ALBERT

Description: To study the effects of ocean acidification on the physiology of phytoplankton requires that the key chemical parameters of the growth medium, pCO2, pH and Ω (the saturation state of calcium carbonate) be carefully controlled. This is made difficult by the interdependence of these parameters. Moreover, in growing batch cultures of phytoplankton, the fixation of CO2, the uptake of nutrients and, for coccolithophores, the precipitation of calcite all change the inorganic carbon and acid-base chemistry of the medium. For example, absent pH-buffering or CO2 bubbling, a sizeable decrease in pCO2 occurs at a biomass concentration as low as 50 μM C in non-calcifying cultures. Even in cultures where pCO2 or pH is maintained constant, other chemical parameters change substantially at high cell densities. The quantification of these changes is facilitated by the use of buffer capacities. Experimentally we observe that all methods of adjustment of pCO2/pH can be used, the choice of one or the other depending on the specifics of the experiments. The mechanical effect of bubbling of cultures seems to induce more variable results than other methods of pCO2/pH control. While highly convenient, the addition of pH buffers to the medium induces changes in trace metal availability and cannot be used under trace metal-limiting conditions.

Description: Effective use of ocean colour and other bio-optical observations is dependent upon an ability to understand and characterise the angular scattering properties of phytoplankton populations. The two-layered sphere appears to offer the simplest heterogeneous geometry capable of simulating the observed angular scattering of phytoplankton cells. A study is made of the twolayered spherical model for the simulation of the inherent optical properties of algal populations, with a particular focus on backscattering as causal to ocean colour. Homogenous and two-layered volume-equivalent single particle models are used to examine the effects of varying cellular geometry, chloroplast volume, and complex refractive index on optical efficiency factors. A morphology with a chloroplast layer surrounding the cytoplasm is shown to be optimal for algal cell simulation. Appropriate chloroplast volume and refractive index ranges, and means of determining complex refractive indices for cellular chloroplast and cytoplasm material, are discussed with regard to available literature. The approach is expanded to polydispersed populations using equivalent size distribution models: to demonstrate variability in simulated inherent optical properties for phytoplankton assemblages of changing dominant cell size and functional type. Finally, a preliminary validation is conducted of inherent optical properties determined for natural phytoplankton populations with the two-layered model, using the reflectance approximation. The study demonstrates the validity of the two-layered geometry and refractive index structure, and indicates that the combined use of equivalent size distributions with the heterogeneous geometry can be used to establish a quantitative formulation between single particle optics, size and assemblage-specific inherent optical properties, and ocean colour.

Description: The formation of nitrate (nitrification) in soils is an important process that influences the form of N available for plant uptake and the potential off-site N losses. Gross nitrification is one of the main sources of nitrous oxide (N2O) and nitric oxide (NO) from soils. A field experiment was designed to verify the idea that gross nitrification rates in soils can be readily predicted by a model approach where seasonal variability is described only by soil moisture and soil temperature and the magnitude of gross nitrification is controlled by the soil organic matter (SOM). Gross nitrification rates were measured by a Barometric Process Separation (BaPS), first described by Ingwersen et al. (1999). The BaPS measurements were validated with the commonly used 15N pool dilution technique measurements at six times. In general, the rates determined from both measurement approaches were in the same order of magnitude and showed a good correlation. The effects of three different fertilisations (mineral fertiliser, manure and the control) over more than 100 years on gross nitrification rates were investigated. During 2004 soil probes from the long-term "static fertilisation experiment" at Bad Lauchstädt were sampled weekly and were measured in the laboratory under field conditions and subsequently under standardised conditions (16°C soil temperature and −30 kPa matrix potential) with the Barometric Process Separation system (BaPS). Gross nitrification rates determined by the BaPS-method under field conditions showed a high temporal variability and ranged from 5 to 77 μg N h−1 kg−1 dry mass, 2 to 74 μg N h−1 kg−1 dry mass and 0 to 49 μg N h−1 kg−1 dry mass with respect to manure, mineral fertiliser and control. The annual average was 0.32, 0.26 and 0.18 g N a−1 kg−1 dry mass for the manure site, mineral fertiliser site and control site, respectively. On all sites gross nitrification revealed a strong seasonal dynamic. Three different methods (a temperature and soil moisture dependency model from Recous et al., 1998, a multiple linear regression and the method proposed in this paper) were applied for reproducing the measured results. On the manure site 78% to 80%, on the mineral fertiliser site 66% to 72% and on the control site 39% to 56% of the observed variations could be explained by the tested models. Gross nitrification rates determined under standardised conditions did not show any seasonal trends but did also however reveal high temporal variability.

Description: The circulation of the subtropical gyres can be decomposed into a horizontal recirculation along contours of constant Bernoulli potential and an overturning circulation across these contours. While the geometry and topology of Bernoulli contours is more complicated in the subtropical gyres than in the Southern Ocean, these subtropical overturning circulations are very much analogous to the Deacon cell found in the Southern Ocean. This analogy is formalised through an exact integral constraint, including the rectified effects of transient eddies. The constraint can be interpreted either in terms of vertical fluxes of potential vorticity, or equivalently as an integral buoyancy budget for an imaginary fluid parcel recirculating around a closed Bernoulli contour. Under conditions of vanishing buoyancy and mechanical forcing, the constraint reduces to a generalised non-acceleration condition, under which the Eulerian-mean and eddy-induced overturning circulations exactly compensate. The terms in the integral constraint are diagnosed in an eddy-permitting ocean model in both the North Pacific subtropical gyre and the Southern Ocean. The extent to which the Eulerian-mean and eddy-induced overturning circulations compensate is discussed in each case.

Description: Fishery Observing System (FOS) was developed as a first and basic step towards fish stock abundance nowcasting/forecasting within the framework of the EU research program Mediterranean Forecasting System: Toward an Environmental Prediction (MFSTEP). The study of the relationship between abundance and environmental parameters also represents a crucial point towards forecasting. Eight fishing vessels were progressively equipped with FOS instrumentation to collect fishery and oceanographic data. The vessels belonged to different harbours of the Central and Northern Adriatic Sea. For this pilot application, anchovy (Engraulis encrasicolus, L.) was chosen as the target species. Geo-referenced catch data, associated with in-situ temperature and depth, were the FOS products but other parameters were associated with catch data as well. MFSTEP products numerical circulation models provide many of these data. In particular, salinity was extracted from re-analysis data of numerical circulation models. Satellite-derived sea surface temperature (SST) and chlorophyll were also used as independent variables. Catch and effort data were used to estimate an abundance index (CPUE – Catch per Unit of Effort). Considering that catch records were gathered by different fishing vessels with different technical characteristics and operating on different fish densities, a standardized value of CPUE was calculated. A spatial and temporal average CPUE map was obtained together with a monthly mean time series in order to characterise the variability of anchovy abundance during the period of observation (October 2003–August 2005). In order to study the relationship between abundance and oceanographic parameters, Generalized Additive Models (GAM) were used. Preliminary results revealed a complex scenario: the southern sector of the domain is characterised by a stronger relationship than the central and northern sector where the interactions between the environment and the anchovy distribution are hidden by a higher percentage of variability within the system which is still unexplained. GAM analysis showed that increasing the number of explanatory variables also increased the portion of variance explained by the model. Data exchange and interdisciplinary efforts will therefore be crucial for the success of this research activity.

Description: We present an extension to the Data INterpolating Empirical Orthogonal Functions (DINEOF) which allows not only to fill in clouded images but also to provide an estimation of the error covariance of the reconstruction. This additional information is obtained by an analogy with optimal interpolation. It is shown that the error fields can be obtained with a clever rearrangement of calculations at a cost comparable to that of the interpolation itself. The method is presented on the reconstruction of sea-surface temperature in the Ligurian Sea and around the Corsican Island (Mediterranean Sea), including the calculation of inter-annual variability of average surface values and their expected errors. The application shows that the error fields are not only able to reflect the data-coverage structure but also the covariances of the physical fields.

Description: The northward inflow of Atlantic Water through Denmark Strait – the North Icelandic Irminger Current (NIIC) – is simulated with a numerical model of the North Atlantic and Arctic Ocean. The model uses the technique of adaptive grid refinement which allows a high spatial resolution (1 km horizontal, 10 m vertical) around Iceland. The model is used to assess time and space variability of volume and heat fluxes for the years 1997–2003. Passive tracers are applied to study origin and composition of NIIC water masses. The NIIC originates from two sources: the Irminger Current, flowing as part of the sub-polar gyre in 100–500 m depth along the Reykjanes Ridge and the shallow Icelandic coastal current, flowing eastward on the south Icelandic shelf. The ratio between the deep and shallow branch is 0.7/0.2 Sv. The NIIC continues as a warm and saline branch northward through Denmark Strait where it entrains large amounts of polar water due to the collision with the southward flowing East Greenland Current. Tracer model results indicate that north of Denmark Strait at Hornbanki section (at 21°30' W from 66°40' N to 67°30' N), the NIIC is composed of 43% water masses of Atlantic origin (AW) originating from the south and 57% entrained polar or Arctic water masses (PW) coming from the north. After passing Denmark Strait, the NIIC follows the coast line north-eastward where it influences the hydrography of north Icelandic waters. Volume and heat transport is highly variable and depends strongly on the wind field north of Denmark Strait. Highest monthly mean transport rates at Hornbanki occur in summer (0.75 Sv) when northerly winds are weak, lowest transport is observed in winter (0.35 Sv). Summer heat flux rates (14 TW) can be even three times higher than in winter (4 TW). Strong variability can also be observed on the interannual scale. In particular the winter 2002/2003 showed anomalous high transport and heat flux rates. During the period 1997 to 2003 decreasing northerly winds caused an increase of the NIIC volume and heat transport by 30%, leading to a warming of North Icelandic shelf by around 0.5K.

Description: We present results of an implementation of the Elastic Viscous Plastic (EVP) sea ice dynamics scheme into the Hadley Centre coupled ocean-atmosphere climate model HadCM3. Although the large-scale simulation of sea ice in HadCM3 is quite good with this model, the lack of a full dynamical model leads to errors in the detailed representation of sea ice and limits our confidence in its future predictions. We find that introducing the EVP scheme results in a worse initial simulation of the sea ice. This paper documents various improvements made to improve the simulation, resulting in a sea ice simulation that is better than the original HadCM3 scheme overall. Importantly, it is more physically based and provides a more solid foundation for future improvement. We then consider the interannual variability of the sea ice in the new model and demonstrate improvements over the HadCM3 simulation.

Description: In this paper, the impact of assimilating Temperature (T) and Salinity (S) profiles from Argo floats in the Mediterranean Sea (MEDARGO) is quantitatively investigated using the Observing System Simulation Experiments (OSSE) approach. The impact of varying the number of floats and their launch positions is considered, using numerical simulations with a MOM model and a reduced-order multivariate Optimal Interpolation scheme (SOFA) for assimilation. Realistic launch positions used during the first MFSTEP phase are considered, as well as ''ideal'' positions that can be envisioned for the future, along the VOS tracks. The most effective float trajectories are identified, showing that frontal regions play a major role, and that it is crucial to maintain a sufficient coverage of them. In addition to this, also a qualitative comparison is performed between the results obtained from MEDARGO floats in ideal conditions and results from ''ideal'' profiles taken along the VOS (Volunteer Observing Ships) tracks, as for the XBT (Expandable Baththermograph) data.

Description: The transport of fine-grained sediments in the marine environment entails risks of pollutant intrusions from substances absorbed onto the cohesive flocks' surface, gradually released to the aquatic field. These substances include nutrients such as nitrate, phosphate and silicate compounds from drainage from fertilization of adjacent cultivated areas that enter the coastal areas through rivers and streams, or trace metals as remainders from urban and industrial activities. As a consequence, knowledge on the motion and distribution of sediment particles coming from a given pollutant source is expected to provide the ''bulk'' information on pollutant distribution, necessary for determining the region of influence of the source and to estimate probable trophic levels of the seawater and potential environmental risks. In that aim a numerical model has been developed to predict the fate of the sediments introduced to the marine environment from different pollution sources, such as river outflows, erosion of the seabed, aeolian transported material and drainage systems. The proposed three-dimensional mathematical model is based on the particle tracking method, according to which matter concentration is expressed by particles, each representing a particular amount of sedimentary mass, passively advected and dispersed by the currents. The processes affecting characteristics and propagation of sedimentary material in the marine environment, incorporated in the parameterization, apart from advection and dispersion, include cohesive sediment and near-bed processes. The movement of the particles along with variations in sedimentary characteristics and state, carried by each particle as personal information, are traced with time. Specifically, concerning transport processes, the local seawater velocity and the particle's settling control advection, whereas the random Brownian motion due to turbulence simulates turbulent diffusion. The vertical stratification of the water-column is taken into consideration by appropriate damping of the vertical diffusion term. Variations in cohesive sediment properties during the abidance in the aquatic environment include coagulation and flock break-up processes, quantification of the effects of ambient density to the density of the cohesive aggregate and the associated alterations to the falling speed of the particle. In the vicinity of the seabed particles may deposit and gradually consolidate with time, remain settled onto the bed, or renter the flow at a later temporal point. Other particle may enter the water column for the first time, originating from the erosion of the bed. The occurrence of each of the aforementioned near-bed processes is defined accordingly to the prevailing benthic shear stress conditions. The mathematical model has been applied to the Thermaikos Gulf, an area of high environmental and socioeconomic importance but also a region of significant pollutant forcing from various anthropogenic activities taking place in the adjoining land. Various kinds of outputs can be extracted, such as trajectories of the overall movement of specific particles and related alterations of their characteristics with time, snapshots of the domain with respect to suspended or deposited matter and naturally concentrations of sediments at every required temporal and spatial point. Indicative results from yearly and monthly simulations, using input baroclinic circulation data from the North Aegean Sea model and river discharges are presented and discussed, including outputs from a Typical One-Year Simulation (TOYS), the simulation of the period from 3 September 2001 to 31 August 2002 (S1A2) and the January 2003 experiment (J03). The description of the processes that have been incorporated in the parameterization covers the most significant factors controlling transport and mixing of fine grained sediments in the marine environment, thus validating the accuracy and completeness of the model. One of the major advantages, apart from the observation of the phenomena in scales smaller than the grid size, hence describing the natural processes more accurately, is the flexibility in accepting various pollutant sources and the applicability to different domains with minor modifications. The model has been incorporated in the MFSTEP project, as part of the developed operational forecasting system for the Mediterranean Sea. The application can be used for the prognosis of the seawater quality for current and for future conditions, enabling employment as part of a near-real time observation system or to formulate decisions for the protection of the seawater environment.