The current ecological crisis requires changes in our way to make science in order to reduce the ecological footprint of scientific research activities. This is particularly crucial for setting a good example for the rest of society. Here we present the process engaged by an oceanography laboratory to reduce its environmental footprint. Using a tool developed by the French collective Labos 1point5, we calculated the carbon footprint of our laboratory separated by activities (missions, consumables, buildings, campaigns at sea, etc.). This exercise allows us first of all to quantify the contribution of the various components of our scientific activity. It also shows that the environmental footprint of our scientific activities is significant, and that it needs to be taken seriously by the community studying the Earth system. Reducing this footprint highlights different possible scales of action. Some actions involve internal laboratory processes, while others require broader societal changes. The measures implemented by our laboratory members to minimize our activities' impact will be presented, representing a part of a broader initiative under Labos 1point5.

This ocean color dataset is derived from MODIS_Aqua sensor measurements covering the Southern Canary upwelling system. The raw L1A measurements were downloaded from NASA's Ocean Color web site and then processed using the Ocean Biology Processing Group's (OBPG) Multi-Sensor Level-1 to Level-2 (MSL12) code. The l2gen program, based on its standard process, generates Level-2 parameters consisting of the top of atmosphere radiance, the radiance of each ocean and atmosphere component, the measurement angles, Level-2 flags, ... The top of atmosphere radiance is pre-corrected to keep only a dependence on the diffuse transmittance, the aerosol contribution and the water leaving radiance.The pre-corrected product and measurement angles are assimilated using the Self-Organizing MapNeuroVaria (SOM-NV) code (Diouf et al., 2013). SOM-NV is an algorithm based on two statistical modelsthat classify a dataset into a map, and then use the information from that map to deliver atmospheric and oceanic parameters from the satellite observation. The parameters of interest are the remote sensing reflectance spectra (Rrs(λ)) and the aerosol optical thickness (AOT) at 869 nm (aot_869). The Rrs at blue (443 and 488 nm) and green (547 nm) are used to calculate chlorophyll-a concentration from the OBPG OCx algorithm (chl_ocx, O'Reilly et al., 1998; Mobley et al., 2016). These geophysical parameters are projected onto a fixed grid at 1/96° resolution and archived in a daily netcdf format files. Each file contains five visible reflectances Rrs(λ) (with λ = 412, 443, 488, 531, and 547 nm), chl_ocx, aot_869, and latitude and longitude coordinates. These parameters are described in the files, along with the global attributes.The netcdf files are formatted as follows: SOM-NV-Ayyyydddhhmmss.nc; where yyyy = year; ddd = Julianday; hh = hour; mm = minute; ss = second. The extension "Ayyyydddhhmmss.nc", corresponds to the nameof the MODIS_aqua file of the day. When two input files exist for the same day, within 5 minutes, the twoscans are concatenated and the orbit keeps the name of the second file.All files are compressed internally to a size of 4, to facilitate transfers. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Résumé Ce jeu de données de couleur de l’eau est issu des mesures du capteur MODIS_Aqua sur la partie sud du système d’upwelling des Canaries. Les mesures brutes L1A ont été téléchargées du site Ocean Color de la NASA, puis traitées à l’aide du code de traitement « Multi-Sensor Level-1 to Level-2 (MSL12) » du groupe Ocean Biology Processing Group (OBPG). La version standard du programme l2gen génère les paramètres de niveau 2 constitués de la luminance totale mesurée, de la luminance de chaque composante du système océan-atmosphère, des angles de mesures, des masques de niveau 2, …. La luminance totale est pré-corrigée pour ne garder qu’une dépendance à la transmittance diffuse, à la contribution des aérosols et à la luminance marine.Le produit pré-corrigé et les angles de mesure sont assimilés à l’aide du code Self-Organizing Map NeuroVaria (SOM-NV) de Diouf et al. (2013). SOM-NV est un algorithme basé sur deux modèles statistiques qui permettent de classer un ensemble de données sur une carte, puis d’utiliser les informations de cette carte pour restituer les paramètres atmosphériques et océaniques de l’observation satellite.Les paramètres restitués sont les spectres de réflectance marine (Rrs(λ)) et l’épaisseur optique des aérosols (AOT) à 869 nm (aot_869). Les Rrs au bleu (443 et 488 nm) et au vert (547 nm) servent à calculer la concentration en chlorophylle-a à partir de l’algorithme OCx de OBPG (chl_ocx).Ces paramètres géophysiques sont projetés sur une grille fixe à 1/96° de résolution et archivés au format de fichiers netcdf journaliers. Chaque fichier netcdf contient cinq réflectances du visible Rrs(λ) (avec λ = 412, 443, 488, 531 et 547 nm), la chl_ocx, l’aot_869, et les coordonnées latitude et longitude. Ces paramètres sont décrits dans les fichiers, ainsi que les attributs globaux.Les fichiers netcdf sont formatés comme suite : SOM-NV-Ayyyydddhhmmss.nc ; avec yyyy = année ; ddd =jour julien ; hh = heure ; mm = minute ; ss = seconde. L'extension "Ayyyydddhhmmss.nc", correspond aunom du fichier MODIS_aqua du jour. Dans le cas où deux fichiers existent pour un même jour, à 5 minutesprès, les deux scans sont concaténés et l'orbite garde le nom du deuxième fichier.Tous les fichiers sont compressés en interne à un niveau 4, pour faciliter le transfert.

The Sahara desert is a major global source of dust that is mostly transported southwest over the ocean off West Africa. The presence of this dust impacts the remote sensing of ocean surface properties. These aerosols have absorbing properties that are poorly accounted for in the standard ocean color data processing algorithm. This can result in an overestimation of the atmospheric contribution to the ocean color signal and consequently an underestimation of the oceanic contribution. A two-step algorithm initially applied to the Sea-viewing Wide field-of-view Sensor (SeaWiFS) data was adapted to the Moderate Resolution Imaging Spectroradiometer (MODIS-Aqua) sensor in the Northwest African region. The Northwest African region is a very productive region, where pelagic resources are an important socio-economic sector. Improving atmospheric correction of ocean color products is, thus, of particular interest for this oceanic region. The two-step approach of classifying the top-of-atmosphere radiance spectra for a better estimate of aerosol type on the one hand, and using an optimization method to fit the parameters of these aerosols and chlorophyll-a concentration (Chla) on the other hand, allows for a better representation of the optical thickness, a correction of the marine reflectance spectrum, and an increase in the spatio-temporal coverage of the area. To the extent that the properties of the water color signal are improved by this data processing, the Chla estimates should also be improved by this approach. However, it is difficult to conclude on this point from the available in situ observations.

Abstract The Senegalese coastal and shelf systems comprises a southern part of the Canary Islands upwelling system. The present study focuses on the study of phytoplankton from meso- to submesoscale during the transition period from the warm West African monsoon season to the cold upwelling season. This period coincides with the return of sardinella from their northward migration to its second most important spawning area resulting in a high retention on the southern coast, as well as possible events of the Senegalese fishermen's skin disease (as it was the case in November 2020). This is a very poorly documented period. The last studies allowing the study of the phytoplankton compartment date from the 1980s. Several data on phytoplankton were collected during the period from 29 November to 02 December 2017 for addressing phytoplankton distribution and dynamics: pigmentary data, microscopic counts, metabarcoding analysis of plankton diversity, single-cell analysis and characterization of optical groups by automated (in vivo) flow cytometry (CytoSen) as well as in vivo characterization of spectral/pigmentary groups by multispectral fluorometry (Fluoroprobe). Environmental data was supplied by CTD RBR concerto and the analysis of several physical and chemical parameters. In particular, FluoroProbe continuous subsurface measurements and profiles made it possible to considerably improve the spatial and temporal resolution of measurements and the dynamics of phytoplankton groups at submesoscale. Moreover, it was possible to follow spatial and temporal changes in the phytoplankton community, particularly at stations sampled twice at few days interval. Many unknown species characterized this period, especially in the nanophytoplankton size range. Distinct communities were found in the upwelling on the coastal fringe and in the old waters offshore, as shown by multispectral analysis. Phytoplankton blooms were observed, some of which being caused by the upwelling of cold water, but intermittently and weakly. In some stations, toxic species were found, such as species belonging to the genus Pseudo-Nitzschia. Keywords: Upwelling, multi-spectral fluorometry, CTD, automated flow cytometry, metabarcoding, microscopy, phytoplankton diversity and dynamics.

Saharan dust represents more than 50% of the total desert dust emitted around the globe and its radiative effect significantly affects the atmospheric circulation at a continental scale. Atmospheric models often fail to represent the dust vertical distribution and the Saharan Air Layer. They underestimate the effects of deep convection on the vertical transport and of the role of scavenging on the confinement of dust aerosols in this layer. Using multi-year simulations performed with a variable-resolution climate model and processed-based analysis, we show that scavenging in deep convection and further re-evaporation of dusty rainfall in the lower troposphere are critical processes for explaining the vertical distribution of desert dust. They play a key role in maintaining a well-defined dust layer with sharp transition at the top of the SAL and in establishing the seasonal cycle of dust distribution.

The epoch of the Anthropocene, a period during which human activity has been the dominant influence on climate and the environment, has witnessed a decline in oxygen concentrations and an expansion of oxygen-depleted environments in both coastal and open ocean systems since the middle of the 20th century. This paper provides a review of system-specific drivers of low oxygen in a range of case studies representing marine systems in the open ocean, on continental shelves, in enclosed seas and in the coastal environment. Identification of similar and contrasting responses within and across system types and corresponding oxygen regimes is shown to be informative both in understanding and isolating key controlling processes and provides a sound basis for predicting change under anticipated future conditions. Case studies were selected to achieve a balance in system diversity and global coverage. Each case study describes system attributes, including the present-day oxygen environment and known trends in oxygen concentrations over time. Central to each case study is the identification of the physical and biogeochemical processes that determine oxygen concentrations through the tradeoff between ventilation and respiration. Spatial distributions of oxygen and time series of oxygen data provide the opportunity to identify trends in oxygen availability and have allowed various drivers of low oxygen to be distinguished through correlative and causative relationships. Deoxygenation results from a complex interplay of hydrographic and biogeochemical processes and the superposition of these processes, some additive and others subtractive, makes attribution to any particular driver challenging. System-specific models are therefore required to achieve a quantitative understanding of these processes and of the feedbacks between processes at varying scales.

Omega-3 long-chain polyunsaturated fatty acids (hereafter, omega-3), including eicosapentaenoic-acid (EPA) and docosahexaenoic-acid (DHA), are essential nutritional compounds for humans, providing several benefits related to cardiovascular and neural health. Human intake of omega-3 occurs mostly via seafood, particularly fish. The primary source of omega-3 in aquatic systems is represented by primary producers, from which omega-3 are transferred throughout the food web. Nitrogen is an essential nutrient for primary producers and can be supplied to surface waters as nitrate upwelled from below, or as ammonium and other regenerated nitrogen forms recycled in situ . Eastern Boundary Upwelling Systems (EBUS) are the most productive marine systems on Earth, together covering only 2% of the ocean’s surface area but supporting 25% of the global fish catch, thereby providing food for humans. In EBUS, nitrate and other nutrients are advected to the surface to support the proliferation of a phytoplankton community dominated by known omega-3 producers (i.e., diatoms). Given current climate change-related projections of ocean warming, acidification, deoxygenation, and increased upwelling intensity, phytoplankton community composition in EBUS may change. Additionally, the global production of EPA + DHA is expected to decrease by up to 30%, rendering its supply for human consumption insufficient by 2050. Here we discuss the state of knowledge related to omega-3 transfer from phytoplankton to small pelagic fish in EBUS, including factors that can influence omega-3 production, links to nitrogen cycling, climate change implications for the omega-3 supply to humans, and suggestions for future research directions to improve our understanding of omega-3 in the ocean.

Particularly interesting because of its socio-economic contribution, the Canary upwelling system encompasses a number of regions with very special characteristics. The wind that blow over this system induces a permanent upwelling off Mauritania and a seasonal upwelling in the south off Senegal, which boosts the development of phytoplankton. To refine the understanding of the phytoplankton in this region (its distribution, variability, response to physical forcings), we combine a number of tools and methods to arrive at a better estimate, and a better monitoring of the concentration of chlorophyll-a (Chl-a), an input parameter for primary production models. Remote sensing of ocean color has particularly interesting advantages, both in terms of global sampling and data acquisition frequency. This method is all the more interesting since ocean color algorithms can be adapted to reduce bias when standard methods have limitations. The regional ocean color algorithm called SOM-NV (Self-Organized Map-Neuro-variational) offers the advantage of making atmospheric correction in the presence of absorbent aerosols, especially desert dust, which sweeps this area permanently and which compels the standard algorithm to apply a mask when atmospheric optical thickness exceeds a threshold of 0.3. This contribution of SOM-NV in the process of atmospheric correction allowed us to 1 : obtain a better reflectance spectra, and as a consequence offer a better estimate of the Chl-a concentrations ; 2 : acquire a larger number of pixels by processing pixels with an optical thickness greater than 0.3 ; 3 : go beyond the general distribution towards the distribution of dominant groups according to the Physat spectral method. The synthesis of 16 years of data from the MODIS-Aqua sensor, allowed us to revisit the seasonality of Chl-a distribution and its cross-shore particularityand an extension towards the open sea which differs according to the season. The highest coastal values are measured in winter and spring, when upwelling intensifies, while the lowest values are measured in summer, when warm, nutrient-poor equatorial waters freplace upwelling waters along the Senegalese coast. This change in water masses impacts phytoplankton communities. According to the work of some authors, nanoplankton gradually replaces diatoms, known to be present during the upwelling season. This makes this region a particularly interesting zone for monitoring dominant groups of phytoplankton, knowing that the change in community impacts the upper levels of the marine food chain, with phytoplankton playing a leading role. Keywords: Phytoplankton, ocean color, upwelling, atmospheric correction, dust

The Canary Current is a potential hotspot for climate change impacts on the oceans where 63 million people depend upon marine resources for national economies and livelihoods. Their unique vulnerability highlights the key roles of climate services and capacity building in order to develop effective adaptation measures.

In West Africa, as in many other estuaries, enormous volumes of marine water are entering the continent. Fresh water discharge is very low, and it is commonly strongly linked to rainfall level. Some of these estuaries are inverse estuaries. During the Great Sahelian Drought (1968–1993), their hyperhaline feature was exacerbated. This paper aims to describe the evolution of the two main West African inverse estuaries, those of the Saloum River and the Casamance River, since the end of the drought. Water salinity measurements were carried out over three to five years according to the sites in order to document this evolution and to compare data with the historical ones collected during the long dry period at the end of 20th century. The results show that in both estuaries, the mean water salinity values have markedly decreased since the end of the drought. However, the Saloum estuary remains a totally inverse estuary, while for the Casamance River, the estuarine turbidity maximum (ETM) is the location of the salinity maximum, and it moves according to the seasons from a location 1–10 km downwards from the upstream estuary entry, during the dry season, to a location 40–70 km downwards from this point, during the rainy season. These observations fit with the functioning of the mangrove, the West African mangrove being among the few in the world that are markedly increasing since the beginning of the 1990s and the end of the dry period, as mangrove growth is favored by the relative salinity reduction. Finally, one of the inverse estuary behavior factors is the low fresh water incoming from the continent. The small area of the Casamance and Saloum basins (20,150 and 26,500 km² respectively) is to be compared with the basins of their two main neighbor basins, the Gambia River and the Senegal River, which provide significant fresh water discharge to their estuary.

The Westward transport of mineral dust from the North Africa continent to Atlantic Ocean can produce poor air quality, low visibilities, and negatively impacting respiratory and cardiac health due to the optical and physical properties of aerosols. The dynamical impact of the sea-breeze on the dust vertical distribution in West Africa remains unknown. To investigate this issue, we have used in-situ measurements from lidar. We have focused on the attenuated backscatter of aerosols to study the effect of the local circulation on the vertical profile of mineral dust at land-sea transition. The results highlight a strong diurnal cycle of mineral dust associated with the nocturnal low-level jet (NLLJ). The jet is located between 500 m and 1000 m and crucially affected by the dynamic of the sea-breeze circulation.

Bioaccumulation of toxic metal elements including mercury (Hg) can be highly variable in marine fish species. Metal concentration is influenced by various species-specific physiological and ecological traits, including individual diet composition and foraging habitat. The impact of trophic ecology and habitat preference on Hg accumulation was analyzed through total Hg concentration and stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) in the muscle of 132 fish belonging to 23 different species from the Senegalese coast (West Africa), where the marine ecosystem is submitted to nutrient inputs from various sources such as upwelling or rivers. Species-specific ecological traits were first investigated and results showed that vertical (i.e. water column distribution) and horizontal habitat (i.e. distance from the coast) led to differential Hg accumulation among species. Coastal and demersal fish were more contaminated than offshore and pelagic species. Individual characteristics therefore revealed an increase of Hg concentration in muscle that paralleled trophic level for some locations. Considering all individuals, the main carbon source was significantly correlated with Hg concentration, again revealing a higher accumulation for fish foraging in nearshore and benthic habitats. The large intraspecific variability observed in stable isotope signatures highlights the need to conduct ecotoxicological studies at the individual level to ensure a thorough understanding of mechanisms driving metal accumulation in marine fish. For individuals from a same species and site, Hg variation was mainly explained by fish length, in accordance with the bioaccumulation of Hg over time. Finally, Hg concentrations in fish muscle are discussed regarding their human health impact. No individual exceeded the current maximum acceptable limit for seafood consumption set by both the European Union and the Food and Agriculture Organization of the United Nations. However, overconsumption of some coastal demersal species analyzed here could be of concern regarding human exposure to mercury.

Small pelagic fish (SPF) species are heavily exploited in eastern boundary upwelling systems (EBUS) as their transformation products are increasingly used in the world's food chain. Management relies on regular monitoring, but there is a lack of robust theories for the emergence of the populations' traits and their evolution in highly variable environments. This work aims to address existing knowledge gaps by combining physical and biogeochemical modelling with an individual life-cycle based model applied to round sardinella (Sardinella aurita) off northwest Africa, a key species for regional food security. Our approach focused on the processes responsible for seasonal migrations, spatio-temporal size-structure, and interannual biomass fluctuations. Emergence of preferred habitat resulted from interactions between natal homing behavior and environmental variability that impacts early life stages. Exploration of the environment by the fishes was determined by swimming capabilities, mesoscale to regional habitat structure, and horizontal currents. Fish spatio-temporal abundance variability emerged from a complex combination of distinct life-history traits. An alongshore gradient in fish size distributions is reported and validated by in situ measurements. New insights into population structure are provided, within an area where the species is abundant year-round (Mauritania) and with latitudinal migrations of variable (300-1200 km) amplitude. Interannual biomass fluctuations were linked to modulations of fish recruitment over the Sahara Bank driven by variability in alongshore current intensity. The identified processes constitute an analytical framework that can be implemented in other EBUS and used to explore impacts of regional climate change on SPF.

The impact of desert aerosols on climate, atmospheric processes, and the environment is still debated in the scientific community. The extent of their influence remains to be determined and particularly requires a better understanding of the variability of their distribution. In this work, we studied the variability of these aerosols in western Africa using different types of satellite observations. SeaWiFS (Sea-Viewing Wide Field-of-View Sensor) and OMI (Ozone Monitoring Instrument) data have been used to characterize the spatial distribution of mineral aerosols from their optical and physical properties over the period 2005–2010. In particular, we focused on the variability of the transition between continental western African and the eastern Atlantic Ocean. Data provided by the lidar scrolling CALIOP (Cloud-Aerosol Lidar with Orthogonal Polarization) onboard the satellite CALIPSO (Cloud Aerosol Lidar and Infrared Pathfinder Satellite Observations) for the period 2007–2013 were then used to assess the seasonal variability of the vertical distribution of desert aerosols. We first obtained a good representation of aerosol optical depth (AOD) and single-scattering albedo (SSA) from the satellites SeaWiFS and OMI, respectively, in comparison with AERONET estimates, both above the continent and the ocean. Dust occurrence frequency is higher in spring and boreal summer. In spring, the highest occurrences are located between the surface and 3 km above sea level, while in summer the highest occurrences are between 2 and 5 km altitude. The vertical distribution given by CALIOP also highlights an abrupt change at the coast from spring to fall with a layer of desert aerosols confined in an atmospheric layer uplifted from the surface of the ocean. This uplift of the aerosol layer above the ocean contrasts with the winter season during which mineral aerosols are confined in the atmospheric boundary layer. Radiosondes at Dakar Weather Station (17.5° W, 14.74° N) provide basic thermodynamic variables which partially give a causal relationship between the layering of the atmospheric circulation over western Africa and their aerosol contents throughout the year. A SSA increase is observed in winter and spring at the transition between the continent and the ocean. The analysis of mean NCEP (National Centers for Environmental Prediction) winds at 925 hPa between 2000 and 2012 suggest a significant contribution of coastal sand sources from Mauritania in winter which would increase SSA over the ocean.

Senegal is the southern tip of the Canary upwelling system. Its coastal ocean hosts an upwelling center which shapes sea surface temperatures between latitudes 12° and 15°N. Near this latter latitude, the Cape Verde headland and a sudden change in shelf cross‐shore profile are major sources of heterogeneity in the southern Senegal upwelling sector (SSUS). SSUS dynamics is investigated by means of Regional Ocean Modeling System simulations. Configuration realism and resolution (Δx≈ 2 km) are sufficient to reproduce the SSUS frontal system. Our main focus is on the 3‐D upwelling circulation which turns out to be profoundly different from 2‐D theory: cold water injection onto the shelf and upwelling are strongly concentrated within a few tens of kilometers south of Cape Verde and largely arise from flow divergence in the alongshore direction; a significant fraction of the upwelled waters are retained nearshore over long distances while travelling southward under the influence of northerly winds. Another source of complexity, regional‐scale alongshore pressure gradients, also contributes to the overall retention of upwelled waters over the shelf. Varying the degree of realism of atmospheric and oceanic forcings does not appreciably change these conclusions. This study sheds light on the dynamics and circulation underlying the recurrent sea surface temperature pattern observed during the upwelling season and offers new perspectives on the connections between the SSUS physical environment and its ecosystems. It also casts doubt on the validity of upwelling intensity estimations based on simple Ekman upwelling indices at such local scales.