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A dynamic energy budget (DEB) model was developed to investigate the growth and reproduction of cultured bivalve species raised under different environmental conditions (varying phytoplankton carbon biomass [Phyto-C], particulate organic carbon [POC] and temperature) and tuned against field data for Mytilus galloprovincialis from the Maliakos and Thermaikos Gulfs (Aegean Sea, Greece). Values of most DEB model parameters were adopted from the literature, while half saturation constant (Xk) and initial values of energy reserves (E) and reproductive buffer (R) were calibrated. Different values have been found for Xk in the 2 areas (Maliakos: Xk = 36 mg C m-3; Thermaikos: Xk = 28 mg C m-3), suggesting that Xk should be treated as a site-specific parameter. Food density (X) was adapted to include not only Phyto-C but also POC in the diet of M. galloprovincialis and only when Phyto-C density was low compared to POC density. Results showed a small contribution of POC during spring in the Maliakos Gulf and almost none at Thermaikos Gulf. The simulated mussel growth showed good agreement with field data. Sensitivity tests on the calibrated parameters (E, R and Xk) were performed to investigate model uncertainty. The standard deviation of simulations with perturbed parameter/initial values remained relatively small and appeared to increase as the modeled mussel grew, in agreement with observations.

The historical and future impacts of atmospheric deposition of inorganic nitrogen (N) and phosphorus (P) on the marine ecosystem in the east Mediterranean Sea are investigated by using a 1D coupled physical- biogeochemical model, set up for the Cretan Sea as a representative area of the basin. For the present-day simulation (2010), the model is forced by observations of atmospheric deposition fluxes at Crete, while for the hindcast (1860) and forecast (2030) simulations, the changes in atmospheric deposition calculated by global chemistry-transport models are applied to the present-day observed fluxes. The impact of the atmospheric deposition on the fluxes of carbon in the food chain is calculated together with the contribution of human activities to these impacts. The results show that total phytoplanktonic biomass increased by 16% over the past 1.5 centuries. Small fractional changes in carbon fluxes and planktonic biomasses are predicted for the near future. Simulations show that atmospheric deposition of N and P may be the main mechanism responsible for the anomalous N:P ratio observed in the Mediterranean Sea. [ABSTRACT FROM AUTHOR]

Abstract: The impact of river load variability on the North Aegean ecosystem functioning over the last decades (1980–2000) was investigated by means of a coupled hydrodynamic/biogeochemical model simulation. Model results were validated against available SeaWiFS Chl-a and in situ data. The simulated food web was found dominated by small cells, in agreement with observations, with most of the carbon channelled through the microbial loop. Diatoms and dinoflagellates presented a higher relative abundance in the more productive coastal areas. The increased phosphate river loads in the early 80s resulted in nitrogen and silicate deficiency in coastal, river-influenced regions. Primary production presented a decreasing trend for most areas. During periods of increased phosphate/nitrate inputs, silicate deficiency resulted in a relative decrease of diatoms, triggering an increase of dinoflagellates. Such an increase was simulated in the late 90s in the Thermaikos Gulf, in agreement with the observed increased occurrence of Harmful Algal Blooms. Microzooplankton was found to closely follow the relative increase of dinoflagellates under higher nutrient availability, showing a faster response than mesozooplankton. Sensitivity simulations with varying nutrient river inputs revealed a linear response of net primary production and plankton biomass. A stronger effect of river inputs was simulated in the enclosed Thermaikos Gulf, in terms of productivity and plankton composition, showing a significant increase of dinoflagellates relative abundance under increased nutrient loads. [Copyright &y& Elsevier]

During the second phase (2003-2006) of the Mediterranean ocean Forecasting System Project (MFS) named Toward Environmental Predictions (MFSTEP) one of the three major aims was the development of numerical forecasting systems. In this context a generic Biogeochemical Flux Model (BFM) was developed and coupled with hydrodynamic models already operating at basin scale as well as in regional areas. In the Eastern Mediterranean basin the BFM was coupled with the Aegean Levantine Eddy Resolving MOdel (ALERMO). The BFM is a generic highly complex model based on ERSEM and although a detailed description of the model and its components is beyond the scope of this work, a short overview of the main processes, laying emphasis on the parameter values used is presented. In addition the performance of the model is evaluated with some preliminary results being qualitatively compared against field observations. The model in its present form is rather promising and reproduces all important major features although there are some slight inefficiencies mostly related to primary and bacterial productivity rates. [ABSTRACT FROM AUTHOR]

Petihakis, G., Smith, C. J., Triantafyllou, G., Sourlantzis, G., Papadopoulou, K-N., Pollani, A., and Korres, G. 2007. Scenario testing of fisheries management strategies using a high resolution ERSEM–POM ecosystem model. – ICES Journal of Marine Science, 64: 1627–1640. [ABSTRACT FROM PUBLISHER]

An advanced multivariate sequential data assimilation system has been implemented within the framework of the European MFSTEP project to fit a three-dimensional biogeochemical model of the Eastern Mediterranean to satellite chlorophyll data from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS). The physics are described by the Princeton Ocean Model (POM) while the biochemistry of the ecosystem is tackled with the Biogeochemical Flux Model (BFM). The assimilation scheme is based on the Singular Evolutive Extended Kalman (SEEK) filter, in which the error statistics were parameterized by means of a suitable set of Empirical Orthogonal Functions (EOFs). To avoid spurious long-range correlations associated with the limited number of EOFs, the filter covariance matrix was given compact support through a radius of influence around every data point location. Hindcast experiments were performed for one year over 1999 and forced with ECMWF 6 h atmospheric fields. The solution of the assimilation system was evaluated against the assimilated data and the MedAtlas climatology, and by assessing the impact of the assimilation on non-observed biogeochemical processes. It is found that the assimilation of SeaWiFS data improves the overall behavior of the BFM model and efficiently removes long term biases from the model despite some difficulties during the spring bloom period. Results, however, suggest the need of subsurface data to enhance the estimation of the ecosystem variables in the deep layers. [ABSTRACT FROM AUTHOR]

A network of three multi-sensor timeseries stations able to deliver real time physical and biochemical observations of the upper thermocline has been developed for the needs of the Mediterranean Forecasting System during the MFSTEP project. They follow the experience of the prototype M3A system that was developed during the MFSPP project and has been tested during a pilot pre-operational period of 22 months (2000-2001). The systems integrate sensors for physical (temperature, salinity, turbidity, current speed and direction) as well as optical and chemical observations (dissolved oxygen, chlorophyll-a, PAR, nitrate). The south Aegean system (E1-M3A) follows a modular design using independent mooring lines and collects biochemical data in the upper 100m and physical data in the upper 500m of the water column. The south Adriatic buoy system (E2- M3A) uses similar instrumentation but on a single mooring line and also tests a new method of pumping water samples from relatively deep layers, performing analysis in the protected "dry" environment of the buoy interior. The Ligurian Sea system (W1-M3A) is an ideal platform for air-sea interaction processes since it hosts a large number of meteorological sensors while its ocean instrumentation, with real time transmission capabilities, is confined in the upper 50m layer. Despite their different architecture, the three systems have common sampling strategy, quality control and data management procedures. The network operates in the Mediterranean Sea since autumn 2004 collecting timeseries data for calibration and validation of the forecasting system as well for process studies of regional dynamics. [ABSTRACT FROM AUTHOR]

Within the framework of the European MFSTEP project, an advanced multivariate sequential data assimilation system has been implemented to assimilate real chlorophyll data from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) into a three-dimensional biochemical model of the Eastern Mediterranean. The physical ocean is described through the Princeton Ocean Model (POM) while the biochemistry of the ecosystem is tackled with the Biochemical Flux Model (BFM). The assimilation scheme is based on the Singular Evolutive Extended Kalman (SEEK) filter, in which the error statistics were parameterized by means of a suitable set of Empirical Orthogonal Functions (EOFs). A radius of influence was further selected around every data point to limit the range of the EOFs spatial correlations. The assimilation experiment was performed for one year over 1999 and forced with ECMWF 6 hour atmospheric fields. The accuracy of the ecological state identification by the assimilation system is assessed by the relevance of the system in fitting the data, and through the impact of the assimilation on non-observed biochemical processes. Assimilation of SeaWiFS data significantly improves the forecasting capability of the BFM model. Results, however, indicate the necessity of subsurface data to enhance the controllability of the ecosystem model in the deep layers. [ABSTRACT FROM AUTHOR]

During the Pilot Phase of the Mediterranean Forecasting System (MFSPP) (1998-2001) a prototype observing system (Mediterranean Moored Multi-sensor Array -- M3A) was designed, developed and operated in the Cretan Sea for continuous oceanographic measurements in real time. The main problems encountered were associated 5 with biofouling, underwater and aerial communication and with the design of the surface buoy. In the second phase of the MFS project named Mediterranean Forecasting System Towards Environmental Predictions (MFSTEP) (2001-2005), the aim was to solve those problems and to consolidate the M3A. During the approximately five years of operation there were 13 scheduled and 15 emergency visits with a total duration of 10 65 days. The acquired experience through the maintenance program proved that the continuous observation of a so important system with a relative low cost is feasible. [ABSTRACT FROM AUTHOR]

Gialova Lagoon, a coastal marine ecosystem in the Ionian Sea, suffered the impact of an oil spill incident in October 1993, leading to the extensive fish deaths when the oil tanker “Iliad” hit bottom in the entrance of the neighbouring Navarino Bay. A multidisciplinary study investigating the structure and functioning of Gialova Lagoon for the development of an integrated economic, social, and environmental management policy consistent with its conservation was carried out on a seasonal basis during 1995/1996. One of the research priorities was to investigate the structure and dynamics of the macrozoobenthic communities and assess whether these communities had recovered from the impact of the oil spill. The various methods applied (abundance/biomass comparison, distribution of species in geometric abundance and geometric size classes) revealed no detectable disturbance of the macrobenthic communities due to anthropogenic impact. However, it was proved that the lagoonal macrofauna suffered extreme natural disturbance due to a dystrophic crisis that occurred during autumn although they successfully recovered in subsequent seasons. Different sets of environmental factors were found to be highly correlated with the temporal and spatial distribution pattern of the macrobenthic communities and are discussed in detail. The coenocline observed in Gialova Lagoon appears to be strongly correlated with the degree of water exchange with adjacent marine and continental environments. [ABSTRACT FROM PUBLISHER]

A generic complex ecological model, the European Regional Seas Ecosystem Model (ERSEM), was applied to a shallow lagoon system in the Eastern Mediterranean. Model results depicting the seasonal variation of nutrients and Chl-α in the water column, as well as three benthic functional groups (suspended feeders, deposit feeders, and benthic carnivores), are validated with in situ data. The likely effect of a technical intervention (river input) increasing the freshwater nutrient inputs on ecosystem functioning is also investigated. Detailed annual carbon fluxes and benthic fauna biomasses are calculated, before and after the river input. The importance of external physical/chemical forcing on the pelagic system and its subsequent effect on the benthic system are demonstrated. Model experiments indicate the shift of the ecosystem from nitrate limitation to predator control with external inputs. Model experiments also show a significant increase in the amount of carbon entering the benthic system through the activity of filter feeders when river inputs are implemented. [ABSTRACT FROM PUBLISHER]

A new approach for processing the remote sensing chlorophyll-α (Chl-α) before assimilating into an ecosystem model is applied in two contrasting, regarding productivity and nutrients availability, Mediterranean sites: the DYFAMED and POSEIDON E1-M3A fixed point open ocean observatories. The new approach derives optically weighted depth-distributed Chl-α profiles from satellite data based on the model simulated Chl-α vertical distribution and light attenuation coefficient. We use the 1D version of the operational ecological 3D POSEIDON model, based on the European Regional Seas Ecosystem Model (ERSEM). The required hydrodynamic properties are obtained (off-line) from the POSEIDON operational 3D hydrodynamic Mediterranean basin scale model. The data assimilation scheme is the singular evolutive interpolated Kalman (SEIK) filter, the ensemble variant of the singular evolutive extended Kalman (SEEK) filter. The performance of the proposed assimilation approach was evaluated against the Chl-α satellite data and the seasonal averages of available in situ data for nitrate, phosphate and Chl-α. An improvement of the model simulated near-surface and subsurface maximum Chl-α concentrations is obtained, especially at the DYFAMED site. Model nitrate is improved with assimilation, particularly with the new approach assimilating depth-distributed Chl-α, while model phosphate is slightly worse after assimilation. Additional sensitivity experiments were performed, showing a better performance of the new approach under different scenarios of model Chl-α deviation from pseudo-observations of surface Chl-α. [ABSTRACT FROM AUTHOR]

A three-dimensional coupled hydrodynamic/biogeochemical numerical model, currently in operation as part of the POSEIDON forecasting system, was implemented in the Mediterranean Sea. The model was assessed regarding its efficacy in representing the main biogeochemical components and seasonal dynamics of the Mediterranean planktonic system. Model outputs were compared with available historical data in a proposed objective eco-regionalisation of the Mediterranean basin, based on productivity. The simulated production (primary, bacterial) and planktonic biomass (phytoplankton, zooplankton and bacteria), as well as particulate and dissolved organic carbon, were found consistent with observational estimates in different areas of the Mediterranean Sea, following large scale productivity gradients. Although some limitations of the model were identified, the observed variability of the phytoplanktonic community structure was reasonably well-reproduced, simulating a dominant microbial food web with an intermittent development of the classical food web. The generic POSEIDON ecosystem model skill assessment provides a benchmark for future model improvement, highlighting the need to expand the range of biological variables sampled for further model calibration and validation. [ABSTRACT FROM AUTHOR]

Ecosystem models are recognized as valuable tools to understand marine ecosystem dynamics and address management questions, requiring an integrated approach of physical and biotic processes. In the present study, a three-dimensional basin scale Mediterranean hydrodynamic/biogeochemical model, currently operational as part of the POSEIDON forecasting system, was extensively validated against available in-situ and satellite data. The generic POSEIDON ecosystem model skill was objectively assessed, in capturing the observed seasonal variability of the main chemical ecosystem components within the planktonic food web. A cluster K-means analysis was applied to obtain an objective 'biogeography' of the Mediterranean Sea, allowing a more efficient validation of model outputs against observational data. The model presented a reasonable skill in reproducing the seasonal cycle and observed patterns of the Mediterranean inorganic nutrients and chlorophyll-a, characterized by a prominent west-to-east gradient and their increase in areas receiving lateral nutrient inputs. Despite some model deviations, validation results have demonstrated the capability of the model to represent the Mediterranean ecosystem, ranging from oligotrophic open ocean to mesotrophic conditions in productive coastal areas. [ABSTRACT FROM AUTHOR]

Operational monitoring and forecasting of marine environmental conditions is a necessary tool for the effective management and protection of the marine ecosystem. It requires the use of multi-variable real-time measurements combined with advanced physical and ecological numerical models. Towards this, a FerryBox system was originally installed and operated in the route Piraeus–Heraklion in 2003 for one year. Early 2012 the system was upgraded and moved to a new high-speed ferry traveling daily in the same route as before. This route is by large traversing the Cretan Sea being the largest and deepest basin (2500 m) in the south Aegean Sea. The HCMR Ferry Box is today the only one in the Mediterranean and thus it can be considered as a pilot case. The analysis of FerryBox SST and SSS in situ data revealed the presence of important regional and sub-basin scale physical phenomena, such as wind-driven coastal upwelling and the presence of a mesoscale cyclone to the north of Crete. In order to assess the impact of the FerryBox SST data in constraining the Aegean Sea hydrodynamic model which is part of the POSEIDON forecasting system, the in situ data were assimilated using an advanced multivariate assimilation scheme based on the Singular Evolutive Extended Kalman (SEEK) filter, a simplified square-root extended Kalman filter that operates with low-rank error covariance matrices as a way to reduce the computational burden. Thus during the period mid-August 2012–mid January 2013 in addition to the standard assimilating parameters, daily SST data along the ferryboat route from Piraeus to Heraklion were assimilated into the model. Inter-comparisons between the control run of the system (model run that uses only the standard data set of observations) and the experiment where the observational data set is augmented with the FerryBox SST data produce interesting results. Apart from the improvement of the SST error, the additional assimilation of daily of FerryBox SST observations is found to have a significant impact on the correct representation of the dynamical dipole in the central Cretan Sea and other dynamic features of the South Aegean Sea, which is then depicted in the decrease of the basin wide SSH RMS error. [ABSTRACT FROM AUTHOR]

Abstract: An application of an ensemble-based robust filter for data assimilation into an ecosystem model of the Cretan Sea is presented and discussed. The ecosystem model comprises two on-line coupled sub-models: the Princeton Ocean Model (POM) and the European Regional Seas Ecosystem Model (ERSEM). The filtering scheme is based on the Singular Evolutive Interpolated Kalman (SEIK) filter which is implemented with a time-local H ∞ filtering strategy to enhance robustness and performances during periods of strong ecosystem variability. Assimilation experiments in the Cretan Sea indicate that robustness can be achieved in the SEIK filter by introducing an adaptive inflation scheme of the modes of the filter error covariance matrix. Twin-experiments are performed to evaluate the performance of the assimilation system and to study the benefits of using robust filtering in an ensemble filtering framework. Pseudo-observations of surface chlorophyll, extracted from a model reference run, were assimilated every two days. Simulation results suggest that the adaptive inflation scheme significantly improves the behavior of the SEIK filter during periods of strong ecosystem variability. [Copyright &y& Elsevier]