Sequential data assimilation in an upwelling influenced estuary

We have evaluated the impact of assimilating chlorophyll, nitrate, phosphate, silicate and ammonium into a coupled 1D hydrodynamic ecosystem model (GOTM-ERSEM) in an upwelling influenced estuary. The assimilation method chosen is the Ensemble Kalman Filter (EnKF), which has been demonstrated to improve field estimates of key variables (chlorophyll, nutrients) for bulk algal bloom prediction. The 1D model has been set up for a central station inside the Ría de Vigo (Spain). Data from bi-weekly surveys are used to constrain the model. Temperature and salinity profiles are used to ensure the correct representation of the water structure through a relaxation scheme. Chlorophyll extracts and nutrients at three depths are assimilated sequentially during 1 year simulation (1991). The assimilation period includes episodes of active upwelling and downwelling. All five assimilated variables are successfully constrained and represent a large improvement on the reference simulation (without assimilation). Small divergences can be related to poorly resolved physical processes in the model. The assimilation was further evaluated by comparing observed biomass partitioning with model results. Diatoms accounted for the largest biomass update and the largest improvement in terms of percentage of variance explained (R²). This is particularly significant as they represent the 46% of the yearly integrated observed biomass of the planktonic autotrophs. Nonetheless the R² value was low for all phytoplankton groups. Bacteria and nanoflagellates showed an improvement with respect to their yearly Root Mean Square (RMS), while the other functional groups worsen or remained unaffected. Chlorophyll assimilation was responsible for most of the impact on the phytoplankton biomass with small contributions from the silicate. It had minor impact on the updates of nutrients which in turn corrected the state variables related to the detrital pool. In this current setting, combined assimilation of chlorophyll and nutrients is not sufficient to produce a skillful simulation of the phytoplankton succession.     

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.     

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.     

Modelling the effects of physical–biological interactions and spatial variability in spawning and nursery areas on transport and retention of sardine Sardinops sagax eggs and larvae in the southern Benguela ecosystem

A particle-tracking individual-based model (IBM) coupled with a 3-D hydrodynamic model was used to investigate how spatial variability in spawning and nursery grounds may influence transport and retention of sardine (Sardinops sagax) eggs and larvae in the southern Benguela ecosystem. A temperature-dependent Bělehrádek development model based on laboratory growth data was used to determine the duration of one egg and two larval stages. Successful transport/retention depended on each particle's stage of development rather than its age. Results show that recruitment could occur in two distinct nursery areas on the west and south coasts of South Africa. Three viable recruitment ‘systems’ were identified: two are retention-based (spawned and retained on the west coast (WC–WC) or the south coast (SC–SC)) and one is transport-based (spawned on the south coast and transported to the west coast (SC–WC)). In the WC–WC system, the vertical distribution of eggs influenced retention; at intermediate depths of spawning (25–50 m) eggs avoided both offshore Ekman drift and deep cold water. In the SC–SC system, the area of spawning was important; > 50% of eggs from the eastern Agulhas Bank (EAB) were retained in the south coast nursery grounds, whereas very few eggs were transported there from west of Cape Agulhas. In the SC–WC system, area of spawning was also important; 40% of the eggs spawned on the western Agulhas Bank (WAB) were transported to the west coast nursery ground. Sardine life history strategy could be divided between two main systems: the west coast system (spawning on the WAB and WC, and recruiting to the WC) and the Agulhas Bank system (spawning on the central and eastern Agulhas Bank, and recruiting to the SC).     

Planktonic community structure and carbon cycling in the Arabian Sea as a result of monsoonal forcing: the application of a generic model

The Arabian Sea exhibits a complex pattern of biogeochemical and ecological dynamics, which vary both seasonally and spatially. These dynamics have been studied using a one-dimensional vertical hydrodynamic model coupled to a complex ecosystem model, simulating the annual cycle at three contrasting stations. These stations are characterised by seasonally upwelling, mixed-layer-deepening and a-seasonal oligotrophic conditions, respectively, and coincide with extensively measured stations on the two JGOFS ARABESQUE cruises in 1994. The model reproduces many spatial and temporal trends in production, biomass, physical and chemical properties, both qualitatively and quantitatively and so gives insight into the main mechanisms responsible for the biogeochemical and ecological complexity. Monsoonal systems are typified by classical food web dynamics, whilst intermonsoonal and oligotrophic systems are dominated by the microbial loop. The ecosystem model (ERSEM), developed for temperate regions, is found to be applicable to the Arabian Sea system with little reparameterisation. Differences in in-situ physical forcing are sufficient to recreate contrasting eutrophic and oligotrophic systems, although the lack of lateral terms are probably the greatest source of error in the model. Physics, nutrients, light and grazing are all shown to play a role in controlling production and community structure. Small-celled phytoplanktons are predicted to be dominant and sub-surface chlorophyll maxima are robust centers of production during intermonsoon periods. Analysis of carbon fluxes indicate that physically driven outgassing of CO₂ predominates in monsoonal upwelling systems but ecological activity may significantly moderate CO₂ outgassing in the Arabian Sea interior.     

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.     

Patterns and controls of chlorophyll-a and primary productivity cycles in the Southern California Bight

Factors that influence the magnitude and the depth of the chlorophyll maximum layer in the ocean off Southern California are explored using observations from the long-term California Cooperative Oceanic Fisheries Investigations (CalCOFI) program. The data record is sufficiently long to reveal patterns not always evident from single stations or single cruises. Processes such as coastal wind-driven upwelling, geostrophic circulation, and annual physical and chemical cycles are illustrated to demonstrate their effect on euphotic zone nutrient availability, and subsequent phytoplankton biomass and primary productivity. In this area, where the influence of wind-driven upwelling is spatially restricted and advected waters are generally nutrient depleted, geostrophically induced upwelling and winter convection become important in determining spatial and temporal patterns of phytoplankton.     

Offshore export versus in situ fractionated mineralization: a 1-D model of the fate of the primary production of the Rías Baixas (Galicia, NW Spain)

A linked hydrodynamic mineralization model is described and used to evaluate offshelf fluxes and fractionated mineralization of particulate phytogenic materials in the coastal upwelling system of the Rías Baixas (NW Spain), under three different typical situations of the upwelling season. The simulations made indicate that the intensity of upwelling controls: (a) net community production (NCP); (b) particulate organic matter (POM) accumulation; (c) in situ mineralization; and (d) matter export in the ‘Rías Baixas.’ Under strong upwelling conditions, there is an important horizontal offshelf flux, having only a small mineralization effect on NCP; if weak upwelling conditions are simulated, POM export is dramatically reduced and in situ mineralization is significantly enhanced; finally, under average upwelling conditions, the offshelf export of POM is about one third of the POM accumulation inside the domain, evidencing its importance in the productivity enhancement of near-shore areas. According to our sensitivity tests, the net vertical velocity (water velocity plus sinking velocity) has a critical role in the C/N/P stoichiometry of POM.     

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.     

Climate–ocean variability and Pacific hake: A geostatistical modeling approach

Climate forcing of the California Current has been known to impact the distribution and abundance of a number of local fish populations, but the mechanisms involved remain poorly understood. Climate metrics such as the Pacific Decadal Oscillation (PDO) and the El Niño Southern Oscillation (ENSO) are usually used to represent climate processes and direct links are made between climate forcing and production variability. This involves aggregation of impacts across large spatial scales and range of species. However, fluctuations in productivity are often the result of changes in physical habitat. In order to fully understand the relationship between climate and productivity, habitat changes should be addressed. In this study we use a geostatistical approach to quantify adult Pacific hake habitat during different climate regimes. Several authors have suggested that the distribution and intensity of the sub-surface poleward flow (the undercurrent) plays a key role in defining adult hake habitat along the west coast of North America. Here we build a model designed to predict hake habitat distribution in space based on sub-surface poleward flow distribution and bottom depth. Our results show that hake habitat expands in 1998 El Niño year compared to 1995. Given the important predatory role that hake plays in the CC, the amount and distribution of adult hake habitat has large implications for the Pacific Northwest food web and could thus serve as an ecosystem indicator representing important physical–biological interactions. Spatially based ecosystem indicators such as the one we develop here address two important yet neglected areas in the ‘Ecosystem Indicators debate’: the importance of developing metrics explicitly representing spatial and environmental processes shaping ecosystem structure. Without these, our power to fully describe ecosystems will be limited.     

Using a random displacement model to simulate turbulent particle motion in a baroclinic frontal zone: A new implementation scheme and model performance tests

Numerical artifacts can limit accurate simulation of turbulent particle motion when Lagrangian particle-tracking models are implemented in hydrodynamic models with stratified conditions like fronts. Yet, modeling of individual particle motion in frontal regions is critical for understanding sediment dynamics as well as the transport and retention of planktonic organisms. The objective of this research was to develop a numerical technique to accurately simulate turbulent particle motions in a particle-tracking model embedded within a hydrodynamic model of a frontal zone. A new interpolation scheme, the ‘water column profile’ scheme, was developed and used to implement a random displacement model for turbulent particle motions. A new interpolation scheme was necessary because linear interpolation schemes caused artificial aggregation of particles where abrupt changes in vertical diffusivity occurred. The new ‘water column profile’ scheme was used to fit a continuous function (a tension spline) to a smoothed profile of vertical diffusivities at the x–y particle location. The new implementation scheme was checked for artifacts and compared with a standard random walk model using (1) Well Mixed Condition tests, and (2) dye-release experiments. The Well Mixed Condition tests confirmed that the use of the ‘water column profile’ interpolation scheme for implementing the random displacement model significantly reduced numerical artifacts. In dye-release experiments, high concentrations of Eulerian tracer and Lagrangian particles were released at the same location up-estuary of the salt front and tracked for 4 days. After small differences in initial dispersal rates, tracer and particle distributions remained highly correlated (r = 0.84 to 0.99) when a random displacement model was implemented in the particle-tracking model. In contrast, correlation coefficients were substantially lower (r = 0.07 to 0.58) when a random walk model was implemented. In general, model performance tests indicated that the ‘water column interpolation’ scheme was an effective technique for implementing a random displacement model within a hydrodynamic model, and both could be used to accurately simulate diffusion in a highly baroclinic frontal region. The new implementation scheme has the potential to be a useful tool for investigating the influence of hydrodynamic variability on the transport of sediment particles and planktonic organisms in frontal zones.     

The winter St. Helena climate index and extreme Benguela upwelling

Climate changes in the subtropical South-east Atlantic turn out to be well described by the St. Helena Island Climate Index (HIX) and observed fluctuations are in good agreement with inter-decadal variability of the entire South Atlantic Ocean. Year-to-year variations of the averaged austral winter HIX (July–September), representative of the main upwelling season, were compared with (i) corresponding averages of the geostrophic alongshore component of the south-east trade wind (SET) between St. Helena Island in the south-west and Luanda/Angola in the north-east, (ii) the meridional distribution of surface waters colder than 13 °C to characterise intense Benguela upwelling (IBU), and (iii) the meridional position of the Angola-Benguela Frontal Zone (ABFZ) determined by means of sea surface temperature images for offshore distances between 50 and 400 km. Temporal changes of these parameters were investigated and showed that the frequency of consecutive years of strong and relaxed Benguela upwelling is characterised by a quasi-cycle of about 11–14 years. It is proposed that the index of the winter HIX may be used as a ‘surveyor’s rod' to describe interannual changes in the Benguela upwelling regime as well as those of the embedded marine ecosystem.     

A study of the response of chlorophyll-a biomass to a winter upwelling event off Western Iberia using SeaWiFS and in situ data

Observations of a winter upwelling event off Western Iberia shelf/slope in the area of influence of the Western Iberia Buoyant Plume (WIBP) were conducted in February 2000. Spatial patterns and time evolution of the chlorophyll-a (chl-a) biomass are analysed, based on in situ and satellite data. SeaWiFS-derived chl-a concentration L2 products were used to track the chlorophyll front and estimate its westward migration velocity (maximum up to 29 km day⁻¹), as well as to characterize the frontal system and its evolution. A method associating the type of spectral signature of a pixel to the fraction of chlorophyll probed by SeaWiFS enabled the estimation of the chl-a biomass within error intervals. High chlorophyll concentrations (for wintertime) were observed over the shelf and slope, up to large distances to the coast. Due to the WIBP, a shallow Ekman layer developed, being nearly coincident with the stratified upper meters. The transport comprised westward advection and stretching of the plume, with little entrainment with the offshore deep mixed layer waters. The relative enlargement of the total area of the Inside-Front Zone (IFZ) during the upwelling event was roughly accompanied by the maintenance of the average biomass per unit of area, considering the water column up to depths of interest. This suggests that there was a net increase of chl-a biomass inside the water column associated with the IFZ, roughly proportional to the increase in the IFZ area. Retention of phytoplankton in the shallow stratified nutrient-rich waters of the WIBP was a key factor for this increase in chl-a biomass.     

Environmental changes in the western Black Sea related to anthropogenic and natural conditions

The Black Sea northwestern shelf (NWS) ecosystem has been subjected to the strongest anthropogenic pressure of the entire Black Sea as about 80% of the freshwater runoff is discharged there.This paper presents a review of the global environmental changes related mainly to increased eutrophication in the western Black Sea basin.A case study (CoMSBlack 92a cruise) attempts to highlight the interaction of some natural and anthropogenic factors responsible for specific chemical and biological features in the western Black Sea environment. The significance of processes located near the Danube river mouth, which, due to their relatively small space scale, have not been recognized before, is clarified. Hydrological processess of specific importance to the distribution and transformation of antropogenic inputs are river plume dynamics, coastal upwelling and mixing and downwelling over the shelf break and slope in this part of the basin. A layer of low hydrological variability (“conservative layer”) appears to be a natural feature of the area, hypothesized to precondition specific biological and chemical processes there.The results suggest that the interplay between the Danube anthropogenic nutrient load with the natural hydrological fronts and gradients provides opportunities for enhanced biological activity thus contributing to the global environmental changes in the Black Sea NWS.     

Exploring relationships between recruitment of European hake (Merluccius merluccius L. 1758) and environmental factors in the Ligurian Sea and the Strait of Sicily (Central Mediterranean)

This paper explores the relationships between the spatial patterns of the distribution of the young hakes of the year (YOY) and the oceanographical features in two areas of the Central Mediterranean (the Ligurian Sea and the Strait of Sicily), characterised by the occurrence of straits and channels. Comparative and correlative approaches were used to investigate coupling between biological and physical patterns. Density indices of the YOY were derived from annual trawl surveys from 1994 to 2004 in spring and autumn. Mean patterns of the YOY distributions were compared with the mesoscale oceanographical features reported in literature. No evident trends in recruitment strength were found in either areas. Inter-annual variability in YOY abundance in the Ligurian Sea was higher than in the Strait of Sicily. The location of nursery grounds in the study areas coincides with zones of relatively higher production, where upwelling and other enrichment processes regularly occur. The presence of predictable eddies and the frontal systems play a major role in the localization of nursery areas in the Strait of Sicily, maintaining their stable position throughout the years. The strongest transport of southern waters from the Tyrrhenian to the Ligurian Sea, due to the East Corsica Current, which is negatively correlated to winter North Atlantic Oscillation, is associated with the highest abundance of hake recruits in the nurseries of the Northern Ligurian Sea.     

One-dimensional modelling of the plankton ecosystem of the north-western Corsican coastal area in relation to meteorological constraints

In order to study the influence of wind mixing on the spring variability of the plankton production of the north western Corsican coastal area, a one-dimensional (1D), vertical, coupled hydrodynamic/biological model (ECOHYDROMV) is used. A hydrodynamic 1D model of the water column with a k–l turbulent closure is applied. The biological model comprises six state variables, representing the plankton ecosystem in the spring period: phytoplankton, copepods, nitrate, ammonium, particulate organic matter of phytoplanktonic origin and particulate organic matter of zooplanktonic origin. The system is influenced by turbulence (expressed by the vertical eddy diffusivity), temperature and irradiance. The model takes into account momentum and heat surface fluxes computed from meteorological data in order to simulate a typical spring atmospheric forcing for the considered area. Results show that primary production vertical structure is characterised by a subsurface maximum which deepens with time and is regulated by the opposite gradients of nitrate concentration and irradiance. Surface plankton productivity is mainly controlled by turbulent vertical transport of nutrients into the mixed layer. The short time scale variability of turbulent mixing generated by the wind appears to be responsible for the plurimodal shape of plankton blooms, observed in the considered area. Furthermore, the model is applied to the study of the spring evolution of the plankton communities off the bay of Calvi (Corsica) for the years 1986 and 1988. In order to initiate and validate the model, time series of hydrological, chemical and biological data have been used. The model reproduces accurately the spring evolution of the phytoplankton biomass measured in situ and illustrates that its strong variability in those years was in close relation to the variability of the wind intensity.     

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.     

The use of digital filter initialization to diagnose the mesoscale circulation and vertical motion in the California coastal transition zone

A dynamical method of initializing the primitive equations is tested and used to diagnose the three-dimensional circulation associated with jets and eddies as found in the California coastal transition zone (CTZ). The initialization method, referred to as digital filter initialization (DFI), was recently developed by [Monthly Weather Review 120 (1992) 1019] for use in an intermittent data assimilation system in the atmosphere. The ability of DFI to recover the mesoscale ageostrophic circulation associated with finite amplitude jets and eddies in the ocean is first demonstrated using control data produced by simulations with a primitive equation model. The DFI method is then applied to synoptic hydrographic data collected during several California CTZ surveys in the summer of 1988. The diagnostic results indicate the existence of jets, eddies, and filaments in the CTZ domain with maximum horizontal currents of the order of 0.6 m/s at the surface. Currents associated with such jets and filaments are coherent to a depth of over 500 m. The surface currents associated with a prominent cool filament are generally confluent, and weakly convergent on average, along the 270 km offshore extent of the filament. Meanders in the jet display convergence and downwelling upstream of pressure troughs and divergence and upwelling downstream of the troughs. Maximum vertical velocities at 100 m are of the order of 10 m/day. This result is consistent with independent estimates of subduction rates made from biological studies in this and similar coastal filaments in the CTZ program.     

Upwelling mechanisms in the northwestern Alboran Sea

From April 1996 to July 1997, a series of hydrographic surveys were carried out in the Northwestern part of the Alboran Sea to investigate the upwelling that is an almost permanent feature in this area. Simultaneously a mooring line was deployed in the north part of the eastern section of the Strait of Gibraltar to monitor the variability of the Atlantic Jet (AJ). Two mechanisms are shown to be relevant for the upwelling dynamic in the region: the southward drifting of the AJ and wind stress. A linear relation between the angle under which the Jet enters the Alboran Sea and the distance from the coastline to the front associated with the Jet has been found. This angle that has been estimated from the low passed time series of current velocity measured by the uppermost instrument of the moored line has been then used to identify the onshore–offshore excursions of the Jet. Both upwelling mechanisms are identified from hydrographic data, because each of them has associated a different type of water mass, and they take place in different locations. Wind-driven upwelling dominates in coastal zones, on the shelf, while upwelling associated with southward drifting of the AJ prevails further offshore. The amount of sub-surface water brought up to the surface by each one is of the same order. However, wind-driven upwelling contributes to the fertilization of this region in a major extent because water upwelled by wind is richer in nutrient concentration.