ABSTRACTAim The oceans harbour a great diversity of organisms whose distribution and ecological ... more ABSTRACTAim The oceans harbour a great diversity of organisms whose distribution and ecological preferences are often poorly understood. Species distribution modelling (SDM) could improve our knowledge and inform marine ecosystem management and conservation. Although marine environmental data are available from various sources, there are currently no user-friendly, high-resolution global datasets designed for SDM applications. This study aims to fill this gap by assembling a comprehensive, uniform, high-resolution and readily usable package of global environmental rasters.Location Global, marine.Methods We compiled global coverage data, e.g. satellite-based and in situ measured data, representing various aspects of the marine environment relevant for species distributions. Rasters were assembled at a resolution of 5 arcmin (c. 9.2 km) and a uniform landmask was applied. The utility of the dataset was evaluated by maximum entropy SDM of the invasive seaweed Codium fragile ssp. fragile.Results We present Bio-ORACLE (ocean rasters for analysis of climate and environment), a global dataset consisting of 23 geophysical, biotic and climate rasters. This user-friendly data package for marine species distribution modelling is available for download at http://www.bio-oracle.ugent.be. The high predictive power of the distribution model of C. fragile ssp. fragile clearly illustrates the potential of the data package for SDM of shallow-water marine organisms.Main conclusions The availability of this global environmental data package has the potential to stimulate marine SDM. The high predictive success of the presence-only model of a notorious invasive seaweed shows that the information contained in Bio-ORACLE can be informative about marine distributions and permits building highly accurate species distribution models.
The Data Interpolating Variational Analysis (DIVA) is a method designed to interpolate irregularl... more The Data Interpolating Variational Analysis (DIVA) is a method designed to interpolate irregularly-spaced, noisy data onto any desired location, in most cases on regular grids. It is the combination of a particular methodology, based on the minimisation of a cost function, and a numerically efficient method, based on a finite-element solver. The cost function penalises the misfit between the observations and the reconstructed field, as well as the regularity or smoothness of the field. The method bears similarities to the smoothing splines, where the second derivatives of the field are also penalised.The intrinsic advantages of the method are its natural way to take into account topographic and dynamic constraints (coasts, advection, etc.) and its capacity to handle large data sets, frequently encountered in oceanography. The method provides gridded fields in two dimensions, usually in horizontal layers. Three-dimension fields are obtained by stacking horizontal layers.In the present work, we summarize the background of the method and describe the possible methods to compute the error field associated to the analysis. In particular, we present new developments leading to a more consistent error estimation, by determining numerically the real covariance function in DIVA, which is never formulated explicitly, contrarily to Optimal Interpolation. The real covariance function is obtained by two concurrent executions of DIVA, the first providing the covariance for the second. With this improvement, the error field is now perfectly consistent with the inherent background covariance in all cases.A two-dimension application using salinity measurements in the Mediterranean Sea is presented. Applied on these measurements, Optimal Interpolation and DIVA provided very similar gridded fields (correlation: 98.6%, RMS of the difference: 0.02). The method using the real covariance produces an error field similar to the one of OI, except in the coastal areas.► The covariance function in DIVA is influenced by the physical boundaries (coastline, bottom) and by dynamics (current, diffusion). ► The analysis performed using DIVA and OI in an infinite domain are equivalent. ► The real data covariance can be accessed using two concurrent executions of DIVA. ► The error fields provided by OI and DIVA are similar.
The Canary Island region is rich in mesoscale phenomena that affect cycles of physical and biolog... more The Canary Island region is rich in mesoscale phenomena that affect cycles of physical and biological processes. A 1D version of the Regional Oceanic Modeling System (ROMS) is used south of the Gran Canaria Island to simulate seasonal climatologies of these cycles. The model is forced with monthly air–sea fluxes averaged from 1993 to 2002 and initialized with mean in situ profiles of temperature, salinity, oxygen and nitrate concentrations. The K-Profile Parameterization (KPP) mixed layer submodel is compared with other submodels using idealized numerical experiments. When forced with realistic air–sea fluxes, the model correctly reproduces the annual cycle of temperature (mixed layer depth), with minimum surface values of 18 °C (maximal depth > 105 m) in February during convective mixing resulting from a negative heat flux. Maximum temperatures above 23 °C (minimal depth < 20 m) are simulated from September to October after strong summer heating and a decrease in Trade Winds intensity. A simple ecosystem model is coupled to the physical model, which provides simulated biological cycles that are in agreement with regional observations. A phytoplankton bloom develops in late winter, driven by the injection of new nutrients into the euphotic layer. Simulated chlorophyll shows a deep maximum fluctuating around 100 m with concentrations around 1 mg Chla m− 3, while surface values are low (around 0.1 mg Chla m− 3 ) during most of the year. The physical and biological model results are validated by comparisons with data from regional studies, climatological fields and time-series from the ESTOC station.
Glider data were acquired along a SARAL/AltiKa track in August 2013 in the Ibiza Channel.Satellit... more Glider data were acquired along a SARAL/AltiKa track in August 2013 in the Ibiza Channel.Satellite altimetry, HF radar and glider data are interpolated and filtered to compute the cross-track velocity.All the platforms showed the existence of a 25–30 km width coastal jet with velocities larger than 20 cm/s.Filtered 40 Hz data provided geostrophic current about 10 km from the coast.Satellite altimetry measurements from SARAL-AltiKa are analysed in the coastal ocean using the results of the G-AltiKa mission (1–5 August 2013), which combined altimeter, HF radar and glider data coincident with the satellite track, south-west of Ibiza Island, in the Western Mediterranean Sea.The absolute dynamic topography, computed from 1 Hz and 40 Hz altimetry data, and the dynamic height, computed from glider temperature and salinity, both exhibited a weak signal with amplitudes of order 2 cm. The resulting geostrophic and HF radar velocities along the track depicted a north-westward coastal current with a maximal velocity larger than 20 cm s−1.This demonstrates that the AltiKa altimeter is able to resolve SLA signals of more than 2 cm, and gradients in those signals over several tens of kilometres. After filtering, the 40 Hz data depicted a signal consistent with the other platforms, up to a distance of order 10 km from the coast.
Filaments are narrow, shallow structures of cool water originating from the coast. They are typic... more Filaments are narrow, shallow structures of cool water originating from the coast. They are typical features of the four main eastern boundary upwelling systems (EBUS). In spite of their significant biological and chemical roles, through the offshore exportation of nutrient-rich waters, the physical processes that generate them are still not completely understood. This paper is a process-oriented study of filament generation mechanisms. Our goal is twofold: firstly, to obtain a numerical solution able to correctly represent the characteristics of the filament off Cape Ghir (30°38′N, northwest Africa) in the Canary EBUS and secondly, to explain its formation by a simple mechanism based on the balance of potential vorticity.The first goal is achieved by the use of the ROMS model (Regional Ocean Modeling System) with embedded domains around Cape Ghir, with a horizontal resolution going up to 1.5 km for the finest domain. The latter gets its initial and boundary conditions from a parent solution and is forced by climatological, high-resolution atmospheric fields. The modeled filaments display spatial, temporal and physical characteristics in agreement with the available in situ and satellite observations. This model solution is used as a reference to compare the results with a set of process-oriented experiments. These experiments allow us to reach the second objective. The solutions serve to highlight the contributions of various processes on the filament generation. Since the study is focused on general processes present under climatological forcing conditions, inter-annual forcing is not necessary.The underlying idea for the filament generation is the balance of potential vorticity in the Canary EBUS: the upwelling jet is characterized by negative relative vorticity and flows southward along a narrow band of uniform potential vorticity. In the vicinity of the cape, an injection of relative vorticity induced by the wind breaks the existing vorticity balance. The upwelling jet is prevented from continuing its way southward and has to turn offshore to follow lines of equal potential vorticity.The model results highlight the essential role of wind, associated with the particular topography (coastline and bottom) around the cape. The mechanism presented here is general and thus can be applied to other EBUS.► The results of a regional model around Cape Ghir are presented and validated. ► An original mechanism based on potential vorticity balance is proposed to explain the filament generation. ► Process-oriented experiments underline the role of the wind in the filament generation.
The SOCIB Glider Toolbox covers all the glider data management process, from raw files to final p... more The SOCIB Glider Toolbox covers all the glider data management process, from raw files to final product in NetCDF.It works both for real-time and delayed mode data, for two of the most used glider types.It solves most of the time-consuming issues that users have to face when processing glider data.We present a complete set of freely available MATLAB/Octave scripts called the SOCIB Glider Toolbox (https://github.com/socib/glider_toolbox). This new toolbox automates glider data processing functions, including thermal lag correction, quality control and graphical outputs. While the scientific value of the glider platform has been proven, the experience for the glider data user is far from perfect or routine. Over the last 10 years, ocean gliders have evolved such that they are now considered as a core component of multi-platform observing systems and multi-disciplinary process studies; we now have a generic processing system that appropriately complements glider capability.In an ideal world, a simple connection to a glider would provide oceanographic data ready for scientific application in an intuitive, familiar format; the reality has been somewhat different. Up till now users have faced several time-consuming tasks that prevent them from directly and efficiently extracting new oceanographic knowledge from the acquired data. The SOCIB glider toolbox covers all stages of the data management process, including: metadata aggregation, raw data download, data processing, data correction and the automatic generation of data products and figures. It is designed to be operated either in real-time or in delayed mode, and to process data from two of the most widely used and commercially exploited glider platforms, Slocum gliders and SeaGliders. The SOCIB glider toolbox is ready to accelerate glider data integration and promote oceanographic discovery.
AbstractIn the framework of the Canaries-Iberian marine ecosystem Exchanges (CAIBEX) experiment, ... more AbstractIn the framework of the Canaries-Iberian marine ecosystem Exchanges (CAIBEX) experiment, an interdisciplinary high-resolution survey was conducted in the NW African region of Cape Ghir (30°38′N) during August 2009. The anatomy of a major filament is investigated on scales down to the submesoscale using in situ and remotely sensed data. The filament may be viewed as a system composed of three intimately connected structures: a small, shallow, and cold filament embedded within a larger, deeper, and cool filament and an intrathermocline anticyclonic eddy (ITE). The cold filament, which stretches 110 km offshore, is a shallow feature 60 m deep and 25 km wide, identified by minimal surface temperatures and rich in chlorophyll a. This structure comprises two asymmetrical submesoscale (∼18 km) fronts with jets flowing in opposite directions. The cold filament is embedded near the equatorward boundary of a much broader region of approximately 120 km width and 150 m depth that forms the cool filament and stretches at least 200 km offshore. This cool region, partly resulting from the influence of cold filament, is limited by two asymmetrical mesoscale (∼50 km) frontal boundaries. At the ITE, located north of the cold filament, we observe evidence of downwelling as indicated by a relatively high concentration of particles extending from the surface to more than 200 m depth. We hypothesize that this ITE may act as a sink of carbon and thus the filament system may serve dual roles of offshore carbon export and carbon sink.
Abstract[1] A high-resolution numerical model study of the Canary Basin in the northeast subtropi... more Abstract[1] A high-resolution numerical model study of the Canary Basin in the northeast subtropical Atlantic Ocean is presented. A long-term climatological solution from the Regional Oceanic Modeling System (ROMS) reveals mesoscale variability associated with the Azores and Canary Current systems, the northwest African coastal upwelling, and the Canary Island archipelago. The primary result concerns the Canary Current (CanC) which, in the solution, transports ∼3 Sv southward in line with observations. The simulated CanC has a well-defined path with pronounced seasonal variability. This variability is shown to be mediated by the westward passage of two large annually excited counterrotating anomalous structures that originate at the African coast. The anomalies have a sea surface expression, permitting their validation using altimetry and travel at the phase speed of baroclinic planetary (Rossby) waves. The role of nearshore wind stress curl variability as a generating mechanism for the anomalies is confirmed through a sensitivity experiment forced by low-resolution winds. The resulting circulation is weak in comparison to the base run, but the propagating anomalies are still discernible, so we cannot discount a further role in their generation being played by annual reversals of the large-scale boundary flow that are known to occur along the African margin. An additional sensitivity experiment, where the Azores Current is removed by closing the Strait of Gibraltar presents the same anomalies and CanC behavior as the base run, suggesting that the CanC is rather insensitive to upstream variability from the Azores Current.
New altimetry products in semi-enclosed seas are of major interest given the importance of the co... more New altimetry products in semi-enclosed seas are of major interest given the importance of the coastal-open ocean interactions. This study shows how reprocessed altimetry products in the Mediterranean Sea from Archiving, Validation and Interpolation of Satellite Oceanographic data (AVISO) have improved the representation of the surface circulation over the 1993–2012 period. We focus on the Alboran Sea, which is the highest mesoscale activity area of the western Mediterranean. The respective impacts of the new mean dynamic topography (MDT) and mapped sea level anomaly (MSLA) on the description of the Western Alboran Gyre (WAG) are quantitatively evaluated. The temporal mean and variability of the total kinetic energy have been significantly increased in the WAG considering both the new MDT and MSLA (by more than 50%). The new MDT has added 39% to the mean kinetic energy, while the new MSLA has increased the eddy kinetic energy mean (standard deviation) by 53% (30%). The new MSLA has yielded higher variability of total (eddy) kinetic energy, especially in the annual frequency band by a factor of 2 (3). The MDT reprocessing has particularly increased the low-frequency variability of the total kinetic energy by a factor of 2. Geostrophic velocities derived from the altimetry products have also been compared with drifter data. Both reprocessed MDT and MSLA products intensify the velocities of the WAG making them closer to the in situ estimations, reducing the root mean square differences and increasing the correlation for the zonal and meridional components. The results obtained using refined coastal processing of altimetry products and new observational data are very encouraging to better understand the ocean circulation variability and coastal-open ocean interactions, and for potential improvements in other sub-basins, marginal seas and coastal global ocean.
AbstractWe investigate the extent to which the recently upgraded version of the Ssalto/Duacs sea ... more AbstractWe investigate the extent to which the recently upgraded version of the Ssalto/Duacs sea level anomaly product affects the description of mesoscale activity in the Eastern Boundary Upwelling Systems (EBUS). Drifter observations confirm that the new data set released by Archiving, Validation and Interpretation of Satellite Oceanographic data (AVISO) in April 2014 (DT14) offers an enhanced description of mesoscale activity for the four EBUS. DT14 returns significantly higher eddy kinetic energy levels (+80%) within a 300 km coastal band, where mesoscale structures are known to induce important lateral physical and biogeochemical fluxes. When applied to DT14, an automatic eddy detection algorithm detects more eddies in the EBUS (+37%), and lower eddy radius estimates, in comparison with results using the former altimetry product (DT10). We show that despite higher eddy densities, the smaller eddy radii result in westward eddy transport estimates that are smaller than those obtained from DT10 (−12%).
We measured new and regenerated production and nitrogen excess in the Canary Current region.N2 fi... more We measured new and regenerated production and nitrogen excess in the Canary Current region.N2 fixation contributes <1% to new production during the summer off the western Iberian peninsula.We estimate a new nitrogen excess rate of 22±19×1010 mol N yr−1.We used 15N-labeled substrates to measure dinitrogen (N2) fixation, nitrate (NO3−)(NO3−) and ammonium (NH4+)(NH4+) uptake, regeneration and associated dissolved organic nitrogen (DON) release in a coastal upwelling system (Cape Ghir, ∼31°N) and an open ocean grid (bounded between 25°–42°N and 20°W) in the Canary Current region during the summer of 2009. New production (Pnew=NO3−NO3− uptake+N2 fixation+DON released from NO3−NO3− uptake−NO3−NO3− regeneration) was higher in the upwelling than in the open ocean zone (0.126 and 0.014 µmol N L−1 h−1, respectively), while regenerated production (Preg=NH4+NH4+ uptake+DON released from NH4+NH4+ uptake+NH4+NH4+ regeneration) was similar in both zones (0.157 and 0.133 µmol N L−1 h−1, respectively). The resulting f-ratio (Pnew/Pnew+Preg) for the open ocean and upwelling zones was 0.08 and 0.48, respectively. The availability of nitrogen in excess of that expected from Redfield stoichiometry is generally attributed to N2 fixation. A previous study indicated that our open ocean grid zone had an excess nitrogen production rate of 40±22×1010 mol N yr−1. We revisited this budget including new dissolved organic matter and NO3−NO3− fluxes through the Strait of Gibraltar and estimated a revised nitrogen excess rate of 22±19×1010 mol N yr−1. The average volumetric rate of N2 fixation for this zone was only 1.3×10−3 nmol N L−1 d−1, indicating that its influence in Pnew and nitrogen excess production in this part of the Atlantic is negligible.
ABSTRACTAim The oceans harbour a great diversity of organisms whose distribution and ecological ... more ABSTRACTAim The oceans harbour a great diversity of organisms whose distribution and ecological preferences are often poorly understood. Species distribution modelling (SDM) could improve our knowledge and inform marine ecosystem management and conservation. Although marine environmental data are available from various sources, there are currently no user-friendly, high-resolution global datasets designed for SDM applications. This study aims to fill this gap by assembling a comprehensive, uniform, high-resolution and readily usable package of global environmental rasters.Location Global, marine.Methods We compiled global coverage data, e.g. satellite-based and in situ measured data, representing various aspects of the marine environment relevant for species distributions. Rasters were assembled at a resolution of 5 arcmin (c. 9.2 km) and a uniform landmask was applied. The utility of the dataset was evaluated by maximum entropy SDM of the invasive seaweed Codium fragile ssp. fragile.Results We present Bio-ORACLE (ocean rasters for analysis of climate and environment), a global dataset consisting of 23 geophysical, biotic and climate rasters. This user-friendly data package for marine species distribution modelling is available for download at http://www.bio-oracle.ugent.be. The high predictive power of the distribution model of C. fragile ssp. fragile clearly illustrates the potential of the data package for SDM of shallow-water marine organisms.Main conclusions The availability of this global environmental data package has the potential to stimulate marine SDM. The high predictive success of the presence-only model of a notorious invasive seaweed shows that the information contained in Bio-ORACLE can be informative about marine distributions and permits building highly accurate species distribution models.
The Data Interpolating Variational Analysis (DIVA) is a method designed to interpolate irregularl... more The Data Interpolating Variational Analysis (DIVA) is a method designed to interpolate irregularly-spaced, noisy data onto any desired location, in most cases on regular grids. It is the combination of a particular methodology, based on the minimisation of a cost function, and a numerically efficient method, based on a finite-element solver. The cost function penalises the misfit between the observations and the reconstructed field, as well as the regularity or smoothness of the field. The method bears similarities to the smoothing splines, where the second derivatives of the field are also penalised.The intrinsic advantages of the method are its natural way to take into account topographic and dynamic constraints (coasts, advection, etc.) and its capacity to handle large data sets, frequently encountered in oceanography. The method provides gridded fields in two dimensions, usually in horizontal layers. Three-dimension fields are obtained by stacking horizontal layers.In the present work, we summarize the background of the method and describe the possible methods to compute the error field associated to the analysis. In particular, we present new developments leading to a more consistent error estimation, by determining numerically the real covariance function in DIVA, which is never formulated explicitly, contrarily to Optimal Interpolation. The real covariance function is obtained by two concurrent executions of DIVA, the first providing the covariance for the second. With this improvement, the error field is now perfectly consistent with the inherent background covariance in all cases.A two-dimension application using salinity measurements in the Mediterranean Sea is presented. Applied on these measurements, Optimal Interpolation and DIVA provided very similar gridded fields (correlation: 98.6%, RMS of the difference: 0.02). The method using the real covariance produces an error field similar to the one of OI, except in the coastal areas.► The covariance function in DIVA is influenced by the physical boundaries (coastline, bottom) and by dynamics (current, diffusion). ► The analysis performed using DIVA and OI in an infinite domain are equivalent. ► The real data covariance can be accessed using two concurrent executions of DIVA. ► The error fields provided by OI and DIVA are similar.
The Canary Island region is rich in mesoscale phenomena that affect cycles of physical and biolog... more The Canary Island region is rich in mesoscale phenomena that affect cycles of physical and biological processes. A 1D version of the Regional Oceanic Modeling System (ROMS) is used south of the Gran Canaria Island to simulate seasonal climatologies of these cycles. The model is forced with monthly air–sea fluxes averaged from 1993 to 2002 and initialized with mean in situ profiles of temperature, salinity, oxygen and nitrate concentrations. The K-Profile Parameterization (KPP) mixed layer submodel is compared with other submodels using idealized numerical experiments. When forced with realistic air–sea fluxes, the model correctly reproduces the annual cycle of temperature (mixed layer depth), with minimum surface values of 18 °C (maximal depth > 105 m) in February during convective mixing resulting from a negative heat flux. Maximum temperatures above 23 °C (minimal depth < 20 m) are simulated from September to October after strong summer heating and a decrease in Trade Winds intensity. A simple ecosystem model is coupled to the physical model, which provides simulated biological cycles that are in agreement with regional observations. A phytoplankton bloom develops in late winter, driven by the injection of new nutrients into the euphotic layer. Simulated chlorophyll shows a deep maximum fluctuating around 100 m with concentrations around 1 mg Chla m− 3, while surface values are low (around 0.1 mg Chla m− 3 ) during most of the year. The physical and biological model results are validated by comparisons with data from regional studies, climatological fields and time-series from the ESTOC station.
Glider data were acquired along a SARAL/AltiKa track in August 2013 in the Ibiza Channel.Satellit... more Glider data were acquired along a SARAL/AltiKa track in August 2013 in the Ibiza Channel.Satellite altimetry, HF radar and glider data are interpolated and filtered to compute the cross-track velocity.All the platforms showed the existence of a 25–30 km width coastal jet with velocities larger than 20 cm/s.Filtered 40 Hz data provided geostrophic current about 10 km from the coast.Satellite altimetry measurements from SARAL-AltiKa are analysed in the coastal ocean using the results of the G-AltiKa mission (1–5 August 2013), which combined altimeter, HF radar and glider data coincident with the satellite track, south-west of Ibiza Island, in the Western Mediterranean Sea.The absolute dynamic topography, computed from 1 Hz and 40 Hz altimetry data, and the dynamic height, computed from glider temperature and salinity, both exhibited a weak signal with amplitudes of order 2 cm. The resulting geostrophic and HF radar velocities along the track depicted a north-westward coastal current with a maximal velocity larger than 20 cm s−1.This demonstrates that the AltiKa altimeter is able to resolve SLA signals of more than 2 cm, and gradients in those signals over several tens of kilometres. After filtering, the 40 Hz data depicted a signal consistent with the other platforms, up to a distance of order 10 km from the coast.
Filaments are narrow, shallow structures of cool water originating from the coast. They are typic... more Filaments are narrow, shallow structures of cool water originating from the coast. They are typical features of the four main eastern boundary upwelling systems (EBUS). In spite of their significant biological and chemical roles, through the offshore exportation of nutrient-rich waters, the physical processes that generate them are still not completely understood. This paper is a process-oriented study of filament generation mechanisms. Our goal is twofold: firstly, to obtain a numerical solution able to correctly represent the characteristics of the filament off Cape Ghir (30°38′N, northwest Africa) in the Canary EBUS and secondly, to explain its formation by a simple mechanism based on the balance of potential vorticity.The first goal is achieved by the use of the ROMS model (Regional Ocean Modeling System) with embedded domains around Cape Ghir, with a horizontal resolution going up to 1.5 km for the finest domain. The latter gets its initial and boundary conditions from a parent solution and is forced by climatological, high-resolution atmospheric fields. The modeled filaments display spatial, temporal and physical characteristics in agreement with the available in situ and satellite observations. This model solution is used as a reference to compare the results with a set of process-oriented experiments. These experiments allow us to reach the second objective. The solutions serve to highlight the contributions of various processes on the filament generation. Since the study is focused on general processes present under climatological forcing conditions, inter-annual forcing is not necessary.The underlying idea for the filament generation is the balance of potential vorticity in the Canary EBUS: the upwelling jet is characterized by negative relative vorticity and flows southward along a narrow band of uniform potential vorticity. In the vicinity of the cape, an injection of relative vorticity induced by the wind breaks the existing vorticity balance. The upwelling jet is prevented from continuing its way southward and has to turn offshore to follow lines of equal potential vorticity.The model results highlight the essential role of wind, associated with the particular topography (coastline and bottom) around the cape. The mechanism presented here is general and thus can be applied to other EBUS.► The results of a regional model around Cape Ghir are presented and validated. ► An original mechanism based on potential vorticity balance is proposed to explain the filament generation. ► Process-oriented experiments underline the role of the wind in the filament generation.
The SOCIB Glider Toolbox covers all the glider data management process, from raw files to final p... more The SOCIB Glider Toolbox covers all the glider data management process, from raw files to final product in NetCDF.It works both for real-time and delayed mode data, for two of the most used glider types.It solves most of the time-consuming issues that users have to face when processing glider data.We present a complete set of freely available MATLAB/Octave scripts called the SOCIB Glider Toolbox (https://github.com/socib/glider_toolbox). This new toolbox automates glider data processing functions, including thermal lag correction, quality control and graphical outputs. While the scientific value of the glider platform has been proven, the experience for the glider data user is far from perfect or routine. Over the last 10 years, ocean gliders have evolved such that they are now considered as a core component of multi-platform observing systems and multi-disciplinary process studies; we now have a generic processing system that appropriately complements glider capability.In an ideal world, a simple connection to a glider would provide oceanographic data ready for scientific application in an intuitive, familiar format; the reality has been somewhat different. Up till now users have faced several time-consuming tasks that prevent them from directly and efficiently extracting new oceanographic knowledge from the acquired data. The SOCIB glider toolbox covers all stages of the data management process, including: metadata aggregation, raw data download, data processing, data correction and the automatic generation of data products and figures. It is designed to be operated either in real-time or in delayed mode, and to process data from two of the most widely used and commercially exploited glider platforms, Slocum gliders and SeaGliders. The SOCIB glider toolbox is ready to accelerate glider data integration and promote oceanographic discovery.
AbstractIn the framework of the Canaries-Iberian marine ecosystem Exchanges (CAIBEX) experiment, ... more AbstractIn the framework of the Canaries-Iberian marine ecosystem Exchanges (CAIBEX) experiment, an interdisciplinary high-resolution survey was conducted in the NW African region of Cape Ghir (30°38′N) during August 2009. The anatomy of a major filament is investigated on scales down to the submesoscale using in situ and remotely sensed data. The filament may be viewed as a system composed of three intimately connected structures: a small, shallow, and cold filament embedded within a larger, deeper, and cool filament and an intrathermocline anticyclonic eddy (ITE). The cold filament, which stretches 110 km offshore, is a shallow feature 60 m deep and 25 km wide, identified by minimal surface temperatures and rich in chlorophyll a. This structure comprises two asymmetrical submesoscale (∼18 km) fronts with jets flowing in opposite directions. The cold filament is embedded near the equatorward boundary of a much broader region of approximately 120 km width and 150 m depth that forms the cool filament and stretches at least 200 km offshore. This cool region, partly resulting from the influence of cold filament, is limited by two asymmetrical mesoscale (∼50 km) frontal boundaries. At the ITE, located north of the cold filament, we observe evidence of downwelling as indicated by a relatively high concentration of particles extending from the surface to more than 200 m depth. We hypothesize that this ITE may act as a sink of carbon and thus the filament system may serve dual roles of offshore carbon export and carbon sink.
Abstract[1] A high-resolution numerical model study of the Canary Basin in the northeast subtropi... more Abstract[1] A high-resolution numerical model study of the Canary Basin in the northeast subtropical Atlantic Ocean is presented. A long-term climatological solution from the Regional Oceanic Modeling System (ROMS) reveals mesoscale variability associated with the Azores and Canary Current systems, the northwest African coastal upwelling, and the Canary Island archipelago. The primary result concerns the Canary Current (CanC) which, in the solution, transports ∼3 Sv southward in line with observations. The simulated CanC has a well-defined path with pronounced seasonal variability. This variability is shown to be mediated by the westward passage of two large annually excited counterrotating anomalous structures that originate at the African coast. The anomalies have a sea surface expression, permitting their validation using altimetry and travel at the phase speed of baroclinic planetary (Rossby) waves. The role of nearshore wind stress curl variability as a generating mechanism for the anomalies is confirmed through a sensitivity experiment forced by low-resolution winds. The resulting circulation is weak in comparison to the base run, but the propagating anomalies are still discernible, so we cannot discount a further role in their generation being played by annual reversals of the large-scale boundary flow that are known to occur along the African margin. An additional sensitivity experiment, where the Azores Current is removed by closing the Strait of Gibraltar presents the same anomalies and CanC behavior as the base run, suggesting that the CanC is rather insensitive to upstream variability from the Azores Current.
New altimetry products in semi-enclosed seas are of major interest given the importance of the co... more New altimetry products in semi-enclosed seas are of major interest given the importance of the coastal-open ocean interactions. This study shows how reprocessed altimetry products in the Mediterranean Sea from Archiving, Validation and Interpolation of Satellite Oceanographic data (AVISO) have improved the representation of the surface circulation over the 1993–2012 period. We focus on the Alboran Sea, which is the highest mesoscale activity area of the western Mediterranean. The respective impacts of the new mean dynamic topography (MDT) and mapped sea level anomaly (MSLA) on the description of the Western Alboran Gyre (WAG) are quantitatively evaluated. The temporal mean and variability of the total kinetic energy have been significantly increased in the WAG considering both the new MDT and MSLA (by more than 50%). The new MDT has added 39% to the mean kinetic energy, while the new MSLA has increased the eddy kinetic energy mean (standard deviation) by 53% (30%). The new MSLA has yielded higher variability of total (eddy) kinetic energy, especially in the annual frequency band by a factor of 2 (3). The MDT reprocessing has particularly increased the low-frequency variability of the total kinetic energy by a factor of 2. Geostrophic velocities derived from the altimetry products have also been compared with drifter data. Both reprocessed MDT and MSLA products intensify the velocities of the WAG making them closer to the in situ estimations, reducing the root mean square differences and increasing the correlation for the zonal and meridional components. The results obtained using refined coastal processing of altimetry products and new observational data are very encouraging to better understand the ocean circulation variability and coastal-open ocean interactions, and for potential improvements in other sub-basins, marginal seas and coastal global ocean.
AbstractWe investigate the extent to which the recently upgraded version of the Ssalto/Duacs sea ... more AbstractWe investigate the extent to which the recently upgraded version of the Ssalto/Duacs sea level anomaly product affects the description of mesoscale activity in the Eastern Boundary Upwelling Systems (EBUS). Drifter observations confirm that the new data set released by Archiving, Validation and Interpretation of Satellite Oceanographic data (AVISO) in April 2014 (DT14) offers an enhanced description of mesoscale activity for the four EBUS. DT14 returns significantly higher eddy kinetic energy levels (+80%) within a 300 km coastal band, where mesoscale structures are known to induce important lateral physical and biogeochemical fluxes. When applied to DT14, an automatic eddy detection algorithm detects more eddies in the EBUS (+37%), and lower eddy radius estimates, in comparison with results using the former altimetry product (DT10). We show that despite higher eddy densities, the smaller eddy radii result in westward eddy transport estimates that are smaller than those obtained from DT10 (−12%).
We measured new and regenerated production and nitrogen excess in the Canary Current region.N2 fi... more We measured new and regenerated production and nitrogen excess in the Canary Current region.N2 fixation contributes <1% to new production during the summer off the western Iberian peninsula.We estimate a new nitrogen excess rate of 22±19×1010 mol N yr−1.We used 15N-labeled substrates to measure dinitrogen (N2) fixation, nitrate (NO3−)(NO3−) and ammonium (NH4+)(NH4+) uptake, regeneration and associated dissolved organic nitrogen (DON) release in a coastal upwelling system (Cape Ghir, ∼31°N) and an open ocean grid (bounded between 25°–42°N and 20°W) in the Canary Current region during the summer of 2009. New production (Pnew=NO3−NO3− uptake+N2 fixation+DON released from NO3−NO3− uptake−NO3−NO3− regeneration) was higher in the upwelling than in the open ocean zone (0.126 and 0.014 µmol N L−1 h−1, respectively), while regenerated production (Preg=NH4+NH4+ uptake+DON released from NH4+NH4+ uptake+NH4+NH4+ regeneration) was similar in both zones (0.157 and 0.133 µmol N L−1 h−1, respectively). The resulting f-ratio (Pnew/Pnew+Preg) for the open ocean and upwelling zones was 0.08 and 0.48, respectively. The availability of nitrogen in excess of that expected from Redfield stoichiometry is generally attributed to N2 fixation. A previous study indicated that our open ocean grid zone had an excess nitrogen production rate of 40±22×1010 mol N yr−1. We revisited this budget including new dissolved organic matter and NO3−NO3− fluxes through the Strait of Gibraltar and estimated a revised nitrogen excess rate of 22±19×1010 mol N yr−1. The average volumetric rate of N2 fixation for this zone was only 1.3×10−3 nmol N L−1 d−1, indicating that its influence in Pnew and nitrogen excess production in this part of the Atlantic is negligible.
A comparison between satellite and in situ sea surface temperature (SST) data in the Western Medi... more A comparison between satellite and in situ sea surface temperature (SST) data in the Western Mediterranean Sea in 1999 is realised. The aim of this study is to better understand the differences between these two data sets, in order to realise merged maps of SST using satellite and in situ data. When merging temperature from different platforms, it is crucial to take the expected RMS error of the observations into account and to correct for possible biases. Advanced Very High Resolution Radiometer (AVHRR) SST day-time and night-time satellite data are used, and the in situ data have been obtained from various databases (World Ocean Database'05, Coriolis, Medar/Medatlas and ICES). Statistics about the differences due to the hour of the day, the month of the year, the type of sensor/platform used (CTD, XBT, drifter, etc) and the spatial distribution are made using a combination of error measures, diagrams and statistical hypothesis testing. In addition to quantify the errors between different platforms, several assumptions often made when creating gridded analyses will be critically reviewed: unbiased data sets, non-correlated errors of the observations, spatially uniform variance, and Gaussian-distributed data.
ABSTRACT This paper presents a detrending method that eliminates the potential bias in current sp... more ABSTRACT This paper presents a detrending method that eliminates the potential bias in current spatial interpolation products caused by measurements unevenly distributed in time. The method estimates a trend component in addition to the spatial structure and has been implemented within the Data Interpolating Variational Analysis (DIVA) analysis tool. It is used to produce monthly climatologies of the Black Sea Cold Intermediate Layer (CIL) cold content while recognizing its seasonal and inter-annual variability. The analysis of the inter-annual trends, given as a by-product of the method, allows one to relate the CIL inter-annual variability to the cumulated air temperature and wind curl anomalies, resolving 79% of its variation and providing a partial (29%) predictive ability for the CIL intensity in the year to come.
ABSTRACT This paper presents the results of the G-AltiKa mission conducted along a SARAL-AltiKa t... more ABSTRACT This paper presents the results of the G-AltiKa mission conducted along a SARAL-AltiKa track south-west of Ibiza (Balearic Islands, Western Mediterranean Sea) from 1 to 5 August 2013. The main feature of the mission is that the glider measurements are almost synchronous with the altimeter pass. The HF radar system operated by the Balearic Islands Coastal Observing and Forecasting System (SOCIB) constitutes a complementary tool to describe the circulation in the study area. The work is focused on the data processing step (interpolation, filtering, corrections) applied to the measurements and on the comparison of the geostrophic velocity across the satellite track. The absolute dynamic topography, computed by adding filtered 1 Hz and 40 Hz along-track sea-level anomalies Mediterranean Sea Mean Dynamic Topography, and the dynamic height, computed from glider temperature and salinity, both exhibited a signal characterized by weak gradients and amplitudes (2 cm), close to the expected accuracy of the AltiKa instrument. The corresponding geostrophic velocities and the HF radar velocities projected on the SARAL/AltiKa track all depicted a northwestward coastal current with a maximal velocity larger than 20 cm/s. The lack of synopticity due to the time interval between the satellite pass (August 1, 2013, 18:26:12 UTC) and the end of the glider transect (August 5, 2013, 04:17:22 UTC) resulted in a spatial shift between the glider and the altimeter along-track signal, around 5 km. The time evolution of the HF radar currents during the mission duration confi rmed the plausibility of such a shift. After the application of a 5 km lag to the glider dynamic height, the correlation and RMS dif ference between the different platforms were computed. The agreement between the altimetry, glider and HF radar cross-track velocities was synthesized in a Taylor diagram that evidenced the lowest root mean square di fference (9.72 cm/s) and the highest correlation (0.64) between the velocities obtained from the glider dynamic height and those from the filtered 40 Hz sea-level anomalies. The 40 Hz data are particularly valuable as they enable us to use the SARAL-AltiKa data closer to the coast than typically possible with altimetry.
Upwelling filaments are typical features in Eastern Boundary Upwelling Systems and were the objec... more Upwelling filaments are typical features in Eastern Boundary Upwelling Systems and were the object of numerous in situ or numerical studies. However physical processes that generates filaments are not perfectly understood. Recent works suggest that tehy arise from a combination of three phenomena: baroclinic instability of the coastal upwelling jet; interaction of the flow with coastline and topography shape; coastal convergence due to wind stress. In order to explain the generation process with a simple theory, we assume that filament arise from an injection of positive vorticity; as the flow gains positive vorticity, it becomes unable to continue southward and detaches from the coast. The filament-rich region of Cape Ghir (NW Africa) acts as a suitable zone for testing our hypothesis. Several numerical experiments with ROMS model were carried out to assess the role of various process (wind curl, bottom friction, variable topography etc) which may be responsible for positive vorticity injection. The model reference configuration allows us to reproduce the filament with spacial and time scales compatible with in situ observations. Results of the experiments highlight the role of wind stress, since it is at the origin of the upwelling itself. Decreased coastal winds caused multiple filaments around Cape Ghir. Smoothed topography has significant effects on the solution, meaning that the model is sensitive to this parameter. With flattened bathymetry, filaments tend to be much weaker and have lower extension.
Egu General Assembly Conference Abstracts, May 1, 2014
The Data-Interpolating Variational Analysis (DIVA) software is a tool designed to reconstruct a c... more The Data-Interpolating Variational Analysis (DIVA) software is a tool designed to reconstruct a continuous field from discrete measurements. This method is based on the numerical implementation of the Variational Inverse Model (VIM), which consists of a minimization of a cost function, allowing the choice of the analyzed field fitting at best the data sets. The problem is solved efficiently using a finite-element method. This statistical method is particularly suited to deal with irregularly-spaced observations, producing outputs on a regular grid. Initially created to work in a two-dimensional way, the software is now able to handle 3D or even 4D analysis, in order to easily produce ocean climatologies. These analyzes can easily be improved by taking advantage of the DIVA's ability to take topographic and dynamic constraints into account (coastal relief, prevailing wind impacting the advection,...). In DIVA, we assume errors on measurements are not correlated, which means we do not consider the effect of correlated observation errors on the analysis and we therefore use a diagonal observation error covariance matrix. However, the oceanographic data sets are generally clustered in space and time, thus introducing some correlation between observations. In order to determine the impact of such an approximation and provide strategies to mitigate its effects, we conducted several synthetic experiments with known correlation structure. Overall, the best results were obtained with a variant of the covariance inflation method. Finally, a new application of DIVA on satellite altimetry data will be presented : these data have particular space and time distributions, as they consist of repeated tracks (~10-35 days) of measurements with a distance lower than 10 km between two successive measurements in a given track. The tools designed to determine the analysis parameters were adapted to these specificities. Moreover, different weights were applied to measurements in order to take the different times of measurements into account. This application focused on daily fields of sea level anomalies in the Mediterranean Sea.
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articles by Charles Troupin