The PFFP deceleration profiles also suggest the presence of layering within the seabed, a situation at the field site that could arise from environmental factors, such as winter ice formation and seasonal erosion. The coefficients of horizontal consolidation estimated with the PFFP (5.4x10-6-1.7x10-5 m2/s) were 1-2 orders of magnitude greater than the coefficients of vertical consolidation measured during oedometer testing (9.51x10-8-1.78x10-6 m2/s across all samples and load steps). Effects impacting the coefficient of consolidation such as to mismatches between sample depths and the resting depth of the penetrometer, sample disturbance, anisotropy, differences in loading conditions, and limitations associated with deriving values from literature charts are discussed. The results suggest that PFFPs are able to well-characterize the geotechnical properties of tidal mudflat soils and contribute to improving the understanding of the geotechnical parameters of undrained shear strength and coefficients of consolidation.

The new velocity fields based on the Generalized Ekman (GE) theory to trace floating algae were derived and verified by drifter observations and compared to reanalysis datasets in the Yellow Sea (YS). Two velocity fields using diagnostic approaches and two velocity fields from reanalysis datasets were examined. The results revealed that the diagnostic velocity fields had comparable accuracy to the reanalysis datasets, even locally better. Then, we applied each velocity field to trace green algae, Ulva prolifera, in July 2011 and brown algae, Sargassum horneri, in May 2017 using particle tracking experiments. In addition, drifter trajectories were simulated, and error accumulation speed was estimated for each velocity field. Simulation results using the diagnostic velocity fields consistently showed better agreement with satellite images and in situ observations than those using reanalysis datasets, demonstrating that the diagnostic velocity could be a superior tool for simulating surfacefloating substances and organisms. The approach to derive diagnostic velocity fields can be easily applied instead of relying on heavy computing numerical models.

A perturbative solution of simplified primitive equations for nonlinear weakly stratified upwelling over a frictional slope is found that resolves the vertical structure of velocity fields and can satisfy Ertel's potential vorticity conservation in the stratified inviscid interior. The solution uses assumptions consistent with the model proposed by Lentz and Chapman, including a steady-state, constant cross-shore density gradient, no alongshore gradients, laterally inviscid, and consideration of cross-shore advection of alongshore momentum. The solution resolves the vertical structure of velocity fields (including subsurface maxima of compensational flow, not resolved by Lentz and Chapman) and can satisfy Ertel's potential vorticity conservation in the stratified inviscid interior. The dynamics are similar to Lentz and Chapman; bottom stress balances alongshore wind stress in a homogeneous density ocean and is replaced by nonlinear cross-shore transport of alongshore momentum as the Burger number (S 5 aN/f, where a, N, and f are the bottom slope, buoyancy frequency, Coriolis frequency, respectively) increases. When the solution uses the empirical relation between cross-shore and vertical density gradients proposed by Lentz and Chapman, vorticity conservation is not satisfied and the nonlinear momentum transport estimated by the solution linearly increases with S, asymptotically matching Lentz and Chapman for S <1. When the solution conserves interior potential vorticity, the momentum transport is proportional to S-2 for S < 1 and is in better agreement with numerical simulations.

A modified version of the NPZD ecosystem model is used to analytically examine the effects of predation avoidance, a possible mechanism for triggering harmful algal blooms (HAB). To resolve HAB development caused by predation avoidance, an additional phytoplankton functional group is considered, one that has slower nutrient uptake and better predation avoidance characteristics than the non-harmful phytoplankton group used in traditional NPZD models. Because the two phytoplankton groups (one non-harmful and one HAB) compete for only one resource within the same system, steady state (equilibrium) conditions cannot occur without the presence of zooplankton; only the non-harmful phytoplankton group, which defeats the HAB group in the resource competition, can survive in the equilibrium. The presence of sufficient zooplankton effectively acts to replenish the nutrient pool by consuming the non-harmful phytoplankton. When this occurs, two equilibrium states are found: one with both phytoplankton groups coexisting, and one that only includes the HAB group. The condition required for equilibrium is that the total nitrogen within the system should be larger than a threshold determined by model coefficients. The threshold and feasibility of the equilibrium are sensitive to the relative HAB predation avoidance coefficient. If the coefficient is larger than the ratio of net growth rates between the HAB and non-harmful phytoplankton group, the threshold becomes infinite, and an equilibrium is not feasible. The time scale for the system to reach an equilibrium state that includes a HAB group is determined asymptotically. The dependence of a threshold condition as a controlling factor may explain the regime shift of dominant species causing HABs. The ecosystem model is fully implemented into the Regional Ocean Modeling System and applied to an idealized coastal embayment (with depths and geometry taken from San Francisco Bay) to show numerically the dominance of prey avoidance dynamics in a natural shallow water environment that includes advection and diffusion. The analytical results improve strategies for HAB modeling and provide guidance for setting model coefficients necessary to resolve a HAB event.

Climate change is likely to have a dramatic impact on many animals, including American lobsters (Homarus americanus). Lobsters are very sensitive to water temperature, and they will move to avoid water that is too warm or too cold. While this behavior has served them well for 1,000’s of years, as the oceans warm up, they might seek new habitats, which might disrupt aspects of their life cycle and lead to a decline in their numbers. In this article, we aim to explain some facts about American lobsters and tell you about several ways that climate change might have an impact on these fascinating and valuable creatures.

Wind influence on tidal inlet hydrodynamics is examined using 40 days of wind, water level, and current observations collected in Spring 2019 at Oregon Inlet, NC, a large (1 km wide, 1-13 m deep) meso-tidal inlet with complex delta systems. Wind velocities through the inlet (ranging 0-18 m/s) are modulated at subtidal timescales and are well correlated (R = 0.87) to a subtidal component of the water level slope through the inlet. The subtidal wind and water level slope are also well correlated to the subtidal current along the principal flow axis in the main inlet channel (R = 0.92 and 0.96, respectively). In combination with findings from previous studies, these findings suggest that regional winds induce the subtidal water level slope through the inlet by causing opposing setup/setdown to either side of the inlet. A force balance at the inlet demonstrates that the wind-induced pressure gradient forces the subtidal currents, with wave forcing and local wind shear acting as lower-order influences. The magnitude of the subtidal current is substantial, exceeding that of the tidal currents 45% of the time. Cumulatively, these findings indicate that regional winds exert a first-order control on the currents at Oregon Inlet and cause irregular hydrodynamic patterns not well described by the traditional inlet classification scheme. Regional geographic characteristics may contribute to the high level of wind influence at Oregon Inlet, but similar processes are likely to be important to net flow dynamics at other inlets with large, shallow inland water bodies.

A characteristic feature of the eastern Bering Sea (EBS) is a subsurface layer linked to seasonal sea ice (SSI) and defined by bottom temperatures less than 2 °C, which is termed the cold pool. Cold pool variability is directly tied to regional zooplankton and fish dynamics. Multifrequency (200 and 460 kHz) acoustic backscatter data were collected remotely using upward looking echosounders along the EBS shelf from 2008 and 2018 and used as a proxy of biological abundance. Acoustic data were coupled with bottom temperature and regional SSI data from the cold (2006-2013) and warm (2014-2018) regimes to assess the relationship between biological scattering communities and cold pool variation. Acoustic backscatter was 2 orders of magnitude greater during the cold regime than during the warm regime, with multifrequency analysis indicating a shift in the warm regime frequency-dependent scattering communities. Cold pool proxy SSI was a stronger predictor for biological scattering than bottom temperature in the cold regime, while warm regime bottom temperature and SSI were equal in predictive power and resulted in improved predictive model performance. Results suggest coupled cold pool and frequency-dependent scattering dynamics are a potential regime shift indicator and may be useful for management practices in surrounding Arctic ecosystems.

Field observations of small scale seabed morphology were obtained over 4 weeks at two locations separated 66 m along a cross-shore transect during the 2014 MEGAPEX Experiment conducted as part of the longer term Sand Engine mega-nourishment project along the North Sea Coast of The Netherlands. The seafloor was continuously covered by dynamic bedforms with amplitudes ranging 0.02-0.40 m and wavelengths ranging 0.20-2.5 m. Ripple migration rates were up to 3.6 m/h, dependent on the energy of the waves and currents. Under the assumption of bedload dominant transport, cross-shore and alongshore sediment volume flux by ripples was estimated from observations at the spatially separated imaging locations. The average and maximum ripple sediment volume flux was found to be 0.22 and 1.7 m3/m/day, respectively, with larger fluxes during spring flood tides and storm wave conditions. The daily averaged fluxes were usually oriented about 30 degrees north of shorenormal, moving in the same direction as a nearby transverse sandbar migration direction. Estimated gradients in the sediment flux within the surfzone were computed from bed level change measurements of the inner surfzone including a larger scale transverse sandbar measured from subsequent jetski surveys. We find that the estimated gradients in surfzone sediment flux are conceivably driven by small variations in the sediment flux driven by sand ripple migration, supported by our observations of ripple driven sediment flux at the two ripple imaging stations. A simple conceptual model is presented that shows how small scale bedforms may contribute to the growth and decay of larger scale bathymetric features, such as sandbars. Results suggest that sediment flux by small scale sand ripples and megaripples could significantly contribute to larger scale morphologic development in the surfzone.

We extracted and analyzed microplastics (MP) in archived sediment cores from Great Bay Estuary (GBE) in the Gulf of Maine region of North America. Results indicated that MP are distributed in GBE sediments, 0-30 cm, at an average occurrence of 116 ± 21 particles g-1 and that morphology varies by site and depth. Analysis by sediment depth and age class indicated that MP accumulation increased over several decades but recently (5-10 years) has likely begun to decrease. Hydrodynamic and particle transport modeling indicated that bed characteristics are a more controlling factor in MP distribution than typical MP properties and that the highest accumulation likely occurs in regions with weaker hydrodynamic flows and lower bed shear stress, e.g., eelgrass meadows and along fringes of the Bay. These results provide a baseline and predictive understanding of the occurrence, morphology, and sedimentation of MP in the estuary.

The effects of sea level rise on storm surge energy transformation and flood and ebb current magnitudes are examined in two distinct New Hampshire estuarine systems. The Great Bay estuary is characterized by strong tidal dissipation along a long (13 km) and deep (20-25 m) rocky channel (ebb-dominated Piscataqua River) that connects to a large (flood-dominated) estuarine bay with extensive mudflat areas, whereas the (ebb-dominated) Hampton/Seabrook estuary has minimal tidal dissipation through a short (1 km) and shallow (5-7 m) sandy inlet that connects to an extensive salt marsh with narrow tidal channels. Numerical simulations are conducted using the finite-volume coastal ocean model (FVCOM) with forcing provided by the tides, with and without 0.01 annual exceedance probability storm surge estimated by the North Atlantic Comprehensive Coastal Study (NACCS) and further with and without sea level rise scenarios for year 2060 in Hampton/Seabrook (0.73 m) and 2100 in Great Bay (1.92 m). Results for the Great Bay estuary show that although the maximum sea surface elevation is higher during storm events, upstream linear wave energy loss (about 50%) of the storm surge with and without sea level rise is similar to tidal wave energy loss under present nonstorm conditions. Corresponding depth-integrated currents increase by 10%-30% with sea level rise, 23%-52% with the storm surge, and 32%-97% for the combined event. However, results from the Hampton/Seabrook estuary show that energy loss through the inlet increases from 2% to 4% for no storm and present-day sea level to 30%-40% for storm surge with sea level rise, partially mitigating inland inundation. Depth-integrated current magnitudes in the Hampton/Seabrook inlet increase by a factor of 4 under sea level rise and storm surge. Model results suggest that sea level rise has significant impacts on current speeds in both estuaries and that the energy decay of the tidal wave and storm surge depends on the nature of the estuarine system, with greater change associated with estuaries with shallow, narrow inlets somewhat reducing the effects of inland flooding.

Bedload transport is an important mechanism for sediment flux in the nearshore. Yet few studies examine the relationship between bedform evolution and net sediment transport. Our work contributes concurrent observations of bedform mobility and bedload transport in response to wave dominant, current dominant, and combined wave-current flows in the nearshore. Bedload sediment flux from migrating bedforms during combined wave-current conditions accounted for at least 20% more bedload transport when compared with wave dominant flows and at least 80% more than current-dominant flows. Bedforms were observed to transport the most sediment during periods with strong currents, with high-energy skewed waves, and while bedform orientation and transport direction were aligned. Regardless of flow type, bedform migration rates were directly proportional to the total kinetic energy contained in the flow field. Eleven bedload transport models formulated to be used in combined flows (both shear and energetics based) were compared with sediment flux estimated from measured bedform migration. An energetics based sediment transport model was most representative for our data.

Time series spanning 22 years of monthly conductivity-temperature-depth profiles are used to examine upper water column temperature interannual variability near the Ecuador coastline. The sampling program began in 1992 (and continues) by Ecuador's National Institute of Oceanography of the Navy and National Fisheries Institute. The five coastal stations are located 8 NM away from the coast and extend from 2 degrees S to 1 degrees N. The anomaly data show marked interannual variations with distinct characteristics associated with El Nino Southern Oscillation (ENSO) indices. Heat content and the 20 degrees C isotherm depth are both largest during El Nino periods and weakest during La Nina periods. The first mode empirical orthogonal function (EOF) decomposition of the anomaly coastal station data represents bulk variations of the thermocline depth and has temporal variability coupled to Nino 3.4 and 1+2 indices. Coastal observations are compared with observations obtained from the offshore TAO/Triton buoys located along 95 degrees W from 2 degrees S to 2 degrees N. The EOF decomposition of TAO buoy time series shows similar spatial EOF structure. The first EOF amplitude time series from coastal and TAO station decomposition is correlated, showing that the dominant variability of the upper water column near the coast is coupled to variations along the equator and seaward of the Galapagos. Coupling between ENSO indices and ERA-1 zonal wind stress from the central Pacific (Nino 4) with observed coastal temperature structure shows that effects of El Nino forcing are strongly influencing the Ecuadorian Sea eastward of the Galapagos Islands.