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Over the past years, a large number of new approaches in the domain of ocean-color have been developed, leading to a variety of innovative descriptors for phytoplankton communities. One of these methods, named PHYSAT, currently allows for the qualitative detection of five main phytoplankton groups from ocean-color measurements. Even though PHYSAT products are widely used in various applications and projects, the approach is limited by the fact it identifies only dominant phytoplankton groups. This current limitation is due to the use of biomarker pigment ratios for establishing empirical relationships between \textit{in-situ} information and specific ocean-color radiance anomalies in open ocean waters. However, theoretical explanations of PHYSAT suggests that it could be possible to detect more than dominance cases but move more towards phytoplanktonic assemblage detection. Thus, to evaluate the potential of PHYSAT for the detection of phytoplankton assemblages, we took advantage of the Continuous Plankton Recorder (CPR) survey, collected in both the English Channel and the North Sea. The available CPR dataset contains information on diatom abundance in two large areas of the North Sea for the period 1998-2010. {Using this unique dataset, recurrent diatom assemblages were retrieved based on classification of CPR samples}. Six diatom assemblages were identified \textit{in-situ}, \textcolor{blue}{each having indicators taxa or species}. Once this first step was completed, the \textit{in-situ} analysis was used to empirically associate the diatom assemblages with specific PHYSAT spectral anomalies. This step was facilitated by the use of previous classifications of regional radiance anomalies in terms of shape and amplitude, coupled with phenological tools. Through a matchup exercise, three CPR assemblages were associated \textcolor{blue}{with} specific radiance anomalies. The maps of detection of these specific radiances anomalies are in close agreement with current \textit{in-situ} ecological knowledge.

International audience; PurposeMarine mangrove sediments in the Manche-à-Eau lagoon (Guadeloupe, Caribbean Sea) harbor locally extensive, white microbial mats. These mats cover the surface of reduced sediments near the roots of red mangrove trees, Rhizophora mangle, and are mainly composed of sulfur-oxidizing bacteria belonging to the Beggiatoaceae family, with some filamentous cyanobacteria. The goal of this study was to investigate the possible influence of sediment characteristics on the presence of these microbial mats.Materials and methodsFour push cores were collected in April 2013, two from zones with microbial mats and two from zones without mats. Sediment characteristics (grain-size distribution, mineralogy, total organic carbon (TOC) and total nitrogen (TN) contents, atomic TOC/TN ratios, and organic matter (OM) δ13C values) were compared for all four cores.Results and discussionSignificant differences were observed between sediments below microbial mats and those without mats. Sediments with microbial mats contained greater amounts of clay, and higher TOC, TN, and TOC/TN ratios, with lower total carbonate content and δ13C values. The higher clay content most likely results from lower fluid flow velocity near to mangrove roots, while higher TOC/TN ratios and lower δ13C values indicate higher inputs of OM from mangrove trees. These results are consistent with the fact that microbial mats were observed near the roots of mangrove trees, which trap OM from terrestrial vegetation and fine sediments.ConclusionsThe grain-size distribution of sediment particles, the total carbonate content, and the δ13C values are the main parameters discriminating between zones with microbial mats and those without mats. Variations in total carbonate content, which is mainly of biogenic origin, result from conditions that are more favorable for benthic organisms in zones without microbial mats. Variations of the TOC/TN ratios are controlled by the presence of a non-negligible amount of inorganic nitrogen bound to surface clay mineral particles and/or by microbial processes.

International audience; From 1998 to 2011, the effects of environmental conditions on the spatial and temporal trends of sardine and sardinella catch rates in the Mauritanian waters were investigated using generalized additive models. Two models were used: a global model and an oceanographic model. The global models explained more of the variability in catch rates (60.4% for sardine and 40% for sardinella) than the oceanographic models (42% for sardine and 32.4% for sardinella). Both species showed clear and inverse seasonal variations in abundances corresponding to their main spawning activities and the hydrologic seasons off the Mauritanian waters. Sardine prefer colder waters and seem to occupy the ‘gap’ in the northern part of the Mauritanian waters as soon as sardinella has left the area because of to lower water temperatures. Unlike sardinella, sardine showed a gradual southward extension between 2002 and 2009. The oceanographic model revealed that a high proportion of catch variability for the two species could be explained by environmental variables. The main environmental parameters explaining the variability are sea surface temperature (SST) and the upwelling index for sardinella, and the chlorophyll-a (Chl-a) concentration, the upwelling index and SST for sardine. The sardinella spatio-temporal variations off Mauritania seem to be more controlled by thermal than productivity gradients, probably linked to the species physiological constraints (thermal tolerance) whereas sardine seems to be more controlled by an ‘optimal upwelling and temperature’ windows. The results presented herein may be useful for understanding the movement of these species along the Mauritanian coast and hence their management under a changing climate.

Spatio-temporal patterns of the chlorophyll- a concentration, Chla , have been assessed from the MEdium Resolution Imaging Spectrometer (MERIS) over the whole Vietnamese coastal waters from 2002 to 2012. For that purpose, six bio-optical algorithms already documented and based on different approaches have been tested over a large in situ data set collected at different seasons and locations along the Vietnamese coast. The OC5 algorithm (Gohin, Druon, and Lampert, 2002) presents the best performances and has been selected to assess Chla in the studied region. The notion of optimal bio-optical environment associated with the best performance of OC5 has been introduced. For suspended particulate matter concentration, SPM , lower than 100 g·m − 3 , and colored dissolved organic matter, a cdom (443), lower than 0.5 m − 1 , Chla is estimated with an uncertainty of 36% and a bias of 5%. A Chla climatology has been generated and the temporal patterns (seasonal variability, long term trend, and irregular component) have been described using the Census-X-11 time series decomposition method. Three-dimensional hydrodynamical numerical simulations have been used to analyze the spatio-temporal patterns of Chla . The seasonal contribution dominates the variance of the signal, in good relationship with the dynamic of the mixed layer depth as well as with the occurrence of a seasonal upwelling induced by the summer monsoon. The irregular variability of Chla which may reach up to 35% of the total variance in the central part of the Vietnamese coast, can be explained through the surface kinetic energy and its standard deviation which is associated with small scales processes. A long term monotonic trend from about 2 to > 5%·yr − 1 (that is 20 to > 50% from 2002 to 2012) have been noticed in different coastal areas where aquaculture activities exhibit a concurrence increase, ranging from 31% to 113% (in production weight) over the same time period. In situ measurements, and especially of nutrients, are however necessary to confirm the link between aquaculture activities and phytoplankton biomass long term evolutions.

International audience; The European sardine, Sardina pilchardus, exhibits a complex population structure, which has produced conflicting results in previous genetic studies. Despite its importance in the fisheries industry, stock delineation for management and conservation purposes is still a matter of debate throughout the distribution range of the species. This study examines whether otolith shapes are more efficient than genetic markers to detect population structure in pelagic species with large population sizes. Sardines were analyzed from 15 sampling localities in the Northeast Atlantic and Mediterranean Sea covering almost the whole distribution range of the species. A combination of otolith shape indices and elliptic Fourier descriptors was investigated by multivariate statistical procedures. Within the studied area, three distinct groups were identified with an overall correct classification of 77%. Group A: northern Mediterranean Sea and Gulf of Gabès; group B: Atlantic Morocco–south Alboran–Algero-provençal coasts; and group C: European Atlantic coast. The Almeria–Oran front and the Gibraltar strait are not an efficient barrier for sardine population separation as there seems to be exchanges between populations of the south-western Mediterranean Sea and those of the Moroccan Atlantic Ocean coast or Gulf of Cadiz. The results are discussed in relation to environmental conditions, oceanographic features, and physical barriers to dispersal in the study area, and compared with those obtained by previous genetic, morphometric, and meristic data. For pelagic species with high gene flow, present results highlighted the need to take into account the identification of phenotypic stocks to ensure sustainable fishery benefits and efficient conservation as they may have unique demographic properties and responses to exploitation.

International audience; Phytoplankton observation in the ocean can be a challenge in oceanography. Accurate estimations of its biomass and dynamics will help to understand ocean ecosystems and refine global climate models. Relevant data sets of phytoplankton defined at a functional level and on a sub-meso-and daily scale are thus required. In order to achieve this, an automated, high-frequency, dedicated scanning flow cytometer (SFC, Cytobuoy b.v., the Netherlands) has been developed to cover the entire size range of phytoplankton cells whilst simultaneously taking pictures of the largest of them. This cytometer was directly connected to the water inlet of a PocketFerryBox during a cruise in the North Sea, 08–12 May 2011 (DYMAPHY project, INTERREG IV A " 2 Seas "), in order to identify the phytoplankton community structure of near surface waters (6 m) with a high spatial resolution basis (2.2 ± 1.8 km). Ten groups of cells, distinguished on the basis of their optical pulse shapes, were described (abundance, size estimate, red fluorescence per unit volume). Abundances varied depending on the hydrological status of the traversed waters, reflecting different stages of the North Sea blooming period. Comparisons between several techniques analysing chlorophyll a and the scanning flow cytometer, using the integrated red fluorescence emitted by each counted cell, showed significant correlations. For the first time, the community structure observed from the automated flow cytometry data set was compared with PHYSAT reflectance anomalies over a daily scale. The number of matchups observed between the SFC automated high-frequency in situ sampling and remote sensing was found to be more than 2 times better than when using traditional water sampling strategies. Significant differences in the phyto-plankton community structure within the 2 days for which matchups were available suggest that it is possible to label PHYSAT anomalies using automated flow cytometry to resolve not only dominant groups but also community structure .

International audience; Remote sensing of ocean color is a powerful tool for monitoring phytoplankton in the ocean with a high spatial and temporal resolution. Several methods were developed in the past years for detecting phytoplankton functional types from satellite observations. In this paper, we present an automatic classification method based on a neural network clustering algorithm in order to classify the anomalies of water leaving radiance spectra (Ra), introduced in the PHYSAT method by Alvain et al. (2005), and analyze their variability at the global scale. The use of an unsupervised classification aims at improving the characterization of the spectral variability of Ra in terms of shape and amplitude as well as the expansion of its potential use to larger in situ datasets for global phytoplankton remote sensing. The Self-Organizing Map algorithm (SOM, Kohonen, 1984) aggregates similar spectra into a reduced set of pertinent groups, allowing the characterization of the Ra variability, which is known to be linked with phytoplankton community composition (Alvain et al., 2012). Based on the same sample of Ra spectra, a comparison between the previous version of PHYSAT (Alvain et al., 2005, 2008) and the new one using SOM shows that it is now possible to take into consideration all the types of spectra. This was not possible with the previous approach, based on thresholds, defined in order to avoid overlaps between the spectral signatures of each phytoplankton group. The SOM-based method is relevant for characterizing a wide variety of Ra spectra through its ability to handle large amounts of data, in addition to its statistical reliability and processing speed compared to the previous PHYSAT. The former approach might have introduced potential biases and thus, its extension to larger databases was very restricted. This is not the case with the new statistical design presented in this work. In the second step, some new Ra spectra have been related to phytoplankton groups using collocated field pigment inventories from a large in situ database. Phytoplankton groups were identified based on biomarker pigment ratio thresholds taken from the literature. SOM was then applied to the global daily SeaWiFS (Sea-viewing Wide Field-of-view Sensor) imagery archive between 1997 and 2010. Global distributions of major phytoplankton groups were analyzed and validated against in situ data. Thanks to its ability to capture a wide range of spectra and to manage a larger in situ pigment dataset, the neural network tool allows to classify a much higher number of pixels (2 times more) than the previous PHYSAT method for the five phytoplankton groups taken into account in this study (Synechococcus-like-cyanobacteria, diatoms, Prochlorococcus, Nanoeucaryotes and Phaeocystis-like). In addition, different Ra spectral signatures have been associated to diatoms. These signatures are located in various environments where the inherent optical properties affecting the Ra spectra are likely to be significantly different. Local phenomena such as diatom blooms in the upwelling regions or during climatic events (i.e. La Niña) are more clearly visible with the new method.

International audience; Knowledge on absorption by colored dissolved organic matter, acdom, spatio-temporal variability in coastal areas is of fundamental importance in many field of researches related to biogeochemical cycles studies, coastal areas management, as well as land and water interactions in the coastal domain. A new method, based on the theoretical link between the vertical attenuation coefficient, Kd, and the absorption coefficient, has been developed to assess acdom. This method, confirmed from radiative transfer simulations and in situ measurements, and tested on an independent in situ data set (N = 126), allows acdom to be assessed with a Mean Relative Absolute Difference, MRAD, of 33% over two order of magnitude (from 0.01 to 1.16 m−1). In the frame of ocean color observation, Kd is not directly measured but estimated from the remote sensing reflectance, Rrs. Based on 109 satellite (SeaWiFS) and in situ coincident (i.e. match-up) data points acdom is retrieved with a MRAD value of 37%. This simple model generally presents slightly better performances than recently developed empirical or semi-analytical algorithms.

International audience; Particulate suspended matter concentration (SPM) were estimated over a 8 year time period (2002-2010) in the coastal waters of French Guiana from a regional algorithm applied to the MODIS monthly reflectance measurements. Comparison between SPOT images and MODIS-SPM maps revealed the strong spatio-temporal coupling between in water SPM and the dynamics of local (i.e. Kourou and Cayenne) mud banks. Highest MODIS SPM values (>13 g m−3 approximately) can be significantly associated with the subtidal part of the banks as well as to the related turbid plume. The migration of these mud banks induces strong interannual changes in SPM reaching up to 6% year−1 within increasing and decreasing patchy areas distributed alternatively along the coastline of French Guiana. Mud banks migration rates derived from MODIS SPM data reach in average about 2 km year−1 in agreement with previous studies. The MODIS time series have allowed for a detailed description of the seasonality and interannual variations in the in-water SPM loads. Seasonal changes in SPM are related to the onset of the trade wind season. Marked non-linear patterns including a sharp evolution in the SPM values around 2005 as well as additional high frequency modulations have been emphasized within the upward and downward SPM trend regions. Concurrent temporal variations in the frequency of northward swells (favoring mud banks migration and reworking) as well as interannual changes in the amount of sediment delivered by the Amazon River have been shown to play a major role in the SPM temporal patterns observed in the French Guiana coastal waters. Our results clearly demonstrate the advantage for ocean color data to describe mud banks dynamics through the assessment of in water SPM temporal variability.

International audience; Optical water types were identified from an in situ data set of concomitant biogeochemical and optical parameters collected in contrasted turbid coastal areas of the eastern English Channel, southern North Sea and French Guiana at different seasons (211 stations). Four optical classes have been defined using a clustering approach performed on the spectrally normalized reflectance spectra. Normalization of the reflectance spectra was carried out during the statistical analysis to emphasize the shape of the reflectances rather than their magnitude. Each optical water type is associated with a specific bio-optical environment, in agreement with previous works. Two classes present a very marked optical character, one being mostly determined by strong phytoplankton and dissolved material loads, and the other one by a high proportion of mineral particles. The two remaining classes are related to optically mixed situations although there are some differences in the relative proportion of particulate mineral material. Applying this optical typology to the SeaWiFS daily reflectance data, we emphasized the high representativeness of these 4 optical water types which allow to describe about two thirds of the reflectance spectra found within the development sites whatever the season. The adequacy of optical water type definition for monitoring the spatio-temporal variability of coastal water masses optical quality, which reflects the impact of biological and hydrodynamic processes occurring at different time scales (i.e. from high frequency to seasonal processes), has been demonstrated. The four optical classes' typology has been shown to remain highly representative at global scale. This underlines the effective optical vicinity of some parts of the coastal ocean during some periods of the year, in spite of the recognized high optical diversity of coastal waters. This further demonstrates the high pertinence of class-based approach for large scale coastal applications. Finally, the potential for class-based inversion algorithms for improving ocean color products retrieval, as well as the applicability of such class-specific algorithms with respect to satellite information have been illustrated from the estimation of the suspended matter concentration. This work provides very encouraging evidence of the potential and adequacy of class-based inversion methods for deriving bio-optical products in optically complex waters such as the coastal ocean.

The influences of physico-chemical and biological processes on dimethylsulfide (DMS) dynamics in the most oligotrophic subtropical zones of the global ocean were investigated. As metrics for the dynamics of DMS and the so-called ‘summer DMS paradox’ of elevated summer concentrations when surface chlorophyll a (Chl) and particulate organic carbon (POC) levels are lowest, we used the DMS-to-Chl and DMS-to-POC ratios in the context of three independent and complementary approaches. Firstly, field observations of environmental variables (such as the solar radiation dose, phosphorus limitation of phytoplankton and bacterial growth) were used alongside discrete DMS, Chl and POC estimates extracted from global climatologies (i.e., a ‘station based’ approach). We then used monthly climatological data for DMS, Chl, and POC averaged over the biogeographic province wherein a given oligotrophic subtropical zone resides (i.e., a ‘province based’ approach). Finally we employed sensitivity experiments with a new DMS module coupled to the ocean general circulation and biogeochemistry model PISCES to examine the influence of various processes in governing DMS dynamics in oligotrophic regions (i.e., a ‘model based’ approach). We find that the ‘station based’ and ‘province based’ approaches yield markedly different results. Interestingly, the ‘province based’ approach suggests the presence of a ‘summer DMS paradox’ in most all of the oligotrophic regions we studied. In contrast, the ‘station based’ approach suggests that the ‘summer DMS paradox’ is only present in the Sargasso Sea and eastern Mediterranean. Overall, we found the regional differences in the absolute and relative concentrations of DMS between 5 of the most oligotrophic regions of the world’s oceans were better accounted for by their nutrient dynamics (specifically phosphorus limitation) than by physical factors often invoked, e.g., the solar radiation dose. Our ‘model based’ experiments suggest that it is the limitation of phytoplankton/bacterial production and bacterial consumption of DMS by pervasive phosphorus limitation that is responsible for the ‘summer DMS paradox’.

Time series of chlorophyll-a concentration (chl a), backscattering coefficient at 490 nm (bbp(490)) and spectral slope of bbp (γ) derived from satellite imagery of ocean color were used to study the aquatic ecosystem of the Southern Yellow Sea during the time period of 1997–2007. Our study indicated that chl a increased in offshore waters by 0.02 mg m−3 y −1 (p < 0.05), in contrast to a decline observed in the middle and low-latitude global waters. bbp(490), a proxy of total suspended particulate matter concentration did not have any significant trend, while γ, a proxy of the relative proportion of small-sized and larger particles in the surface ocean, decreased significantly. Annual spring phytoplankton blooms occurred in nearshore and offshore waters of the central Southern Yellow Sea; while autumn blooms only occurred in nearshore waters.

The variability of inherent optical properties is investigated in the ultra-oligotrophic waters of the Mediterranean Sea sampled during the BOUM experiment performed during early summer 2008. Bio-optical relationships found for ultra-oligotrophic waters of the three anticyclonic gyres sampled significantly depart from the mean standard relationships provided for the global ocean, confirming the peculiar character of these Mediterranean waters. These optical anomalies are diversely related to the specific biological and environmental conditions occurring in the studied ecosystem. Specifically, the surface specific phytoplankton absorption coefficient exhibits values lower than those expected from the general relationships mainly in relation with a high contribution of relatively large sized phytoplankton. Conversely, the particulate backscattering coefficient, bbp, values are much higher than the mean standard values for a given chlorophyll-a concentration, TChl-a. This feature can presumably be related to the relevant influence of highly refractive submicrometer particles of Saharan origin in the surface layer of the water column. The present measurements also show that the Mediterranean Sea is greener than TChl-a alone indicates, as already stressed in previous studies. This color anomaly is partly explained by the estimated colored dissolved organic matter and submicrometer particles absorption coefficients, and to a greater extent by the high bbp/TChl-a values assuming that these particles backscatter light similarly in the green and blue parts of the visible spectrum. The diel variation of both the particulate matter attenuation and backscattering coefficients were also investigated specifically. Despite some differences in the timing and the magnitude of the daily oscillations found for these optical parameters, potential for the backscattering coefficient daily oscillation to be used, similarly to that for the attenuation coefficient, as a proxy for estimating carbon community production budget has been highlighted for the first time. This result is particularly relevant for present and future geostationary spatial ocean color missions.

Knowledge of the oceanic particulate organic carbon (POC) pool and of its spatio-temporal variability is important for understanding the oceanic carbon cycle. Until now, POC estimates from space have been restricted to the surface layer. An empirical algorithm is developed to derive the POC content integrated over the euphotic layer ( POC Zeu ) from the near-surface POC concentration ( POC surf ). The relationship follows a power-law distribution, POC Zeu = A × POC surf B , with A and B depending on the type of waters (stratified or well-mixed) and on the near-surface chlorophyll concentration. A global climatology of POC surf and POC Zeu is generated from the SeaWiFS archive between 1998 and 2006. The global patterns of POC surf and POC Zeu follow the major gyre systems and other large-scale circulation features. High surface and integrated POC content, around 150 mg m − 3 and 6000 mg m − 2 , are encountered at high latitude, whereas low content, 50 mg m − 3 and 2000 mg m − 2 , are observed in subtropical gyres. The mean global values of POC surf and POC Zeu over the global ocean are 53 mg m − 3 and 3742 mg m − 2 . The standing stocks of POC are 3.92 × 10 14 and 1.19 × 10 15 g over the first penetration and euphotic depth, respectively.

International audience; A methodology is proposed to infer the altitude of aerosol plumes over the ocean from reflectance ratio measurements in the O2 absorption A-band (759 to 770 nm). The reflectance ratio is defined as the ratio of the reflectance in a first spectral band, strongly attenuated by O2 absorption, and the reflectance in a second spectral band, minimally attenuated. For a given surface reflectance, simple relations are established between the reflectance ratio and the altitude of an aerosol layer, as a function of atmospheric conditions and the geometry of observation. The expected accuracy for various aerosol loadings and models is first quantified using an accurate, high spectral resolution, radiative transfer model that fully accounts for interactions between scattering and absorption. The method is developed for POLDER and MERIS, satellite sensors with adequate spectral characteristics. The simulations show that the method is only accurate over dark surfaces when aerosol optical thickness at 765 nm is relatively large (> 0.3). In this case, the expected accuracy is on the order of ± 0.5 km or ± 0.2 km for POLDER or MERIS respectively. More accurate estimates are obtained with MERIS, since in this case the spectral reflectance ratio is more sensitive to aerosol altitude. However, a precise spectral calibration is needed for MERIS. The methodology is applied to MERIS and POLDER imagery acquired over marine surfaces. The estimated aerosol altitude is compared with in situ lidar profiles of backscattering coefficient measured during the AOPEX-2004 experiment for MERIS, or obtained with the space-borne lidar CALIOP for POLDER. The retrieved altitudes agree with lidar measurements in a manner consistent with theory. These comparisons demonstrate the potential of the differential absorption methodology for obtaining information on aerosol altitude over dark surfaces