The influence of upwelling and entrainment on the algal bloom in the Baltic Sea

Hydrodynamic processes control many geochemical and ecological processes in the sea. In this paper, the influence of up- and downwelling and entrainment on the ecosystem components are studied. The ecohydrodynamic model was initially used to simulate the whole Baltic Sea to get the boundary conditions for the Gulf of Riga. Then, to study the influence of different hydrodynamic conditions on the algal bloom, three simulations were made for the Gulf of Riga using different boundary and entrainment conditions. It appears that upwelling in the gulf was strongly dependent on open boundary conditions between the Baltic Proper and the gulf. The vertical transport in the Gulf of Riga was many times more intensive in the calculation system Baltic Proper and Gulf of Riga, than in the case where only the Gulf of Riga was simulated. The blue–green algal bloom was influenced by the vertical transport due to different nutrients' limitation mechanism.     

Behavioral modeling of Pagrus major in the East Seto Inland Sea

Evaluation of the behaviors of fish that belong to higher levels of the food web is important from the viewpoint of resource management and other environmental issues. Especially for adult fish that can swim against the surrounding currents, it is quite important to consider migration effects when modeling fish behavior. In the present study, a model of fish behavior is developed that considers the migration effect by incorporating a preference for various environmental factors. The species to be modeled, Pagrus major, was chosen because its high value as a food makes it representative of an exploited fish species. In the developed model, the direction of the fish movement is determined by the strength of preference for environmental factors of water temperature, salinity, dissolved oxygen, and prey density. The model is coupled with a hydrodynamic model and a lower-trophic ecosystem model, which predict the physical environment and water quality of the target area. Numerical simulations are carried out to reproduce the spatial distribution and seasonal variations of the ecosystem in the East Seto Inland Sea. Proper parameters for fish behavior were obtained through the processes of model tuning. As a result of the simulations, we clarified that the environmental conditions have a sizeable influence on the migration and distribution of Pagrus major. The developed model is also able to reproduce the fish biomass variation in time and space, which will provide more detailed information for resource management of the fish.     

Spatial and temporal variability in the pelagic ecosystem of the East Sea (Sea of Japan): A review

The East Sea (Sea of Japan) is a unique marginal sea because it exhibits features of oceanic dynamics of much larger ocean basins. This semi-enclosed basin may be considered as a model or microcosm for understanding of how biological processes and distributions in pelagic ecosystem are interacting with physical processes in highly dynamic ocean regions. This overview summarizes the recent progresses concerning spatial and temporal variability of pelagic ecosystem components form an interdisciplinary point of view. Spatial characteristics of physical environments and biogeography in the region are distinguished mainly by the subpolar front. It was also found that long-term changes in biomass and community structure as well as those in the physical and biological environments are associated with climate variability in the region. We conclude by identifying main needs for the information and researches, particularly regular and long-term sampling, and permanent monitoring if possible.     

Study of the seasonal cycle of the biogeochemical processes in the Ligurian Sea using a 1D interdisciplinary model

A one-dimensional coupled physical–biogeochemical model has been built to study the pelagic food web of the Ligurian Sea (NW Mediterranean Sea). The physical model is the turbulent closure model (version 1D) developed at the GeoHydrodynamics and Environmental Laboratory (GHER) of the University of Liège. The ecosystem model contains 19 state variables describing the carbon and nitrogen cycles of the pelagic food web. Phytoplankton and zooplankton are both divided in three size-based compartments and the model includes an explicit representation of the microbial loop including bacteria, dissolved organic matter, nano-, and microzooplankton. The internal carbon/nitrogen ratio is assumed variable for phytoplankton and detritus, and constant for zooplankton and bacteria. Silicate is considered as a potential limiting nutrient of phytoplankton's growth. The aggregation model described by Kriest and Evans in (Proc. Ind. Acad. Sci., Earth Planet. Sci. 109 (4) (2000) 453) is used to evaluate the sinking rate of particulate detritus. The model is forced at the air–sea interface by meteorological data coming from the “Côte d'Azur” Meteorological Buoy. The dynamics of atmospheric fluxes in the Mediterranean Sea (DYFAMED) time-series data obtained during the year 2000 are used to calibrate and validate the biological model. The comparison of model results within in situ DYFAMED data shows that although some processes are not represented by the model, such as horizontal and vertical advections, model results are overall in agreement with observations and differences observed can be explained with environmental conditions.     

Short time-scale analysis of the NW Mediterranean ecosystem during summer–autumn transition: A 1D modelling approach

Modelling was used as a tool to better understand the physical and biological processes observed during the multidisciplinary cruise DYNAPROC 2 (DYNAmic of rapid PROCesses in the water column), which took place in the Ligurian Sea in September–October 2004. The aim of the cruise was to study the short time-scale physical and biological processes that occur when the ecosystem switches from summer oligotrophy to autumnal mesotrophy. In this study, we have tested two 1D physical–biological coupled models. The first was a classical model in which surface layer dynamics were obtained using the turbulent kinetic energy model of Gaspar [Gaspar et al., 1990]. The simulated food-web took into account ten state variables: three nutrients, three classes of phytoplankton, two classes of zooplankton and two types of detritus. The second model (called IDA, Isopycnals Depth Adjustment) was based on the initial one but it took into account the measured variations of isopycnals depths. The results showed that the IDA model most efficiently reproduced the observed ecosystem dynamics. We have therefore used the IDA model to show that physical processes observed during the cruise had a major effect on biological compartment, mainly on nano- and picophytoplankton.     

Gulf of Gdansk spring bloom physical, bio-optical, biological modelling and contact data assimilation

In this study we propose a model of phytoplankton population dynamics in the marine ecosystem, which includes physical, biological and bio-optical parts. As an example we simulate the abnormal 1993 Gulf of Gdansk spring bloom, when extremely high chlorophyll concentrations were observed. For the one-dimensional model we use two different methods of contact chlorophyll observation assimilation to fit a model of “in situ” data. The results are compared with two-dimensional ecosystem modelling based on a barotropic model of wind-driven circulation without assimilation.     

A spatially explicit ecosystem model of seston depletion in dense mussel culture

A fully-coupled biological–physical–chemical model of a coastal ecosystem was constructed to examine the impact of suspended mussel culture on phytoplankton biomass in Tracadie Bay, Prince Edward Island, Canada. Due to the extent of mussel culture there, we hypothesised that shellfish filtration would control the concentration and distribution of phytoplankton and other suspended particles in the bay. Circulation was delineated with a tidally-driven 2D numerical model and used to drive an ecosystem model with a focus on pelagic components including phytoplankton production, nutrients, detritus, and mussels. The benthos were treated as a sink. Nutrients and seston were forced by tidal exchange and river input, with phytoplankton additionally forced by light. Boundary conditions of seston and nutrients were derived from field studies with an emphasis on the contrast between spring (high river nutrients, low temperature) and summer (low river inputs and high temperatures). Model output was used to map phytoplankton carbon over the bay for each season and in the presence of mussels and river nutrient input. Results indicate severe depletion effects of mussel culture on overall phytoplankton biomass, but no spatial pattern that can be attributed to grazing alone. Primary production generated by nutrient-rich river water created a mid-bay spike in phytoplankton that dominated the spatial pattern of chlorophyll-based carbon. Model results were validated with surveys from a towed sensor array (Acrobat) that confirmed the river influence and indicated bay-wide depletion of 29% between high and low water. Our model results indicate that the farm-scale depletion emphasised in previous studies cannot simply be extrapolated to seston limitation at the ecosystem level.     

Enrichment, concentration and retention processes in relation to anchovy (Engraulis ringens) eggs and larvae distributions in the northern Humboldt upwelling ecosystem

A Lagrangian model is used to simulate and quantify in the northern Humboldt upwelling ecosystem the processes of enrichment, concentration and retention, identified by Bakun [Bakun, A., 1996. Patterns in the ocean. Ocean processes and marine population dynamics. University of California Sea Grant, California, USA, in cooperation with Centro de Investigaciones Biologicas de Noroeste, La Paz, Baja California Sur, Mexico, 323 pp.] as being important for the survival and recruitment of early life stages of pelagic fish. The method relies on tracking the positions of particles within water velocity fields generated by a three-dimensional hydrodynamic model. Simple criteria for considering particles as participating to enrichment, concentration or retention are used to derive indices of the three processes. We analyse the spatial distribution of and seasonal variability in these indices. The results are discussed in relation to anchovy (Engraulis ringens) eggs and larvae distributions off Peru, and to a comparable study conducted in the southern Benguela upwelling ecosystem.     

Variability in hydrographic conditions to the east and northwest of South Georgia, 1996–2001

Six years of high-resolution hydrographic data from the eastern and northwestern sides of South Georgia (southwest Atlantic) are used to study the changing circulation and water mass properties of the region. One year of data from these locations was used previously to describe the oceanographic conditions at those times; using the much greater volume of data now available, we identify which features appear temporally robust and which are transient, and begin addressing topics relating to the forcing of the inter-annual variability and the potential consequences for the local ecosystem. Waters on the shelf and those over the adjacent deep ocean invariably have different hydrographic properties, though the transition between them can be abrupt or gradual. The onshelf/offshelf differences vary greatly from year to year, due to the combined influences of local and remote processes. There are several instances of strong physical coupling between the eastern and northwestern sides of South Georgia; this offers potential for distinguishing physically-induced ecosystems changes separately from biologically-induced ecosystems changes. On the northeast side of the shelf, close to Cumberland Bay, there is evidence of an often intense, but variable, cyclonic circulation that is the result of interaction with the local bathymetry. This may act as a retention mechanism, and enhance local productivity. Two examples of extreme cold anomalies are present in the series of measurements. One of these (in 2000/2001) affected a limited area at the eastern side of the region surveyed and was due to an intrusion of the Southern Antarctic Circumpolar Current Front. The other (in early 1998) was due to the combined effects of the passage of a large-scale ocean anomaly that had its origins upstream in the Pacific Ocean, and strong air/sea interaction. Both of these were associated with the strong 1997/1998 El Niño event. Whilst previous studies have observed a link between El Niño forcing and ocean response around South Georgia with a temporal lag of around 3 years, we observe a much more rapid response to the extremely strong 1997/1998 El Niño event. This indicates that the ocean and ecosystem around South Georgia are more immediately susceptible to extreme instances of remote climatic forcing than had been supposed.     

Resistance analysis of unsymmetrical trimaran model with outboard sidehulls configuration

The application of multi-hull ship or trimaran vessel as a mode of transports in both river and sea environments have grown rapidly in recent years.Trimaran vessels are currently of interest for many new high speed ship projects due to the high levels of hydrodynamic efficiency that can be achieved,compared to the mono-hull and catamaran hull forms.The purpose of this study is to identify the possible effects of using an unsymmetrical trimaran ship model with configuration（S/L） 0.1-0.3 and R/L=0.1-0.2.Unsymmetrical trimaran ship model with main dimensions： L=2000mm,B=200 mm and T=45 mm.Experimental methods（towing tank） were performed in the study using speed variations at Froude number 0.1-0.6.The ship model was pulled by an electric motor whose speed could be varied and adjusted.The ship model resistance was measured precisely by using a load cell transducer.The comparison of ship resistance for each configuration with mono-hull was shown on the graph as a function of the total resistance coefficient and Froude number.The test results found that the effective drag reduction could be achieved up to 17% at Fr=0.35 with configuration S/L=0.1.     

Modelling the spatial and temporal variability of the Cretan Sea ecosystem

The ecosystem function of the oligotrophic Cretan Sea is explored through the development and application of a 3D ecological model. The simulation system comprises of two on-line coupled submodels: the 3D Princeton Ocean Model (POM) and the 1D European Regional Seas Ecosystem Model (ERSEM) adapted to the Cretan Sea. For the tuning and initialisation of the ecosystem parameters, the 1D version of the biogeochemical model is used.After a model spin up period of 10 years to reach a quasi-steady state, the results from an annual simulation are presented. A cost function is used as validation method for the comparison of model results with field data. The estimated annual primary and bacteria production are found to be in the range of the reported values. Simulation results are in good agreement with in situ data illustrating the role of the physical processes in determining the evolution and variability of the ecosystem.     

Resolving the impact of short-term variations in physical processes impacting on the spawning environment of eastern Baltic cod: application of a 3-D hydrodynamic model

Variations in oxygen conditions below the permanent halocline influence the ecosystem of the Baltic Sea through a number of mechanisms. In this study, we examine the effects of physical forcing on variations in the volume of deep oxygenated water suitable for reproductive success of central Baltic cod. Recent research has identified the importance of inflows of saline and oxygenated North Sea water into the Baltic Sea for the recruitment of Baltic cod. However, other processes have been suggested to modify this reproduction volume including variations in timing and volume of terrestrial runoff, variability of the solubility of oxygen due to variations in sea surface temperature as well as the influence of variations in wind stress. In order to examine the latter three mechanisms, we have performed simulations utilizing the Kiel Baltic Sea model for a period of a weak to moderate inflow of North Sea water into the Baltic, modifying wind stress, freshwater runoff and thermal inputs. The model is started from three-dimensional fields of temperature, salinity and oxygen obtained from a previous model run and forced by realistic atmospheric conditions. Results of this realistic reference run were compared to runs with modified meteorological forcing conditions and river runoff.From these simulations, it is apparent that processes other than major Baltic inflows have the potential to alter the reproduction volume of Baltic cod. Low near-surface air temperatures in the North Sea, the Skagerrak/Kattegat area and in the western Baltic influence the water mass properties (high oxygen solubility). Eastward oriented transports of these well-oxygenated highly saline water masses may have a significant positive impact on the Baltic cod reproduction volume in the Bornholm Basin.Finally, we analysed how large scale and local atmospheric forcing conditions are related to the identified major processes affecting the reproduction volume.     

Description of a flexible and extendable physical–biogeochemical model system for the water column

A modelling system for coupled physical–biogeochemical simulations in the water column is presented here. The physical model component allows for a number of different statistical turbulence closure schemes, ranging from simple algebraic closures to two-equation turbulence models with algebraic second-moment closures. The biogeochemical module consists of models which are based on a number of state variables represented by their ensemble averaged concentrations. Specific biogeochemical models may range from simple NPZ (nutrient–phytoplankton–zooplankton) to complex ecosystem models. Recently developed modified Patankar solvers for ordinary differential equations allow for stable discretisations of the production and destruction terms guaranteeing conservative and non-negative solutions. The increased stability of these new solvers over explicit solvers is demonstrated for a plankton spring bloom simulation. The model system is applied to marine ecosystem dynamics the Northern North Sea and the Central Gotland Sea. Two different biogeochemical models are applied, a conservative nitrogen-based model to the North Sea, and a more complex model including an oxygen equation to the Baltic Sea, allowing for the reproduction of chemical processes under anoxic conditions. For both applications, earlier model results obtained with slightly different model setups could be basically reproduced. It became however clear that the choice for ecosystem model parameters such as maximum phytoplankton growth rates does strongly depend on the physical model parameters (such as turbulence closure models or external forcing).     

Error quantification of a high-resolution coupled hydrodynamic-ecosystem coastal-ocean model: Part 2. Chlorophyll-a, nutrients and SPM

Marine systems models are becoming increasingly complex and sophisticated, but far too little attention has been paid to model errors and the extent to which model outputs actually relate to ecosystem processes. Here we describe the application of summary error statistics to a complex 3D model (POLCOMS-ERSEM) run for the period 1988–1989 in the southern North Sea utilising information from the North Sea Project, which collected a wealth of observational data. We demonstrate that to understand model data misfit and the mechanisms creating errors, we need to use a hierarchy of techniques, including simple correlations, model bias, model efficiency, binary discriminator analysis and the distribution of model errors to assess model errors spatially and temporally. We also demonstrate that a linear cost function is an inappropriate measure of misfit. This analysis indicates that the model has some skill for all variables analysed. A summary plot of model performance indicates that model performance deteriorates as we move through the ecosystem from the physics, to the nutrients and plankton.     

The nitrogen cycle in tidal flats and eelgrass beds of Ise Bay

A tidal flat-sea grass bed ecosystem model was formulated and applied to Ise Bay to evaluate the purification capability of the shallow-water region where a new airport is expected to be built. The model results were in the range of the observed biomass for each state variable in the model. The purification capability of this shallow-water region is estimated from the model results. The inorganic nitrogen removal is estimated at 56 kg N day⁻¹; the organic particulate nitrogen removal by suspension feeders is 95 kg N day⁻¹; the organic nitrogen removal by harvest and fish predation is 25 kg N day⁻¹, and the purification capability of this site is 51 kg N day⁻¹. Potential loss of the sea grass bed by reclamation will reduce the removal ability of inorganic nitrogen as well as food sources for juvenile fishes.     

Improving the physics of a coupled physical–biogeochemical model of the North Atlantic through data assimilation: Impact on the ecosystem

Several studies on coupled physical–biogeochemical models have shown that major deficiencies in the biogeochemical fields arise from the deficiencies in the physical flow fields. This paper examines the improvement of the physics through data assimilation, and the subsequent impact on the ecosystem response in a coupled model of the North Atlantic. Sea surface temperature and sea surface height data are assimilated with a sequential method based on the SEEK filter adapted to the coupling needs. The model domain covers the Atlantic from 20°S to 70°N at eddy-permitting resolution. The biogeochemical model is a NPZD-DOM model based on the P3ZD formulation. The results of an annual assimilated simulation are compared with an annual free simulation.With assimilation, the representation of the mixed layer depth is significantly improved in mid latitudes, even though the mixed layer depth is generally overestimated compared to the observations. The representation of the mean and variance of the currents is also significantly improved.The nutrient input in the euphotic zone is used to assess the data assimilation impact on the ecosystem. Data assimilation results in a 50% reduction of the input due to vertical mixing in mid-latitudes, and in a four- to six-fold increase of the advective fluxes in mid-latitudes and subtropics. Averaged zonally, the net impact is a threefold increase for the subtropical gyre, and a moderate (20–30%) decrease at mid and high latitudes.Surface chlorophyll concentration increases along the subtropical gyre borders, but little changes are detected at mid and high latitudes. An increase of the primary production appears along the Gulf Stream path, but it represents only 12% on average for mid and high latitudes. In the subtropical gyre centre, primary production is augmented but stays underestimated (20% of observations). These experiments show the benefits of physical data assimilation in coupled physical–biogeochemical applications.     

On the key role of nutrient data to constrain a coupled physical–biogeochemical assimilative model of the North Atlantic Ocean

A sequential assimilative system has been implemented into a coupled physical–biogeochemical model (CPBM) of the North Atlantic basin at eddy-permitting resolution (1/4°), with the long-term goal of estimating the basin scale patterns of the oceanic primary production and their seasonal variability. The assimilation system, which is based on the SEEK filter [Brasseur, P., Verron, J., 2006. The SEEK filter method for data assimilation in oceanography: a synthesis. Ocean Dynamics. doi: 10.1007/s10236-006-0080-3], has been adapted to this CPBM in order to control the physical and biogeochemical components of the coupled model separately or in combination. The assimilated data are the satellite Topex/Poseidon and ERS altimetric data, the AVHRR Sea Surface Temperature observations, and the Levitus climatology for salinity, temperature and nitrate.In the present study, different assimilation experiments are conducted to assess the relative usefulness of the assimilated data to improve the representation of the primary production by the CPBM. Consistently with the results obtained by Berline et al. [Berline, L., Brankart, J-M., Brasseur, P., Ourmières, Y., Verron, J., 2007. Improving the physics of a coupled physical–biogeochemical model of the North Atlantic through data assimilation: impact on the ecosystem. J. Mar. Syst. 64 (1–4), 153–172] with a comparable assimilative model, it is shown that the assimilation of physical data alone can improve the representation of the mixed layer depth, but the impact on the ecosystem is rather weak. In some situations, the physical data assimilation can even worsen the ecosystem response for areas where the prior nutrient distribution is significantly incorrect. However, these experiments also show that the combined assimilation of physical and nutrient data has a positive impact on the phytoplankton patterns by comparison with SeaWiFS ocean colour data, demonstrating the good complementarity between SST, altimetry and in situ nutrient data. These results suggest that more intensive in situ measurements of biogeochemical nutrients are urgently needed at basin scale to initiate a permanent monitoring of oceanic ecosystems.     

Modelling Pseudocalanus elongatus stage-structured population dynamics embedded in a water column ecosystem model for the northern North Sea

This paper outlines an approach to couple a structured zooplankton population model with state variables for eggs, nauplii, two copepodites stages and adults adapted to Pseudocalanus elongatus into the complex marine ecosystem model ECOHAM2 with 13 state variables resolving the carbon and nitrogen cycle. Different temperature and food scenarios derived from laboratory culture studies were examined to improve the process parameterisation for copepod stage dependent development processes. To study annual cycles under realistic weather and hydrographic conditions, the coupled ecosystem–zooplankton model is applied to a water column in the northern North Sea. The main ecosystem state variables were validated against observed monthly mean values. Then vertical profiles of selected state variables were compared to the physical forcing to study differences between zooplankton as one biomass state variable or partitioned into five population state variables. Simulated generation times are more affected by temperature than food conditions except during the spring phytoplankton bloom. Up to six generations within the annual cycle can be discerned in the simulation.     

Analysis of the contribution of ice algae to the ice-covered ecosystem in Lake Saroma by means of a coupled ice–ocean ecosystem model

A new coupled ice–ocean ecosystem model that links the pelagic and ice ecosystems was used to clarify the role of ice algae in ice-covered ocean ecosystems. The model was applied to Lake Saroma (Hokkaido, Japan) in 1992. Comparison of the model's results with observational data confirmed that the model reproduced the behavior of the ecosystem with acceptable accuracy during the period from winter to spring. The primary production of the ice algae is effectively transported into the pelagic system by means of physical releasing effects: brine convection, ice melting and freezing, and diffusion generated at the bottom of the ice. Ice algae released from the ice are rapidly exported because of their high sinking speed and the shallow depth of Lake Saroma. For this reason, the zooplankton in Lake Saroma cannot graze these released algae. However, zooplankton actively graze the ice algae living along the bottom of the ice. These results show that, before their release, ice algae play an important role as a food source for overwintering zooplankton. A sensitivity analysis revealed a positive correlation between the sinking speed of the released ice algae and the magnitude of the spring bloom by pelagic phytoplankton, and that the time when secondary production becomes active is an important factor in the linkage between these two algal populations.     

An eddy-permitting, coupled ecosystem-circulation model of the Arabian Sea: comparison with observations

A nitrogen-based, pelagic ecosystem model has been coupled with an eddy-permitting ocean general circulation model of the Arabian Sea, and the results are compared with observations. The seasonal variability simulated by the model is in good agreement with observations: during the southwest monsoon season, phytoplankton increases in the western Arabian Sea due to upwelling along the coast; during the northeast monsoon season, phytoplankton abundance is large in the northern Arabian Sea because of the enhanced nitrate entrained by relatively deep vertical mixing. Two major differences are, however, found in the basin-wide comparison between model results and observations: an unrealistic nitrate maximum in the subsurface layer of the northern Arabian Sea and too low primary production in oligotrophic regimes. The former may be attributed to the lack of denitrification in the model. Possible causes for the latter include the present model's underestimation of fast nutrient recycling, the neglect of carbon fixation decoupled from nitrogen uptake and of nitrogen fixation, and inadequate nitrate entrainment by mixed layer deepening. The rate at which simulated nitrate increases in the northern Arabian Sea is 11–24 TgN/year, and should correspond to the denitrification rate integrated over the northern Arabian Sea assuming that the loss of nitrogen through denitrification is balanced by advective input. The model does not reproduce the observed phytoplankton bloom in the late southwest monsoon season. Possible causes are that the mixed layer may be too shallow in summer and that the horizontal transport of nitrate from the coast of Oman may be too weak. Sensitivity experiments demonstrate a strong dependence of the simulated primary productivity on the vertical mixing scheme and on the inclusion of a fast recycling loop in the ecosystem model.