Tidal flushing and wind driven circulation of Ahe atoll lagoon (Tuamotu Archipelago, French Polynesia) from in situ observations and numerical modelling

Hydrodynamic functioning and water circulation of the semi-closed deep lagoon of Ahe atoll (Tuamotu Archipelago, French Polynesia) were investigated using 1year of field data and a 3D hydrodynamical model. Tidal amplitude averaged less than 30cm, but tide generated very strong currents (2ms(-1)) in the pass, creating a jet-like circulation that partitioned the lagoon into three residual circulation cells. The pass entirely flushed excess water brought by waves-induced radiation stress. Circulation patterns were computed for climatological meteorological conditions and summarized with stream function and flushing time. Lagoon hydrodynamics and general overturning circulation was driven by wind. Renewal time was 250days, whereas the e-flushing time yielded a lagoon-wide 80-days average. Tide-driven flush through the pass and wind-driven overturning circulation designate Ahe as a wind-driven, tidally and weakly wave-flushed deep lagoon. The 3D model allows studying pearl oyster larvae dispersal in both realistic and climatological conditions for aquaculture applications.     

Modelling larval dispersal of the king scallop (Pecten maximus) in the English Channel: examples from the bay of Saint-Brieuc and the bay of Seine

The king scallop (Pecten maximus) is one of the most important benthic species of the English Channel as it constitutes the first fishery in terms of landings in this area. To support strategies of spatial fishery management, we develop a high-resolution biophysical model to study scallop dispersal in two bays along the French coasts of the English Channel (i.e. the bay of Saint-Brieuc and the bay of Seine) and to quantify the relative roles of local hydrodynamic processes, temperature-dependent planktonic larval duration (PLD) and active swimming behaviour (SB). The two bays are chosen for three reasons: (1) the distribution of the scallop stocks in these areas is well known from annual scallop stock surveys, (2) these two bays harbour important fisheries and (3) scallops in these two areas present some differences in terms of reproductive cycle and spawning duration. The English Channel currents and temperature are simulated for 10 years (2000–2010) with the MARS-3D code and then used by the Lagrangian module of MARS-3D to model the transport. Results were analysed in terms of larval distribution at settlement and connectivity rates. While larval transport in the two bays depended both on the tidal residual circulation and the wind-induced currents, the relative role of these two hydrodynamic processes varied among bays. In the bay of Saint-Brieuc, the main patterns of larval dispersal were due to tides, the wind being only a source of variability in the extent of larval patch and the local retention rate. Conversely, in the bay of Seine, wind-induced currents altered both the direction and the extent of larval transport. The main effect of a variable PLD in relation to the thermal history of each larva was to reduce the spread of dispersal and consequently increase the local retention by about 10 % on average. Although swimming behaviour could influence larval dispersal during the first days of the PLD when larvae are mainly located in surface waters, it has a minor role on larval distribution at settlement and retention rates. The analysis of the connectivity between subpopulations within each bay allows identifying the main sources of larvae which depend on both the characteristics of local hydrodynamics and the spatial heterogeneity in the reproductive outputs.     

Modelling larval dispersal and settlement of the reef-building polychaete Sabellaria alveolata: Role of hydroclimatic processes on the sustainability of biogenic reefs

The honeycomb worm Sabellaria alveolata forms biogenic reefs which constitute diversity hotspots on tidal flats. The largest known reefs in Europe, located in the Bay of Mont-Saint-Michel (English Channel), are suffering increasing anthropogenic disturbances which raise the question of their sustainability. As the ability to recover depends partly on the recolonization of damaged reefs by larval supply, evaluating larval dispersal and the connectivity between distant reefs is a major challenge for their conservation. In the present study, we used a 3D biophysical model to simulate larval dispersal under realistic hydroclimatic conditions and estimate larval retention and exchanges among the two reefs of different sizes within the bay. The model takes into account fine-scale hydrodynamic circulation (800×800 m²), advection–diffusion larval transport, and gregarious settlement behaviour. According to the field data, larval dispersal was simulated for a minimal planktonic larval duration ranging from 4 to 8 weeks and the larval mortality was set to 0.09 d⁻¹. The results highlighted the role played by a coastal eddy on larval retention within the bay, as suggested by previous in situ observations. Very different dispersal patterns were revealed depending on the spawning reef location, although the two reefs were located only 15 km apart. The settlement success of the larvae released from the smallest reef was mainly related to tidal conditions at spawning, with the highest settlement success for releases at neap tide. The settlement success of the larvae from the biggest reef was more dependent on meteorological conditions: favourable W and SW winds may promote a ten-fold increase in settlement success. Strong year-to-year variability was observed in settlers’ numbers, with favourable environmental windows not always coinciding with the main reproductive periods of Sabellaria. Settlement kinetics indicated that the ability to delay metamorphosis could significantly improve the settlement success. Although bidirectional exchanges occurred between the two reefs, the highest settlers’ numbers originated from the biggest reef because of its stronger reproductive output. Because of the recent decline of this reef due to increasing anthropogenic disturbances larval supply in the bay may not be sufficient enough to ensure the sustainability of the remarkable habitat formed by Sabellaria alveolata reefs.     

Modelling salmon lice dispersal in Loch Torridon, Scotland

A particle transport model is described that is being used to simulate the dispersal of salmon lice (Lepeophtheirus salmonis) larvae in the waters of Loch Torridon. A hydrodynamic model, forced by tides and winds, drives the transport model. Particle movements are strongly influenced by winds, which can lead to formation of lice concentrations in coastal areas several kilometres from the source. Idealised constant wind simulations have been used to locate areas that larval lice may potentially reach from given source locations. Detailed analysis of simulations forced with real wind data is required to assess areas that larval lice from these sources are likely to reach. Further field and experimental work on the viability of lice is required to assess infection risk.     

Multi-scale distribution and dynamics of bivalve larvae in a deep atoll lagoon (Ahe, French Polynesia)

Bivalve larvae and hydrographic parameters were sampled over a range of spatio-temporal scales in a deep atoll lagoon. Bivalve larvae abundances were very high throughout the year: 18,550 m(-3) in average. Larvae were (i) concentrated at mid-depth with nocturnal ascent and diurnal descent, (ii) heterogeneously dispersed at the lagoon scale, (iii) subject to day-to-day variation in abundance and (iv) transferred between different parts of the lagoon providing evidence of intra-lagoonal connectivity. The primacy of physical factors was seen on large spatial scale with the diluting effect of water renewal and transfers by hydrodynamics. On smaller spatial scale, the primacy of biological processes was recognised, with larval swimming activity leading to dial vertical migration correlated with food concentration. Variations in larval abundance were driven by bivalve reproductive activity correlated with meteorological conditions (i.e. windy periods). Finally, relationship between bivalve larvae patterns and pearl oyster (Pinctada margaritifera) settlement structuring is discussed.     

A numerical study of the dynamics of the wave-driven circulation within a fringing reef system

The circulation driven by wave breaking, tides and winds within a fringing coral reef system (Ningaloo Reef) in Western Australia was investigated using the ocean circulation model ROMS two-way coupled to the wave model SWAN. Currents within the system were dominantly forced by wave breaking, with flow driven over the shallow reefs and towards the lagoon, which returned to the ocean through channels in the reef. Hindcast model simulations were compared against an extensive field dataset, revealing that the coupled wave–circulation model could accurately predict the waves and currents throughout this morphologically complex reef–lagoon system. A detailed momentum budget analysis showed that, over the reef, a dominant cross-shore balance was established between radiation stress gradients and a pressure (mean water level) gradient (similar to a beach). Within the lagoon, alongshore currents were primarily balanced by alongshore gradients in wave setup, which drove flow towards (and ultimately out) the channels. The importance of these wave-driven currents to Ningaloo Reef was quantified over a full seasonal cycle, during periods when wave and wind conditions significantly differed. These results showed that wave breaking still overwhelmingly dominated the circulation and flushing of Ningaloo Reef throughout the year, with winds playing an insignificant role.     

Review of solutions for 3D hydrodynamic modeling applied to aquaculture in South Pacific atoll lagoons

A workshop organized in French Polynesia in November 2004 allowed reviewing the current methods to model the three-dimensional hydrodynamic circulation in semi-enclosed atoll lagoons for aquaculture applications. Mollusk (e.g. pearl oyster, clam) aquaculture is a major source of income for South Pacific countries such as French Polynesia or Cook Islands. This aquaculture now requires a better understanding of circulation patterns to improve the spatial use of the lagoons, especially to define the best area to set larvae collectors. The pelagic larval duration of the relevant species (<20 days) and the size of the semi-closed lagoons (few hundreds of km2) drive the specifications of the model in terms of the spatial and temporal scale. It is considered that, in contrast with fish, mollusk larvae movements are limited and that their cycle occurs completely in the lagoon, without an oceanic stage. Atolls where aquaculture is productive are generally well-bounded, or semi-closed, without significant large and deep openings to the ocean. Nevertheless part of the lagoon circulation is driven by oceanic water inputs through the rim, ocean swells, tides and winds. Therefore, boundary conditions of the lagoon system are defined by the spatial structure of a very shallow rim (exposition and number of hoas), the deep ocean swell climate, tides and wind regimes. To obtain a realistic 3D numerical model of lagoon circulation with adequate forcing, it is thus necessary to connect in an interdisciplinary way a variety of methods (models, remote sensing and in situ data collection) to accurately represent the different components of the lagoon system and its specific boundary conditions. We review here the current methods and tools used to address these different components for a hypothetical atoll of the Tuamotu Archipelago (French Polynesia), representative of the semi-closed lagoons of the South Pacific Ocean. We hope this paper will serve as a guide for similar studies elsewhere and we provide guidelines in terms of costs for all the different stages involved.     

Multi-scale distribution and dynamics of bivalve larvae in a deep atoll lagoon (Ahe,French Polynesia)

Bivalve larvae and hydrographic parameters were sampled over a range of spatio-temporal scales in a deep atoll lagoon. Bivalve larvae abundances were very high throughout the year: 18,550 m⁻³ in average. Larvae were (i) concentrated at mid-depth with nocturnal ascent and diurnal descent, (ii) heterogeneously dispersed at the lagoon scale, (iii) subject to day-to-day variation in abundance and (iv) transferred between different parts of the lagoon providing evidence of intra-lagoonal connectivity. The primacy of physical factors was seen on large spatial scale with the diluting effect of water renewal and transfers by hydrodynamics. On smaller spatial scale, the primacy of biological processes was recognised, with larval swimming activity leading to dial vertical migration correlated with food concentration. Variations in larval abundance were driven by bivalve reproductive activity correlated with meteorological conditions (i.e. windy periods). Finally, relationship between bivalve larvae patterns and pearl oyster (Pinctada margaritifera) settlement structuring is discussed.     

Modelling tidally induced larval dispersal over Anton Dohrn Seamount

Massachusetts Institute of Technology general circulation model is used for the analysis of larval dispersal over Anton Dohrn Seamount (ADS), North Atlantic. The model output validated against the in situ data collected during the 136th cruise of the RRS ‘James Cook’ in May–June 2016 allowed reconstruction of the details of the baroclinic tidal dynamics over ADS. The obtained velocities were used as input data for a Lagrangian-type passive particle tracking model to reproduce the larval dispersal of generic deep-sea water invertebrate species. It was found that the residual tidal flow over ADS has a form of a pair of dipoles and cyclonic and anti-cyclonic eddies located at the seamount periphery. In the vertical direction, tides form upward motions above the seamount summit. These currents control local larval dispersal and their escape from ADS. The model experiment with a large number of particles (7500) evenly seeded on the ADS surface has shown that the trajectory of every individual particle is sensitive to the initial position and the tidal phase where and when it is released. The vast majority of the particles released above 1000 m depth remain seated in the same depth band where they were initially released. Only 8% of passive larvae were able to remain in suspension until competent to settle (maximise dispersal capability) and settle (make contact with the bottom) within the specified limits for this model. It was found that every tenth larval particle could leave the seamount and had a chance to be advected to any other remotely located seamount.     

Hydrodynamic characterization of the Arcachon Bay,using model-derived descriptors

A numerical model (MARS-2D) was developed, with the aim of describing the hydrodynamics that prevail in Arcachon Bay. Direct model results as well as derived mixing and transport time-scales (tidal prism, local and integrated flushing times, age of water masses), were used to understand the behaviour of water masses and exchanges between the Bay and its frontiers. Particular attention was paid to the processes that drive the hydrodynamics (tides, wind and rivers), in order to understand their respective influence.The Arcachon Bay hydrodynamic system appears primarily to be highly influenced by tides; secondarily, by winds. About two third of the lagoon total volume is flushed in and out at each tidal cycle, which represent a mean tidal prism of 384 millions of cubic meters. The percentage of seawater flushed out during the ebb, that returns into the lagoon during the following flood flow is very high (return flow factor=0.95). This pattern leads to calculated integrated flushing times (IFT) ranging from 12.8 to 15.9 days, respectively, for the winter 2001 and summer 2005 simulations (two contrasting climatological situations: in summer, light northwesterly winds and low discharges in the rivers and, in winter, stronger southwesterly winds and higher river flows). Moreover, it has been found that northerly and westerly winds tend to reduce the flushing time, whilst southerly and easterly winds tend to hinder the renewal of the water in the Bay. The behaviour of the waters originating from the two main rivers of the lagoon, was studied also by means of the mean age assessment, under varying conditions of river flow and wind regime.     

Application of a circulation and transport model system to the dispersal of herring larvae in the North Sea

A model system consisting of a three-dimensional circulation and transport model is used to simulate the dispersal of herring larvae in the North Sea. The driving forces of the circulation model are theM₂-tide, time dependent wind stress and air pressure fields, as well as monthly climatological density fields interpolated on a daily basis. The transport model includes advection as well as diffusion and uses a tracer technique to pursue the larvae in the time and space domain. Furthermore, the transport model incorporates a simulation of active vertical movement of the larvae as vertical migration has a marked effect on the drift route of the larvae.Simulated North Sea currents are compared to observed currents gained during the Autumn Circulation Experiment (ACE) which took place from August 1987 to March 1988. The variability in observed currents at the location of the moorings is found to be larger than in the simulated currents. On a larger scale, the simulated circulation in the northern North Sea shows a close correspondence to the inferred circulation from a quasi-synoptic hydrographic survey. The quality of the predictions of larval transport and distribution patterns by the model system is tested using sequential larvae distributions observed during ACE. Common features and discrepancies of observed and simulated distributions are discussed and conclusions for further field investigations and modelling studies are drawn.     

Effect of a kelp forest on coastal currents

Ocean currents supply a kelp ecosystem with nutrients, planktonic food, and larvae. We have found that these currents in a kelp forest (Macrocystis pyrifera) are slower than currents outside. At the Pt. Loma, San Diego, California, site that we studied, current velocities were about a third of those outside. A comparison of frequency spectra shows that semi-diurnal frequencies are preferentially passed by the kelp. This effect of a kelp forest on the currents that nurture it is similar to that of a terrestrial forest on local winds.     

Modelling the impact of a La Niña event on a South West Pacific Lagoon

In view of increasing environmental awareness and biodiversity conservation, understanding the main forcing mechanism driving biogeochemical cycles in coral reefs and lagoon coastal areas is a priority. La Ni?a events cause unbalanced situations in the Equatorial Pacific and result in enhanced precipitation in South West Pacific coastal areas. We investigated the impact of heavy rainfalls during the 2008 La Ni?a event on the New Caledonia lagoon using a 3D coupled on-line hydrodynamic-biogeochemical model. Simulations and data showed that the whole lagoon was impacted by river inputs and stronger hydrodynamics, enhancing chlorophyll-a concentration by a factor between 1.7 and 1.9. The coupled model provided new insights into plume transport, highlighting that eastern plumes can be advected northwards or can reach the South West Lagoon, depending on the balance between regional, tide-induced, and wind-induced surface currents. It also provided a synoptic view of lagoon biogeochemical-hydrodynamic response, when remote sensing data are not available due to cloud coverage.     

Tidal dynamics of the Terminos Lagoon,Mexico: observations and 3D numerical modelling

The tidal circulation patterns in the Terminos Lagoon were studied based on the analysis of 1 year of measurements and numerical simulations using a baroclinic 3D hydrodynamic model, the MARS3D. A gauging network was installed consisting of six self-recording pressure–temperature sensors, a tide gauge station and two current profilers, with pressure and temperature sensors moored in the main lagoon inlets. Model simulations were validated against current and sea level observations and were used to analyse the circulation patterns caused by the tidal forcing. The numerical model was forced with eight harmonic components, four diurnal (K ₁, O ₁, P ₁, Q ₁) and four semi-diurnal (M ₂, S ₂, N ₂, K ₂), extracted from the TPX0.7 database. The tidal patterns in the study area vary from mixed, mainly diurnal in the two main inlets of the lagoon, to diurnal in its interior. The tidal residual circulation inside the lagoon is dominated by a cyclonic gyre. The results indicate a net flux from the southwest Ciudad del Carmen inlet (CdC) towards the northeast Puerto Real inlet (PtR) along the southern side of the lagoon and the opposite in the northern side. The results indicate two areas of strong currents in the vicinity of the inlets and weak currents inside the lagoon. The area of strong currents in the vicinity of the CdC inlet is larger than that observed in the PtR inlet. Nevertheless, the current analysis indicates that the highest current speeds, which can reach a magnitude of 1.9 m s^?1, occurred in PtR. A further analysis of the tide distortion in the inlets revealed that both passages are ebb dominated.     

Remote and local forcing of a coastal lagoon: The Virginia Coast Reserve

The effects of local and remote wind forcing of water level heights in the Virginia Coast Reserve (VCR) are examined in order to determine the significant forces governing estuarine motions over subtidal time scales. Recent (1996–2008) data from tide and wind stations in the lagoon, a tide station to the north at Sandy Hook, NJ, and one offshore wind station at the Chesapeake Light Tower are examined. Sea surface height spectrum calculations reveal significant diurnal and semidiurnal tidal effects along with subtidal variations, but a suppressed inertial signal. Sea-surface heights (SSH) with 2–5 day periods at Wachapreague, VA are coherent with those at Sandy Hook and lag them in time, suggesting that southward-propagating continental shelf waves provide subtidal variability within the lagoon. The coherence between lagoon winds and sea surface height, as well as between winds and cross-lagoon sea height gradient, were significant at a relatively small number of frequency and wind direction combinations. The frequencies at which this wind forcing occurs are the tidal and subtidal bands present to the north, so that lagoon winds selectively augment existing SSH signals, but do not generate them. The impact of the wind direction is closely related to the geometry of the lagoon and bounding landmasses. The effect of wind stress is also constrained by geometry in affecting the cross-lagoon water height gradient. Water levels at subtidal frequencies are likely forced by a combination of local wind forcing, remote wind forcing and oceanic forcing modified by the complex topography of the lagoon, shelf, and barrier islands.     

Exposure to sewage plumes and the incidence of deformities in larval fishes

Point-source impacts such as sewage plumes can cause significant degradation of larval habitat. Data on larval abundance, current speed and the shape of surface and subsurface sewage plumes off the coast of Sydney, Australia, indicated that long-shore currents can transport large numbers of larvae through plumes that can potentially affect the health of larvae. Deformities to the notochord, eyes and head were found in samples of preserved wild larvae. Some deformities (e.g. Lateral curl of the notochord) were probably caused by preservation and ‘packing effects’ (shaped by organisms and objects in the sample), while others (e.g. half-pigmented eyes and corrugated notochord) were unlikely to have been caused by sampling artefacts. Deformed larvae were found in waters around Sydney that are influenced by multiple sewage outfalls, and at locations up to 250 km from Sydney. It was concluded that deformities were caused by natural and potentially anthropogenic factors. Cyto- and histopathological studies of larvae are required. Moreover, relationships between oceanography and concentrations of pollutants in plumes are needed to further assess impacts of pollutants on assemblages of vulnerable planktonic animals.     

Circulation in the Great Barrier Reef Lagoon using numerical tracers and in situ data

Numerical hydrodynamic models of the northeastern Queensland shelf, forced by regional winds and modelled boundary currents in the northern Coral Sea, are used to provide improved estimates of general flow trajectories and water residence times within the Great Barrier Reef (GBR) shelf system. Model performance was checked against a limited set of current metre records obtained at Lark Reef (16°S) and the Ribbon Reefs (15.5°S). Estimates of water parcel trajectories are derived from a series of numerical tracer experiments, with daily releases of neutrally buoyant, un-reactive particles at 320 sites along the coast between Cape York (10.7°S) and Hervey Bay (25°S). Flow trajectories and residence times for tracer particles introduced to the GBR lagoon in the southern—ca. 22°S, central—19°S, and northern reef—14°S are emphasised. For purposes of the analysis, the year was divided into two seasons based on mean alongshore current direction. Most coastal sourced tracers entering the central GBR lagoon between 16° and 20°S during the northward-current season (January–August) primarily encounter the outer-shelf reef matrix after exiting the lagoon at its northern “head” (nominally 16°S), after 50–150 days. Up to 70% of tracer particles entering in the southward-current season (August–December) eventually crossed the lagoon to the outer-shelf reef matrix, with median crossing times between 20 and 330 days. During favourable wind conditions, tracers introduced at the coast may move rapidly across the lagoon into the reef matrix. The tracer experiments indicate that most coastal-sourced tracers entering the GBR lagoon remain near the coast for extended periods of time, moving north and south in a coastal band. Residence times for conservative tracer particles (and implied residence times for water-borne materials) within the GBR shelf system ranged from ca. 1 month to 1 year—time frames that are very long relative to development times of planktonic larvae and cycling times for nutrient materials in the water column, implying they are transformed long before reaching the outer reef matrix.     

Air–sea–river interactions

Extensive recording of currents, collection of water samples and routine meteorological and tide records provide a base for this study of the dynamics of Australia's largest river, the Murray, during one of its rare floods in 1974. The results suggest that the Coorong. a narrow lagoon extending from the river mouth to the Southeast, at right angles to prevailing winds, was formed as a flood escape mechanism. Geological evidence displays the existence of similar geometries formed in the past in an area which at one time was a deep gulf of the Southern Ocean extending into Australia. The same mechanism may have been at work elsewhere in the world.     

Spatial and temporal distribution of zooplankton related to the environmental conditions in the coral reef lagoon of New Caledonia,Southwest Pacific

The distribution of zooplanktonic prey of fish larvae was examined in three bays and two lagoonal stations in the Southwest lagoon of New Caledonia. Water column conditions were characterized by increasing chlorophyll a and particulate organic matter (POM) concentrations from the lagoon to the estuarine bay. The mean zooplankton settled volume and total density were significantly higher in the estuarine bay, reaching 35.1 mL m⁻³ and 3.5 × 10⁵ individuals m⁻³, respectively. The total zooplankton density also progressively increased along the sampling period. The composition of assemblages differed between the lagoon and the bays, and was similar in the three bays. Wind speed, surface temperature, chlorophyll a and POM explained these variations, as revealed by a co-inertia analysis (COIA). The prey preferred by fish larvae, i.e. small crustaceans and small copepods, were more abundant in bays. Sheltered bays, most influenced by terrigenous inputs, are likely to provide the best feeding conditions.