Prediction of near-field shear dispersion in an emergent canopy with heterogeneous morphology

The evaluation of longitudinal dispersion in aquatic canopies is necessary to predict the behavior of dissolved species and suspended particles in marsh and wetland systems. Here we consider the influence of canopy morphology on longitudinal dispersion, focusing on transport before constituents have mixed over depth. Velocity and longitudinal dispersion were measured in a model canopy with vertically varying canopy density. The vertical variation in canopy morphology generates vertical variation in the mean velocity profile, which in turn creates mean-shear dispersion. We develop and verify a model that predicts the mean-shear dispersion in the near field from morphological characteristics of the canopy, such as stem diameter and frontal area. Close to the source, longitudinal dispersion is dominated by velocity heterogeneity at the scale of individual stems. However, within a distance of approximately 1 m, the shear dispersion associated with velocity heterogeneity over depth increases and eclipses this smaller-scale process.     

A mechanism for horizontal zooplankton transport by vertical migration in tidal currents

A mechanism is proposed by which net horizontal transport can be induced in an organism which migrates vertically in a purely oscillatory, vertically sheared tidal current. The mechanism contains two elements. First, for all reasonable tidal current profiles, net horizontal transport is induced in any organism which migrates vertically with a period which is an exact multiple of the tidal period. (This is the basis for the widelyknown process of selective tidal stream transport where the migration period and the tidal period are exactly equal.) The second element in the new mechanism is the observation that diel migration, the most common form of vertical migration, has a period of 24 h and is therefore an exact multiple of the principal solar semi-diurnal tidal constituent (S2) which has a period of 12 h. This relation between the S2 and diel migration periods stems from the fact that both phenomena are independently locked to the solar cycle. Diel vertical migration can therefore interact with the S2 tidal current constituent to induce longterm horizontal transport in migrating organisms. For reasonable tidal current and vertical migration parameters it is found that horizontal transport rates of 4 km d^–1 are possible. The direction of net transport depends upon the phase of the S2 tidal current relative to local noon. The hypothesis is therefore proposed that geographical variation in S2 phase is a factor responsible for creating regions which are either retention-favorable or otherwise for diel-migrating marine organisms.     

Temporal variability of zooplankton biomass (ATP content and dry weight) in the St. Lawrence Estuary: Advective phenomena during neap tide

In order to assess the temporal variability of living zooplankton in a tidal estuary, the ATP content and dry weight of mixed zooplankton populations (mainly copepods) were measured during a period of 175 h at an anchor station in the Upper St. Lawrence Estuary. Vertical tows were made every 30 min. Hourly vertical profiles of the current speed and direction, temperature and salinity were also obtained during the experiment. A strong tidal influence was found in all series. Maxima and minima of the ATP content (living biomass) and the dry weight (total biomass) were correlated with low and high water slacks. The serial autocorrelation and cross-correlation showed, in both series a 12 to 13-h cycle, and the ATP:dry weight ratio showed a significant 24-h cycle. The cross-correlation with the Kendall τ was used to detect the relationship between biological components and physical indices (stratification and Ri). It is suggested that the proportion of living zooplankton biomass in the Upper St. Lawrence Estuary is most likely the result of a combination of diurnal migration and longitudinal advection.     

An individual-based analysis of the dynamics of two coexisting phytoplankton species in the mixed layer

In marine ecosystems ecological and environmental conditions continuously change, possibly supporting the wide range of phytoplankton species coexisting in aquatic environments. Phytoplankton communities are not homogeneously distributed in the water column due to the spatial and temporal variability of turbulent mixing and the concurrent biological response. In this paper an individual-based model (Lagrangian method) simulating the basic physiology of two coexisting phytoplankton species has been developed. The species, sharing the same availability of light and nutrient resource, are characterized by different photo-physiological parameters. The spatial and temporal evolution of turbulent mixing is simulated introducing vertical profiles of measured eddy diffusivity. Three case studies have been examined to analyze the role of environment–individual interactions in determining bloom conditions for both the selected species. The organisms experience recurrent fluctuations of light, temperature, and nutrient concentration gradients, due to the turbulent mixing in the water column, which have significant effects on the growth of the phytoplankton species. In all the numerical experiments, the temporal and spatial variability of different forcings do not support the prevalence of one species over the other over the time scale typical of a phytoplankton bloom.A well mixed water column favours the growth of both the populations while a variable mixing regime limits their growth reducing the photophysiological differences between the species.     

Vertical migration strategies with respect to advection and stratification in a semi-enclosed lough: a comparison of mero- and holozooplankton

Patterns of zooplankton vertical movement are often difficult to interpret because of multiple, complex and confounding environmental factors. Behavioural adaptations to these environmental variables are compared within and between the holo- and meroplankton constituents of a community. We used a nested design to analyse patterns at several scales in time; (semi-diel, diel, spring-neap tidal cycle and season) and two in space; (depth and site). To reduce complexity and aid interpretation we studied a semi-isolated community in a semi-enclosed, seasonally stratified sea lough (Lough Hyne Marine Nature Reserve, Ireland). In this, the main environmental gradient was water flow rate (or water residence time) caused by tidal currents. Vertical profiles of abundance showed that populations of the most abundant species of holo- and meroplankton in the lough have considerable behavioural plasticity, enabling them to switch between sedentary and migratory behaviour and patterns of migration. Some species migrate vertically in synchrony with diel cycles and others in response to semi-diel tidal currents; a few do both, but the majority did neither. It is suggested that water column structure and hydrographic discontinuities caused by flow rate and pycnocline dynamics are responsible for the variable patterns of vertical migration and distribution.Communicated by J.P. Thorpe, Port Erin     

Mass Transport in Vegetated Shear Flows

Submerged aquatic vegetation has the potential to greatly improve water quality through the removal of nutrients, particulates and trace metals. The efficiency of this removal depends heavily upon the rate of vertical mixing, which dictates the timescale over which these constituents remain in the canopy. Continuous dye injection experiments were conducted in a flume with model vegetation to characterize vertical mass transport in vegetated shear flows. Through the absorbance–concentration relationship of the Beer–Lambert Law, digital imaging was used to provide high-resolution concentration profiles of the dye plumes. Vertical mass transport is dominated by the coherent vortices of the vegetated shear layers. This is highlighted by the strong periodicity of the transport and its simple characterization based on properties of the shear layer. For example, the vertical turbulent diffusivity is directly proportional to the shear and thickness of the layer. The turbulent diffusivity depends upon the size of the plume, such that the rate of plume growth is lower near the source. In the far-field, mass is mixed more than twice as rapidly as momentum. Finally, plume size is dictated predominantly by X, a dimensionless distance that scales upon the number of vortex rotations experienced by the plume.     

Eddy diffusivity: a single dispersion analysis of high resolution drifters in a tidal shallow estuary

In an estuary, mixing and dispersion resulting from turbulence and small scale fluctuation has strong spatio-temporal variability which cannot be resolved in conventional hydrodynamic models while some models employs parameterizations large water bodies. This paper presents small scale diffusivity estimates from high resolution drifters sampled at 10 Hz for periods of about 4 h to resolve turbulence and shear diffusivity within a tidal shallow estuary (depth <3 m). Taylor’s diffusion theorem forms the basis of a first order estimate for the diffusivity scale. Diffusivity varied between 0.001 and 0.02 m²/s during the flood tide experiment. The diffusivity showed strong dependence (R² > 0.9) on the horizontal mean velocity within the channel. Enhanced diffusivity caused by shear dispersion resulting from the interaction of large scale flow with the boundary geometries was observed. Turbulence within the shallow channel showed some similarities with the boundary layer flow which include consistency with slope of 5/3 predicted by Kolmogorov’s similarity hypothesis within the inertial subrange. The diffusivities scale locally by 4/3 power law following Okubo’s scaling and the length scale scales as 3/2 power law of the time scale. The diffusivity scaling herein suggests that the modelling of small scale mixing within tidal shallow estuaries can be approached from classical turbulence scaling upon identifying pertinent parameters.     

Analysis of lipid components for determining the condition of anchovy larvae,Engraulis mordax

It has been presumed that intertidal spawning by Limulus polyphemus minimizes the loss of egges to subtidal predators; however, this strategy involves considerable risks. Massive beach strandings of adults accompany seasonal spawning migrations of crabs along Cape May in Delaware Bay, (USA). At least 190000 horseshoe crabs, approximating 10% of the adult population, died from beach stranding along the New Jersey shore of Delaware Bay during the 1986 (May to June) spawning season. Abnormalities of the telson (which is used in righting behavior) were significantly more common among stranded crabs than among individuals actively spawning on the intertidal beach. The number of stranded crabs per day was not correlated with tidal height or environmental variables (wind speed, wave height) which characterized the conditions at spawning. A complex suite of factors, including the size of the available spawning population, tidal and weather conditions, and beach slope, influence the number stranded during the breeding season. Horseshoe crab stranding results in a large loss of gravid females from the population, and may represent a major input of organic matter to intertidal sandy beaches in certain regions of Delaware Bay.     

Modeling and data assessment of longitudinal salinity in a low-gradient estuarine river

Continuous data of vertical-profile salinity were analyzed for four stations located successively upriver in a macrotidal estuary, the lower St. Johns River (Northeast Florida, USA). The data analysis confirmed well-mixed salinity conditions in the river with at most 1.3 ppt of vertical variability at Dames Point (river km 20), where the main variations of salinity are along the longitudinal axis of the river. Given the well-mixed salinity conditions and dominant horizontal structure of salinity variations in the river, we present and apply a barotropic, two-dimensional modeling approach for hydrodynamic-salinity transport simulation in the lower St. Johns River. When properly forced by offshore surge, high-resolution wind fields and freshwater river inflows, the model replicated the salinity measurements remarkably well, including the separation into tidal and sub-tidal components. The data and model results show that, at times, offshore winds and surge can be more influential on longitudinal salinity variations than local winds over the river. We demonstrate the importance of using proper boundary conditions to force the model relative to the minimal sensitivity of the model to parameter adjustment of horizontal mixing and uncertainty-based perturbation of wind and inflow forcings.     

Rhythmic motor activity responses of the California fiddler crab Uca crenulata to artificial light conditions

Uca crenulata, the California species of fiddler crab, was exposed to artificial light conditions to separate the influence of the light cycle from that of the tidal input on its rhythmic motor activity. Under both constant light and light-dark cycles, rhythmic activity was demonstrated in only 50% of the experimental crabs; the activity of the remaining 50% was random. Individuals exposed to constant light conditions after having been subjected to 24 h light-dark cycles demonstrated no significant difference in period length of their rhythmic activity from crabs investigated in constant light immediately after field collection. The mean period did not differ significantly from the tidal period of 24.8 h, but the variation was considerable. In artificial light-dark cycles, the activity rhythms were usually masked but, in some cases, synchronized. The results indicate that U. crenulata has an endogenous rhythm with a period close to the tidal cycle which may be synchronized by light as well as by tidal cues. The display of this endogenous rhythm, however, is poor.     

Deterministic particle tracking simulation of pollutant discharges in rivers and estuaries

A two-dimensional deterministic particle tracking model, in which the anisotropic-dispersive process is described by a particle strength exchange scheme, is established for the simulation of pollutant transport in vertically well-mixed rivers and estuaries. By simulating two benchmark problems with analytic solutions, the PSE scheme is shown to be accurate even if the anisotropic ratio of dispersion coefficients is very high. Further simulations of two specific problems concerning the optimal effluent discharge location and procedure are presented. The major conclusion is that in a tidal estuary with a relatively large fresh-water flow, setting the discharge position at the mixing center and making the discharge rate proportional to flow speed may minimize the peaks of concentration.     

A σ-coordinate transport model coupled with rotational boussinesq-type equations

This paper describes a σ-coordinate scalar transport model coupled with a Boussinesq-type hydrodynamic model. The Boussinesq model has the ability to calculate both three-dimensional velocity distributions and the water surface motion. To capture ‘dispersion’ processes in open channel flow, horizontal vorticity effects induced by a bottom shear stress are included in the Boussinesq model. Thus, a reasonable representation of vertical flow structure can be captured in shallow and wavy flow fields. To solve the coupled Boussinesq and scalar transport system, a finite-volume method, based on a Godunov-type scheme with the HLL Riemann solver, is employed. Basic advection and advection–diffusion numerical tests in a non-rectangular domain were carried out and the computed results show good agreement with analytic solutions. With quantitative comparisons of dispersion experiments in an open channel, it is verified that the proposed coupled model is appropriate for both near and far field scalar transport predictions. From numerical simulations in the surf zone, physically reasonable results showing expected vertical variation are obtained.     

Secondary flow within a river bed and contaminant transport

We have developed a numerical method to simulate the transport of non-sorbing contaminants within the sediment layer of a stream and the leaching of these contaminants in the steam. Typical stream bottom surfaces are uneven with triangularly shaped undulation forms. The flow of the water above such triangular surfaces causes external pressure changes that result in a “pumping effect” and a secondary flow within the sediment. The latter causes a significant contaminant advection within the sediment layer. The flow field in the porous sediment layer is obtained by solving numerically Darcy’s equations. The unsteady mass transfer equation is solved by using a finite-difference method with an up-wind scheme. The effects of parameters, such as channel slope, hydraulic head and dispersion, are studied by quantitatively comparing the numerical results of the total mass flow rate from the contaminant source, the concentration front propagation, and the contaminant mass flow rate into the water column. The “pumping effect,” increases the flow in the vertical direction and, thus, enhances the vertical advective mass transport of the contaminant. This bedform-shape induced flow is largely responsible for the mass transfer of contaminants into the water column. The numerical results also show that the mechanical dispersion inside the sediment bed will significantly increase the contaminant mass flow rate from the source.     

Large Eddy Simulation of turbulence generated by a weak breaking tidal bore

A tidal bore is a natural and fragile phenomenon, which is of great importance for the ecology of an estuary. The bore development is closely linked with the tidal range and the river mouth shape, and its existence is sensitive to any small change in boundary conditions. Despite their ecological and cultural value, little is known on the flow field, turbulent mixing and sediment motion beneath tidal bores. Indeed, some striking features can be highlighted in two-dimensional simulations, such as large velocity fluctuations and flow recirculation structures. Using Large Eddy Simulation method, the numerical results emphasised the complicated turbulent structures and their unsteadiness under a tidal bore.     

A Computational Fluid Dynamics Approach for Urban Area Transport and Dispersion Modeling

A simulation tool has been developed to model the wind fields, turbulence fields, and the dispersion of Chemical, Biological, Radiological and Nuclear (CBRN) substances in urban areas on the building to city blocks scale. A Computational Fluid Dynamics (CFD) approach has been taken that naturally accounts for critical flow and dispersion processes in urban areas, such as channeling, lofting, vertical mixing and turbulence, by solving the steady-state, Reynolds-Averaged Navier–Stokes (RANS) equations. Rapid generation of high quality cityscape volume meshes is attained by a unique voxel-based model generator that directly interfaces with common Geographic Information Systems (GIS) file formats. The flow and turbulence fields are obtained by solving the steady-state RANS equations using a collocated, pressure-based approach formulated for unstructured and polyhedral mesh elements. Turbulence modeling is based upon the Renormalization Group variant of the k–ε model (k–ε RNG). Neutrally buoyant simulations are made by prescribing velocity boundary condition profiles found by a power–law relationship, while turbulence quantities boundary conditions are defined by a prescribed mixing length in conjunction with the assumption of turbulence equilibrium. Dispersion fields are computed by solving an unsteady transport equation of a dilute gas, formulated in a Eulerian framework, using the velocity and turbulence fields found from the steady-state RANS solution. In this paper the model is explained and detailed comparisons of predicted to experimentally obtained velocity, turbulence and dispersion fields are made to neutrally stable wind tunnel and hydraulic flume experiments.     

Measuring mucus thickness in reef corals using a technique devised for vertebrate applications

A method previously used to measure thickness of the surface mucus layer (SML) of the mammalian gastrointestinal tract has been applied to the SML of reef corals. It involves manual measurement of mucus thickness using a micromanipulator and fine glass needle (micropipette) and is non-destructive to the coral, meaning that repeated measurements can be taken. A measurable mucus layer was recorded in all cases in the study, which comprised 450 individual thickness measurements from four coral species. Mucus thickness ranged from 145 to 700 μm. Thus, whatever dynamic processes control mucus synthesis, secretion to the tissue surface and subsequent release into the water column, a continuous mucosal barrier is maintained. A change in SML thickness was recorded as a response to aerial exposure during the natural tidal cycle and to solar exposure-induced bleaching, although the response due to bleaching varied between two studied species. The technique is rapid, cost-effective and a simple means of assessing coral SML thickness, a variable that shows significant variation in relation to environmental conditions and is likely to be an important health indicator in these organisms.     

Effects of depth on the feeding capabilities of two octocorals

Photographic and trap data obtained from the eastern North Atlantic Ocean in 1981 and 1978, respectively, have been combined to document the response of abyssal lysianassid amphipods to large food falls, and the predation on these amphipods by the fish Paraliparis bathybius. The use of a new camera/current meter system has demonstrated that overall numbers of amphipods and presence of fish were related to tidal currents. Species of Paralicella and Orchomene were the most abundant amphipods, and occurred in peak numbers during periods of low current velocity. Variation in abundance of Eurythenes gryllus, a larger species, which occurred in smaller numbers, was apparently not related to tidal currents. Paraliparis bathybius were present only during flood tides.     

A coupled numerical model to investigate the air–sea interaction at the coastal upwelling area of Cabo Frio,Brazil

This work investigates the capability of an oceanic numerical model dynamic and thermodynamically coupled to a three-dimensional mesoscale atmospheric numerical model to simulate the basic features of the air–sea interaction in the coastal upwelling area of Cabo Frio (RJ, Brazil). The upwelling/downwelling regime is an important feature in the oceanic circulation of Cabo Frio and determines the sustainability of local ecosystems. This regime is predominantly driven by the atmospheric circulation and is well documented, being suitable to be used as test reference for atmospheric and oceanic coupled and uncoupled models. The oceanic boundary conditions, coastline shape and coupling effect have been tested. The uncoupled oceanic model forced by a NE (SW) wind field generates a realistic upwelling (downwelling) phenomenon regardless of the proximity of the lateral boundary and how realistic is the shape of the coastline. The atmospheric-oceanic coupled model generates an upwelling location and intensity similar to the uncoupled simulation, but the upwelling is gradually enhanced by the sea-breeze circulation. It also generates vertical profiles of mixing ratio that compare better to the observations than the uncoupled simulation and air potential temperature and wind vertical profiles that represent particular features of the atmospheric circulation at Cabo Frio.     

Short-term temporal patterns of early recruitment of coral reef fishes in the tropical eastern Pacific

Short-term temporal patterns of recruitment have been described in a variety of coral reef fishes and have often been related with lunar and tidal cycles. While the relative importance of lunar and tidal factors in determining recruitment patterns has been difficult to assess, most studies have been done in the Caribbean and Indo-Pacific, where tidal amplitudes are small. We studied the short-term temporal dynamics of fish recruitment at Gorgona Island (tropical eastern Pacific), where there is a large tidal amplitude (~4.4 m). Every other day during three consecutive months in 1998, we directly measured the magnitude of reef fish recruitment to standardized coral units (SCUs) isolated from natural reefs. A total of 40 species from 21 families settled on the SCUs. Of 11 species with sufficient numbers for meaningful statistical analyses, two (Lutjanus guttatus and Pomacanthus zonipectus) had lunar recruitment with peaks near the new moon; three combined species of antennariids showed semilunar recruitment with peaks near moon quarters; and eight other species showed sporadic and aperiodic recruitment pulses. The contribution of lunar (moonlight intensity) and tidal factors (tidal amplitude and net tidal flow) to recruitment dynamics varied among species, although it was generally low (<18%) even among species with periodic patterns, except perhaps in L. guttatus. In this species, recruitment magnitude correlated negatively with moonlight intensity, accounting for 34.5% of the variance. Post-settlement predation by roving predators may be one cause of this relationship. In the remaining species, particularly those with sporadic and aperiodic recruitment pulses, stochastically varying weather and oceanographic events may be more important in determining temporal variation in recruitment.     

Geolocation of free-ranging fish on the European continental shelf as determined from environmental variables II. Reconstruction of plaice ground tracks

Between December 1993 and February 1997, 302 electronic data storage tags (DSTs), programmed to record depth at 10-min intervals and temperature daily, were attached to mature female plaice, Pleuronectes platessa, and released in the southern North Sea. Fifty tags were returned, 38 of which functioned fully and recorded 2,955 days of data. Twenty-seven tags recorded data over the full period at liberty, and 34 geographical ground tracks were reconstructed. Reconstruction was performed using a two-dimensional tidal stream simulation model that translated vertical movement of fish, recorded by DSTs, into horizontal movement assuming an initial down-tide swimming speed of 0.6 body lengths s^–1. Geographical accuracy of reconstructed tracks was assessed based on closeness of fit between (1) reconstruction endpoint and reported recapture position; (2) reconstructed locations and corresponding locations based on tidal data recorded by DSTs using the tidal location method (TLM; location of areas with similar tidal range and time of high water); and (3) DST temperature records and corresponding averaged sea surface temperature data records for corresponding locations. The results demonstrate that the assumptions of the tidal stream simulation model were sufficient to reconstruct geographically accurate representations of the migrations of individual plaice, which have in turn provided new information on the extent, duration, and directionality of movement. Our study demonstrates how DSTs can provide fishery-independent data with direct management applications in behaviourally driven, individual-based predictive models of fish migration.Communicated by J.P. Thorpe, Port Erin