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  • European Marine Science
  • 2018-2022
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Harid, Romaissa; Demarcq, Herve; Houma, Fouzia;

    {"references": ["Cotroneo, Y., Aulicino, G., Ruiz, S., Pascual, A., Budillon, G., Fusco, G., Tintor\u00e9, J. (2016). Glider and satellite high resolution monitoring of a mesoscale eddy in the algerian basin: Effects on the mixed layer depth and biochemistry. Journal of Marine Systems, 162: 73- 88. https://doi.org/10.1016/j.jmarsys.2015.12.004", "Cotroneo, Y., Celentano, P., Aulicino, G., Perilli, A., Olita, A., Falco, P., Sorgente, R., Ribotti, A., Budillon, G., Fusco, G., Pessini, F. (2021). Connectivity Analysis Applied to Mesoscale Eddies in the Western Mediterranean Basin. Remote Sensing, 13: 4228. https://doi.org/10.3390/rs13214228", "Cullen, J.J. (1982). The Deep Chlorophyll Maximum: Comparing Vertical Profiles of Chlorophyll a. Can. J. Fish. Aquat. Sci., 39: 791- 803. https://doi.org/10.1139/f82-108", "Doney, S.C. (2006). Plankton in a warmer world. Nature, 444: 695-696. https://doi.org/10.1038/444695a", "D'Ortenzio, F., Ribera d'Alcal\u00e0, M. (2009). On the trophic regimes of the Mediterranean Sea: a satellite analysis. Biogeosciences: 139-148. https://doi.org/10.5194/bg-6-139-2009", "Hafen, R. (2016). Package 'stlplus', Enhanced Seasonal Decomposition of Time Series by Loess, in: CRAN.", "Harid, R. (2022). \u00c9tude par t\u00e9l\u00e9d\u00e9tection et mesures in situ des efflorescences algales et de la mati\u00e8re en suspension dans le Bassin Alg\u00e9rien (These de doctorat). ENSSMAL, Alger.", "Harid, R., Ait Kaci, M., Keraghel, M.A., Zerrouk\u0131, M., Houma-Bachari, F. (2018). Seasonal and Interannual Variability of Primary Production and Chlorophyll Concentrations in the Algerian Basin: Application of Ocean Color. In: Kallel, A., Ksibi, M., Ben Dhia, H., Kh\u00e9lifi, N. (Eds.), Recent Advances in Environmental Science from the EuroMediterranean and Surrounding Regions, Advances in Science, Technology & Innovation. Springer International Publishing, Cham: 1641-1643. https://doi.org/10.1007/978-3-319-70548- 4_475", "Harid, R., Demarcq, H., Keraghel, M.-A., Ait-Kaci, M., Zerrouki, M., Bachari, N.-E.-I., Houma, F. (2022). Spatio-temporal variability of a chlorophyll-a based biomass index and influence of coastal sources of enrichment in the Algerian Basin. Continental Shelf Research, 232: 104629. https://doi.org/10.1016/j.csr.2021.104629", "Huot, Y., Babin, M., Bruyant, F., Grob, C., Twardowski, M.S., Claustre, H. (2007). Relationship between photosynthetic parameters and different proxies of phytoplankton biomass in the subtropical ocean. Biogeosciences, 4: 853-868. https://doi.org/10.5194/bg-4- 853-2007", "Keraghel, M.A., Louanchi, F., Zerrouki, M., A\u00eft Kaci, M., A\u00eft-Ameur, N., Labaste, M., Legoff, H., Taillandier, V., Harid, R., Mortier, L. (2020). Carbonate system properties and anthropogenic carbon inventory in the Algerian Basin during SOMBA cruise (2014): Acidification estimate. Marine Chemistry, 221: 103783. https://doi.org/10.1016/j.marchem.2020.103783", "Mayot, N., D'Ortenzio, F., Ribera d'Alcal\u00e0, M, M., Lavigne, H., Claustre, H. (2016). Interannual variability of the Mediterranean trophic regimes from ocean color satellites. Biogeosciences, 13: 1901- 1917. https://doi.org/10.5194/bg-13-1901-2016", "Millot, C. (1985). Some features of the Algerian Current. Journal of Geophysical Research: Oceans, 90: 7169-7176. https://doi. org/10.1029/JC090iC04p07169", "Millot, C. (1999). Circulation in the Western Mediterranean Sea. Journal of Marine Systems, 20: 423-442. https://doi.org/10.1016/S0924-7963(98)00078-5", "Millot, C., Candela, J., Fuda, J.-L., Tber, Y. (2006). Large warming and salinification of the Mediterranean outflow due to changes in its composition. Deep Sea Research Part I: Oceanographic Research, 53: 656-666. https://doi.org/10.1016/j.dsr.2005.12.017", "Millot, C., Taupier-Letage, I. (2005). Circulation in the Mediterranean Sea. Hdb Env Chem, 5: 38. https://doi.org/DOI10.1007/b107143", "Millot, C., Taupier-Letage, I., Benzohra, M. (1990). The Algerian eddies. Earth-Science Reviews, 27: 203-219. https://doi.org/10.1016/0012- 8252(90)90003-E", "Mobley, C. (1994). Light and Water: Radiative Transfer in Natural Waters. Academic Press 2.", "Moutin, T., Prieur, L. (2012). Influence of anticyclonic eddies on the Biogeochemistry from the Oligotrophic to the Ultraoligotrophic Mediterranean (BOUM cruise). Biogeosciences, 9: 3827-3855. https://doi.org/10.5194/bg-9-3827-2012", "NASA's Ocean Color Web (2019). Available online: http://oceancolor.gsfc.nasa.gov/ (accessed on 29 October 2019) [WWW Document]. URL https://oceancolor.gsfc.nasa.gov/ (accessed 10.29.19).", "Obaton, D. (1998). Circulation et mod\u00e9lisation de la M\u00e9diterran\u00e9e Occidentale et du Golfe du Lion - Synth\u00e8se des connaisssances et des travaux existants", "Olita, A., Sorgente, R., Ribotti, A., Fazioli, L., Perilli, A. (2011). Pelagic primary production in the Algero-Proven\u00e7al Basin by means of multisensor satellite data: focus on interannual variability and its drivers. Ocean Dynamics, 61: 1005-1016. https://doi.org/10.1007/s10236-011-0405-8", "O'Reilly, J.E., Maritorena, S., Siegel, D., O'Brien, M.C., Toole, D., Mitchell, B.G., Kahru, M., Chavez, F., Strutton, P., Cota, G.F., Hooker, S., McClain, C.R., Carder, K.L., M\u00fcller, W.A., Harding, L., Magnuson, A., Phinney, D., Moore, G.F., Aiken, J., Arrigo, K.R., Letelier, R., Culver, M. (2000). Ocean Color Chlorophyll a Algorithms for SeaWiFS, OC2, and OC4: Version 4. In: Volume 11, SeaWiFS Postlaunch Calibration and Validation Analyses, Part 3, SeaWiFS Postlaunch Technical Report Series. USA.", "Perrot, L., Gohin, F., Ruiz-Pino, D., Lampert, L. (2016). Seasonal and interannual variability of coccolithophore blooms in the North East-Atlantic Ocean from a 18-year time-series of satellite water-leaving radiance (preprint). Remote Sensing/Biological Processes/Surface/Shelf Seas. https://doi.org/10.5194/os-2016- 13", "Pessini, F., Cotroneo, Y., Olita, A., Sorgente, R., Ribotti, A., Jendersie, S., Perilli, A. (2020). Life history of an anticyclonic eddy in the Algerian basin from altimetry data, tracking algorithm and in situ observations. Journal of Marine Systems, 207: 103346. https://doi.org/10.1016/j.jmarsys.2020.103346", "Pessini, F., Olita, A., Cotroneo, Y., Perilli, A. (2018). Mesoscale eddies in the Algerian Basin: do they differ as a function of their formation site? Ocean Science, 14: 669-688. https://doi.org/10.5194/os-14- 669-2018", "Raimbault, P., Coste, B., Boulhadid, M., Boudjellal, B. (1993). Origin of high phytoplankton concentration in deep chlorophyll maximum (DCM) in a frontal region of the Southwestern Mediterranean Sea (algerian current). Deep Sea Research Part I: Oceanographic Research Papers, 40: 791-804. https://doi.org/10.1016/0967- 0637(93)90072-B", "Salgado-Hernanz, P.M., Racault, M.-F., Font-Mu\u00f1oz, J.S., Basterretxea, G. (2019). Trends in phytoplankton phenology in the Mediterranean Sea based on ocean-colour remote sensing. Remote Sensing of Environment, 221: 50-64. https://doi.org/10.1016/j.rse.2018.10.036", "Strickland, J. (1965). Production of organic matter in primary stages of themarine food chain. In: Chemical Oceanography, Academic Press, London, edited by: J. P. Riley and G. Skirrow. Chemical Oceanography, Academic Press: 477-610.", "Taupier-Letage, Millot, C. (1988). Surface circulation in the Algerian basin during 1984. Oceanologia Acta, 9: 79-85. https://archimer.ifremer.fr/doc/00267/37811"]} NASA (National Aeronautics and Space Administration) has acquired to the present-day data on the temporal and spatial distribution of chlorophyll-a (Chl-a) biomass from the Moderate-Resolution Imaging Spectroradiometer (MODIS) Aqua sensor for ocean color. In our work, the daily Chl-a biomass was estimated from the MODIS product OC3M bio-optical standard algorithm. The Seasonal-Trend decomposition of time series based on Loess (STL) identified the temporal variability of the dynamical features in the MODIS products for Chl-a concentration time series in the Algerian Basin (AB) surface waters. The STL has the specificity to identify seasonal components changing over the time series composition, perfectly detects the presence of outliers, and is responsive to nonlinear trends. In the current work, this method was applied to a time series of 16 years in AB (Southwestern Mediterranean Sea) at 120 km offshore [0 to 120 km]. Decomposing the MODIS products into a trend, seasonal, and remainder components, the Chl-a indicated the dominance of the seasonal components with 108.7% from 2003 to 2018. Furthermore, interannual seasonal variation for Chl-a biomass showed the influence of the same sources of enrichment each year in the Algerian Basin.

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    Authors: Dorrell, Richard; Liang, Yue; Gueguen, Nolwenn; Nonoyama, Tomomi; +11 Authors

    Abstract Organic carbon fixed through the Calvin Cycle can be diverted towards different metabolic fates within and beyond the plastids of photosynthetic eukaryotes. These include export to the cytoplasm and mitochondrial respiration; gluconeogenesis of storage compounds; and the anabolic synthesis of lipids, amino acids and cofactors via the plastidial pyruvate hub. In plants, pyruvate is principally synthesised via the lower half of glycolysis-gluconeogenesis in the cytoplasm, although a secondary plastid-targeted pathway in non-photosynthetic tissue directly links glyceraldehyde-3-phosphate to the pyruvate hub. Here, we characterize a complete plastidial lower half glycolytic-gluconeogenic pathway in the photosynthetic plastids of diatoms, obligately photosynthetic eukaryotic algae that are important contributors to marine primary production. We show that the two enzymes required to complete plastidial glycolysis-gluconeogenesis, plastidial Enolase and PGAM ( bis -phospho-glycerate mutase), originated through recent duplications of mitochondria-targeted respiratory glycolytic isoforms. Through CRISPR-Cas9 mutagenesis and integrative ‘omic analyses in the diatom Phaeodactylum tricornutum , we present evidence that this pathway functions to divert excess plastidial glyceraldehyde-3-phosphate into diverse fates accessed from the pyruvate hub, and may potentially also function in the gluconeogenic direction to permit more efficient management of cellular carbon. Considering meta-genomic data, we show that this pathway is of greater importance in polar and sub-polar oceans, in which diatoms dominate primary production; and considering experimental data, we show that this principally relates to the elongated photoperiods present at high latitudes. Our data provide insights into the functions of a poorly understood yet evolutionarily recurrent plastidial metabolic pathway, and a further explanation for the success of diatoms in the contemporary ocean.

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    Authors: Briottet, Xavier; Bajjouk, Touria; Chami, Malik; Delacourt, Christophe; +12 Authors

    L'imagerie hyperspectrale a démontré son intérêt pour la caractérisation des propriétés biochimiques, biophysiques et structurelles de la végétation, des sols naturels et agricoles ainsi que des surfaces artificialisées. A la suite de la mission Hyperion, de nouvelles missions spatiales ont vu le jour (PRISMA, EnMAP), ou sont en phase d'étude (SBG, CHIME). Ces spectro-imageurs ont une résolution spatiale au sol de l'ordre de 30 m, un large champ de vue et peuvent couvrir de vastes zones du globe terrestre afin de caractériser les écosystèmes terrestres et océaniques avec un temps de revisite variant de 4 à 16 jours. Néanmoins, leur résolution spatiale est limitée ce qui induit un nombre important de pixels mixtes réduisant leur potentiel de discrimination pour des zones hétérogènes. La mission BIODIVERSITY a pour objectif de compléter ces missions par des acquisitions de meilleure résolution spatiale (typiquement 8-10 m) avec une revisite de l'ordre de 5 jours sur des sites de référence ciblés possédant des caractéristiques identifiées et bien localisées. Elle permettra ainsi de répondre à deux problématiques scientifiques qui vont dimensionner l'instrument. La première problématique porte sur la distribution spatiale et temporelle des traits de la végétation dans les assemblages d'espèces ; ces traits sont associés à la résilience des écosystèmes terrestres, aux influences anthropiques et à la biodiversité des écosystèmes en termes de composition et d'assemblages en espèces. La seconde problématique porte sur l'amélioration de nos connaissances des zones côtières et des eaux continentales en termes de biodiversité, de qualité des eaux et de bathymétrie, pour ensuite évaluer l'impact de l'activité anthropique sur leurs écosystèmes. Enfin, ces deux applications qui déterminent les spécifications de l'instrument seront complétées par l'étude, à fine résolution spatiale, de l'impact des pratiques de gestion des sols dans un processus environnemental tels que le stockage du carbone dans les sols, l'infiltration et la rétention d'eau en surface ou l'érosion des sols. Elles ouvrent également de nouvelles voies pour évaluer comment les matériaux urbains influencent notre environnement proche et pour caractériser les pollutions urbaine et industrielle. Les défis scientifiques ainsi que les exigences-utilisateurs pour une telle mission sont présentés pour chaque application. Imaging spectroscopy has demonstrated its interest in characterizing the biochemical, biophysical and structural properties of vegetation, natural and agricultural soils, as well as artificial surfaces. Following the Hyperion mission, new space missions have emerged (PRISMA, EnMap), or are under study (CHIME, SBG). However, one of their main limitations lies in their spatial resolution that induces a large number of mixed pixels reducing their potential for discrimination for very heterogeneous areas. The BIODIVERSITY mission aims to complement these space missions with better GSD acquisitions (typically 8-10 m) with a 5-day revisit on targeted reference sites with identified and well-located characteristics. It will thus make it possible, in particular, to answer two scientific issues that will design the instrument. The first issue concerns the spatial and temporal distribution of vegetation traits in species assemblages; these traits are associated with the resilience of terrestrial ecosystems, anthropogenic influences, and the biodiversity of ecosystems in terms of species composition and assemblages. The second issue relates to improving our knowledge of coastal areas and inland waters in terms of biodiversity, water quality and bathymetry, in order to assess the impact of human activity on their ecosytems. The scientific challenges as well as the user requirements for such a mission are presented for each application. International audience

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    Authors: Manca, Eleonora;

    This report details the collaborative effort between partners from Europe and China to deliver the first broad-scale habitat map for a Chinese sea basin, using the EUNIS (European Nature Information System) approach, as part of Task 4.1 of the joint EMOD-PACE/CEMDNET project. Broad-scale habitat models can be useful in data poor regions and, provide a full spatial coverage dataset on the distribution of habitat types, for very large areas (basin wide, national water, European waters) for application such as marine spatial planning or marine protected sites network assessments. EUNIS (European Nature Information System) broad-scale habitat map provide a first general picture of the variety and general types of physical habitats at the seabed and should be based on good understanding of key physical variables that drive the distribution of characteristics benthic communities. The present report introduces the first broad-scale habitat map in an Asian sea basin, based on the EMODnet habitat mapping approach, and associated confidence datasets. The case study site selected for this work covers part of the Beibu Gulf, located in the north-western parts of the South China Sea. We include a summary of the methodology used, as well as a presentation the habitat map, its input layers and associated confidence assessments. Furthermore, we discuss limitations of the approach, applicability to Chinese sea basins and propose the next steps to improve in this work.

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    Authors: Schwab, Romain; Le Roy, Ronan; Marion, Claire; Debese, Nathalie; +1 Authors

    Jedes Jahr schließen rund 60 hochqualifizierte Hydrographen ihre Ausbildung an den französischen Institutionen ENSTA Bretagne, Cnam Intechmer und Shom/UBO ab. Diese sich ergänzenden Ausbildungen decken sowohl den zivilen als auch den militärischen Bedarf ab. Die Vermessungspraxis ist ein zentraler Bestandteil der Ausbildung, um die Studierenden schnell in der Berufswelt einsetzen zu können. In diesem Paper werden die wichtigsten von den einzelnen Schulen durchgeführten Feldarbeiten beschrieben, bei denen die Studierenden technische Fähigkeiten erwerben. Um den hohen Bedarf an Personal und Ausrüstung zu decken, arbeiten die französischen Einrichtungen aktiv zusammen. Insbesondere gibt es einige Brücken zwischen Bildungsprogrammen und auch einen globaleren Austausch von Fachwissen und Materialien. Les établissements français à savoir l’ENSTA Bretagne, Cnam Intechmer et le Shom/UBO forment chaque année une soixantaine d’hydrographes. Ces formations complémentaires répondent à la fois aux besoins civils et militaires. La composante pratique de la formation est fondamentale pour rendre ces futurs diplômés rapidement opérationnels dans le monde du travail. Ce papier présente un projet terrain d’envergure propre à chaque école dans lequel les étudiants développent leurs expertises techniques. Pour faire face aux besoins importants tant en termes d’encadrement que de matériel, les instituts collaborent activement entre eux. Il existe ainsi des passerelles inter-établissements sur la formation, et des partages de compétence sur les enjeux actuels et futurs de l’hydrographie Every year, around 60 highly-qualified hydrographers graduate from the French institutions ENSTA Bretagne, Cnam Intechmer and Shom/UBO. These complementary teachings address both civilian and military demands. The survey practice is a key part of the training which ensure students’ ability to be quickly operational in the professional world. This paper outlines major fieldwork conducted by each school, where trainees acquire technical skills. To face these growing needs in terms of staff and equipment, French facilities actively cooperate. In particular, there are some bridges between educational programmes and also more global expertise and materials sharing.

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    Authors: Lemane, Téo;

    Le 21ème siècle subit un tsunami de données dans de nombreux domaines, notamment en bio-informatique. Ce changement de paradigme nécessite le développement de nouvelles méthodes de traitement capables de passer à l’échelle sur de telles données. Ce travail consiste principalement à considérer des jeux de données massifs provenant du séquençage génomique. Une façon courante de traiter ces données est de les représenter comme un ensemble de mots de taille fixe, appelés k-mers. Les k-mers sont très largement utilisés comme éléments de bases par de nombreuses méthodes d’analyses de données de séquençages. L’enjeu est de pouvoir représenter les k-mers et leurs abondances dans un grand nombre de jeux de données. Une possibilité est la matrice de k-mers, où chaque ligne est un k-mer associé à un vecteur d’abondances. Ces k-mers sont erronées en raison des erreurs de séquençage et doivent être filtrés. La technique habituelle consiste à écarter les k-mers peu abondants. Sur des ensembles de données complexes comme les métagénomes, un tel filtre n’est pas efficace et élimine un trop grand nombre de k-mers. La vision des abondances à travers les échantillons permise par la représentation matricielle permet également une nouvelle procédure de détection des erreurs dans les jeux de données complexes. En résumé, nous explorons le concept de matrice de k-mer et montrons ses capacités en termes de passage à l’échelle au travers de diverses applications, de l’indexation à l’analyse, et proposons différents outils à cette fin. Sur le plan de l’indexation, nos outils ont permis d’indexer un grand ensemble métagénomique du projet Tara Ocean tout en conservant des k-mers rares, habituellement écartés par les techniques de filtrage classiques. En matière d’analyse, notre technique de construction de matrices permet d’accélérer d’un ordre de grandeur l’analyse différentielle de k-mers. The 21st century is bringing a tsunami of data in many fields, especially in bioinformatics. This paradigm shift requires the development of new processing methods capable of scaling up on such data. This work consists mainly in considering massive tera-scaled datasets from genomic sequencing. A common way to process these data is to represent them as a set of words of a fixed size, called k-mers. The k-mers are widely used as building blocks by many sequencing data analysis techniques. The challenge is to be able to represent the k-mers and their abundances in a large number of datasets. One possibility is the k-mer matrix, where each row is a k-mer associated with a vector of abundances and each column corresponds to a sample. Some k-mers are erroneous due to sequencing errors and must be discarded. The usual technique consists in discarding low-abundant k-mers. On complex datasets such as metagenomes, such a filter is not efficient and discards too many k-mers. The holistic view of abundances across samples allowed by the matrix representation also enables a new procedure for error detection on such datasets. In summary, we explore the concept of k-mer matrix and show its scalability in various applications, from indexing to analysis, and propose different tools for this purpose. On the indexing side, our tools have allowed indexing a large metagenomic dataset from the Tara Ocean project while keeping additional k-mers, usually discarded by the classical k-mer filtering technique. The next and important step is to make the index publicly available. On the analysis side, our matrix construction technique enables to speed up a differential k-mer analysis of a state-of-the-art tool by an order of magnitude.

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    Authors: Gnede, Shade; Dayoub, Amal; Hassan, Mohamad;

    The present study aimed at isolating ectoparasite species and blood-sucking parasite- affecting wild Mugil cephalus and Scomber scombrus, and evaluating the impact of infection on the chemical composition of their muscles. A total of 238 individuals of M. cephalus and 224 of S. scombrus were captured from Syrian marine waters (Eastern Mediterranean) through two years, from April 2020 to April 2022. Fish samples were examined for infection, and parasites were isolated according to the wet smears method and identified at species level. Chemical composition: proteins, fats, moisture and ash contents of muscle of two species studied were determined. Variations of these different components in the infected and non-infected samples, and according to months or season, age and sex were assessed. Results showed the infection of M. cephalus by Ligophorus mediterraneus, Ergenstrema sp. (Monogenea) and Caligus pageti (Copepoda), whereas, only one ectoparasite species: Kuhnia scombri (Monogenea) was identified from S. scombrus. This is actually the first record of Ergenstrema sp; C. pageti and K. scombri in the two species studied in Syrian marine waters. This is also the first record of Ergenstrema sp. in wild M. cephalus in the world. No significant differences in the content of moisture, protein and ash were observed between the infected and non-infected fish. Nevertheless, fat content has showed a significant (P-value <0.05) decrease in the samples infected by the blood-sucking parasites- (i.e. C. pageti and K. scombri) in both species studied. In addition, significant differences of the chemical composition according to season and age were also found, but not between females and males.

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    Authors: Alglave, Baptiste;

    La cartographie de la répartition des espèces d’intérêts halieutiques et l’identification de leurs zones fonctionnelles est cruciale pour assurer le renouvellement des espèces et pour l’aménagement de l’espace marin. Pour autant, la localisation des habitats essentiels des poissons, et plus particulièrement des frayères, reste incertaine pour de nombreuses espèces exploitées. Les données de référence pour cartographier la distribution des espèces exploitées et identifier leurs frayères sont issues de campagnes scientifiques qui bénéficient d’un protocole d’échantillonnage standardisé. Ces campagnes ont généralement lieu une ou deux fois par an, elles prélèvent un nombre limité d’échantillons et elles peuvent ne pas correspondre à la période de reproduction des espèces étudiées. Elles sont donc limitées pour identifier les frayères des espèces d’intérêt halieutique. Par ailleurs, les déclarations de capture des pêcheurs (logbook) fournissent des informations sur l’ensemble de l’année avec une densité d’échantillonnage supérieure à celle des données scientifiques. En les combinant aux données de géolocalisation des navires disponibles par le système de surveillance des navires de pêche (VMS), les données de déclarations peuvent permettre de compléter l’information apportée par les données de campagne. Dans cette thèse, nous avons développé un modèle statistique qui permet de combiner les données commerciales et scientifiques pour inférer la distribution des espèces d’intérêt halieutique à une résolution spatio-temporelle fine. Le modèle permet de prendre en compte le comportement de ciblage des pêcheurs (échantillonnage préférentiel) et d’intégrer les données de déclarations qui sont définies à une résolution spatiale grossière pour inférer la distribution des espèces à une résolution fine (changement de support). Les cartes de la distribution des espèces permettent d’identifier les zones d’agrégation pendant la saison de reproduction. Nous décrivons également les applications potentielles du cadre de modélisation pour l’aménagement de l’espace marin et les extensions qui pourraient être ajoutées à la version actuelle du modèle Mapping fish distribution and identifying fish essential habitats grounds is key to ensure species renewal and manage the marine space. Information on the location of fish essential habitats and specifically of fish spawning grounds is still lacking for many harvested species. The reference data to map fish distribution and identify spawning grounds are scientific survey data. These data benefit from a standardized sampling protocol. However, due to their costs, they also generally suffer from a low sampling density in space and time. In particular, they generally occur once or twice a year and they may mismatch fish reproduction. Commercial declarations combined with Vessel Monitoring System data could prove highly valuable to complement the information brought by scientific survey data as fishermen landings provide information on the full year with a much denser sampling density. In this PhD, we developed an integrated statistical framework that allows to combine commercial and scientific data sources to infer fish distribution in space and time. Our approach accounts for fishermen targeting behavior towards areas of higher biomass (preferential sampling) and allows to infer fine scale species distribution based on spatially aggregated declarations data (change of support). We demonstrate the ability of the framework to produce monthly maps of fish distribution and to identify aggregation areas during reproduction season. We also outline the potential applications of the framework for Marine Spatial Planning and discuss several extensions that could be added to the actual model.

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  • Authors: Bazin, Simon; Hemmer-Brepson, Claire; Logez, Maxime; Sentis, Arnaud; +1 Authors

    The reduction of body size with warming has been proposed as the third universal response to global warming, besides geographical and phenological shifts. Observed body size shifts in ectotherms are mostly attributed to the temperature size rule (TSR) stating that warming speeds up initial growth rate but leads to smaller adult size when food availability does not limit growth. Nevertheless, climate warming can decrease food availability by modifying biochemical cycles and primary production. The interactive effects of temperature and food availability on life history traits have been studied in small invertebrate species, but we have limited information on how temperature and food availability jointly influence life history traits in vertebrate predators, despite the observation that TS responses are amplified in larger species. Food availability can also influence growth, fecundity and survival and thus potentially modulate the effect of temperature on life history strategies. In this paper, we filled this gap by investigating under laboratory conditions the independent and interactive effects of temperature (20 or 30 °C) and food availability (restricted or ad libitum) on the growth, fecundity and survival of the medaka fish Oryzias latipes. Our results confirm that warming leads to a higher initial growth rate and lower adult size leading to crossed growth curves between the two temperatures. Food-restricted fish were smaller than ad libitum fed fish throughout the experiment, leading to nested growth curves. In addition, food restriction appears to amplify TSR by decreasing initial growth rate in the cold treatment. Fish reared at 30 °C matured younger, had smaller size at maturity, had a higher fecundity but had a shorter life span than fish reared at 20 °C, suggesting a "live fast die young" strategy under warming. Food restriction increased the survival probability under both temperature conditions corresponding to a "eat little die old" strategy. Finally, food restriction appeared to be advantageous as food restriction largely increased survival while have a weaker negative effect on growth and fecundity and no impact on age and size at maturity. Our results highlight the importance of accounting for the interaction between temperature and food availability to understand body size shifts. This is of importance in the context of global warming as resources (e.g., phytoplankton and zooplankton communities in aquatic ecosystems) are predicted to change in size structure and total abundance with increasing temperatures. Furthermore, we highlight the importance of considering ontogeny when investigating the effects of temperature-induced body size shifts on trophic interactions and community dynamics since thermal effects depend on the life stage of the organisms.

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    Authors: Alban, Frederique; Leonardi, Sophie; Le Floc H, Pascal;

    La question posée porte sur la capacité d’adaptation des halles à marée face aux fluctuations de l’offre et des cours du poisson dans le contexte des confinements en 2020. Le chiffre d’affaires national des premiers marchés a décliné de 18 % par rapport à la moyenne des trois années précédentes. La méthode de décomposition du chiffre d’affaires démontre que la valeur des productions traduit une stratégie de quantité et plus rarement une action sur les prix. Des enquêtes auprès des responsables de halles à marée apportent une lecture complémentaire, voire différente de celle des statistiques de vente. La discussion des résultats soulève d’une part le risque de biais informationnel pour une analyse limitée à une approche quantitative, d’autre part la menace potentielle des ventes directes sur les halles à marée. The question raised concerns the capacity of the fish markets to adapt to the fluctuations in supply and fish prices caused by the first confinement and amplified by the second in 2020. The national turnover of the first markets declined by 18 % compared to the average of the previous three years. The method of breaking down turnover shows that the value of production reflects a strategy on quantity and more rarely a price policy. Surveys of fish market managers provide a complementary even different understanding to that of the sales statistics. The discussion of the results raises two major questions. The first deals with the informational bias when the analysis is limited to a quantitative approach to production statistics. The second is the question of the potential threat of direct sales to fish markets.

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    Authors: Harid, Romaissa; Demarcq, Herve; Houma, Fouzia;

    {"references": ["Cotroneo, Y., Aulicino, G., Ruiz, S., Pascual, A., Budillon, G., Fusco, G., Tintor\u00e9, J. (2016). Glider and satellite high resolution monitoring of a mesoscale eddy in the algerian basin: Effects on the mixed layer depth and biochemistry. Journal of Marine Systems, 162: 73- 88. https://doi.org/10.1016/j.jmarsys.2015.12.004", "Cotroneo, Y., Celentano, P., Aulicino, G., Perilli, A., Olita, A., Falco, P., Sorgente, R., Ribotti, A., Budillon, G., Fusco, G., Pessini, F. (2021). Connectivity Analysis Applied to Mesoscale Eddies in the Western Mediterranean Basin. Remote Sensing, 13: 4228. https://doi.org/10.3390/rs13214228", "Cullen, J.J. (1982). The Deep Chlorophyll Maximum: Comparing Vertical Profiles of Chlorophyll a. Can. J. Fish. Aquat. Sci., 39: 791- 803. https://doi.org/10.1139/f82-108", "Doney, S.C. (2006). Plankton in a warmer world. Nature, 444: 695-696. https://doi.org/10.1038/444695a", "D'Ortenzio, F., Ribera d'Alcal\u00e0, M. (2009). On the trophic regimes of the Mediterranean Sea: a satellite analysis. Biogeosciences: 139-148. https://doi.org/10.5194/bg-6-139-2009", "Hafen, R. (2016). Package 'stlplus', Enhanced Seasonal Decomposition of Time Series by Loess, in: CRAN.", "Harid, R. (2022). \u00c9tude par t\u00e9l\u00e9d\u00e9tection et mesures in situ des efflorescences algales et de la mati\u00e8re en suspension dans le Bassin Alg\u00e9rien (These de doctorat). ENSSMAL, Alger.", "Harid, R., Ait Kaci, M., Keraghel, M.A., Zerrouk\u0131, M., Houma-Bachari, F. (2018). Seasonal and Interannual Variability of Primary Production and Chlorophyll Concentrations in the Algerian Basin: Application of Ocean Color. In: Kallel, A., Ksibi, M., Ben Dhia, H., Kh\u00e9lifi, N. (Eds.), Recent Advances in Environmental Science from the EuroMediterranean and Surrounding Regions, Advances in Science, Technology & Innovation. Springer International Publishing, Cham: 1641-1643. https://doi.org/10.1007/978-3-319-70548- 4_475", "Harid, R., Demarcq, H., Keraghel, M.-A., Ait-Kaci, M., Zerrouki, M., Bachari, N.-E.-I., Houma, F. (2022). Spatio-temporal variability of a chlorophyll-a based biomass index and influence of coastal sources of enrichment in the Algerian Basin. Continental Shelf Research, 232: 104629. https://doi.org/10.1016/j.csr.2021.104629", "Huot, Y., Babin, M., Bruyant, F., Grob, C., Twardowski, M.S., Claustre, H. (2007). Relationship between photosynthetic parameters and different proxies of phytoplankton biomass in the subtropical ocean. Biogeosciences, 4: 853-868. https://doi.org/10.5194/bg-4- 853-2007", "Keraghel, M.A., Louanchi, F., Zerrouki, M., A\u00eft Kaci, M., A\u00eft-Ameur, N., Labaste, M., Legoff, H., Taillandier, V., Harid, R., Mortier, L. (2020). Carbonate system properties and anthropogenic carbon inventory in the Algerian Basin during SOMBA cruise (2014): Acidification estimate. Marine Chemistry, 221: 103783. https://doi.org/10.1016/j.marchem.2020.103783", "Mayot, N., D'Ortenzio, F., Ribera d'Alcal\u00e0, M, M., Lavigne, H., Claustre, H. (2016). Interannual variability of the Mediterranean trophic regimes from ocean color satellites. Biogeosciences, 13: 1901- 1917. https://doi.org/10.5194/bg-13-1901-2016", "Millot, C. (1985). Some features of the Algerian Current. Journal of Geophysical Research: Oceans, 90: 7169-7176. https://doi. org/10.1029/JC090iC04p07169", "Millot, C. (1999). Circulation in the Western Mediterranean Sea. Journal of Marine Systems, 20: 423-442. https://doi.org/10.1016/S0924-7963(98)00078-5", "Millot, C., Candela, J., Fuda, J.-L., Tber, Y. (2006). Large warming and salinification of the Mediterranean outflow due to changes in its composition. Deep Sea Research Part I: Oceanographic Research, 53: 656-666. https://doi.org/10.1016/j.dsr.2005.12.017", "Millot, C., Taupier-Letage, I. (2005). Circulation in the Mediterranean Sea. Hdb Env Chem, 5: 38. https://doi.org/DOI10.1007/b107143", "Millot, C., Taupier-Letage, I., Benzohra, M. (1990). The Algerian eddies. Earth-Science Reviews, 27: 203-219. https://doi.org/10.1016/0012- 8252(90)90003-E", "Mobley, C. (1994). Light and Water: Radiative Transfer in Natural Waters. Academic Press 2.", "Moutin, T., Prieur, L. (2012). Influence of anticyclonic eddies on the Biogeochemistry from the Oligotrophic to the Ultraoligotrophic Mediterranean (BOUM cruise). Biogeosciences, 9: 3827-3855. https://doi.org/10.5194/bg-9-3827-2012", "NASA's Ocean Color Web (2019). Available online: http://oceancolor.gsfc.nasa.gov/ (accessed on 29 October 2019) [WWW Document]. URL https://oceancolor.gsfc.nasa.gov/ (accessed 10.29.19).", "Obaton, D. (1998). Circulation et mod\u00e9lisation de la M\u00e9diterran\u00e9e Occidentale et du Golfe du Lion - Synth\u00e8se des connaisssances et des travaux existants", "Olita, A., Sorgente, R., Ribotti, A., Fazioli, L., Perilli, A. (2011). Pelagic primary production in the Algero-Proven\u00e7al Basin by means of multisensor satellite data: focus on interannual variability and its drivers. Ocean Dynamics, 61: 1005-1016. https://doi.org/10.1007/s10236-011-0405-8", "O'Reilly, J.E., Maritorena, S., Siegel, D., O'Brien, M.C., Toole, D., Mitchell, B.G., Kahru, M., Chavez, F., Strutton, P., Cota, G.F., Hooker, S., McClain, C.R., Carder, K.L., M\u00fcller, W.A., Harding, L., Magnuson, A., Phinney, D., Moore, G.F., Aiken, J., Arrigo, K.R., Letelier, R., Culver, M. (2000). Ocean Color Chlorophyll a Algorithms for SeaWiFS, OC2, and OC4: Version 4. In: Volume 11, SeaWiFS Postlaunch Calibration and Validation Analyses, Part 3, SeaWiFS Postlaunch Technical Report Series. USA.", "Perrot, L., Gohin, F., Ruiz-Pino, D., Lampert, L. (2016). Seasonal and interannual variability of coccolithophore blooms in the North East-Atlantic Ocean from a 18-year time-series of satellite water-leaving radiance (preprint). Remote Sensing/Biological Processes/Surface/Shelf Seas. https://doi.org/10.5194/os-2016- 13", "Pessini, F., Cotroneo, Y., Olita, A., Sorgente, R., Ribotti, A., Jendersie, S., Perilli, A. (2020). Life history of an anticyclonic eddy in the Algerian basin from altimetry data, tracking algorithm and in situ observations. Journal of Marine Systems, 207: 103346. https://doi.org/10.1016/j.jmarsys.2020.103346", "Pessini, F., Olita, A., Cotroneo, Y., Perilli, A. (2018). Mesoscale eddies in the Algerian Basin: do they differ as a function of their formation site? Ocean Science, 14: 669-688. https://doi.org/10.5194/os-14- 669-2018", "Raimbault, P., Coste, B., Boulhadid, M., Boudjellal, B. (1993). Origin of high phytoplankton concentration in deep chlorophyll maximum (DCM) in a frontal region of the Southwestern Mediterranean Sea (algerian current). Deep Sea Research Part I: Oceanographic Research Papers, 40: 791-804. https://doi.org/10.1016/0967- 0637(93)90072-B", "Salgado-Hernanz, P.M., Racault, M.-F., Font-Mu\u00f1oz, J.S., Basterretxea, G. (2019). Trends in phytoplankton phenology in the Mediterranean Sea based on ocean-colour remote sensing. Remote Sensing of Environment, 221: 50-64. https://doi.org/10.1016/j.rse.2018.10.036", "Strickland, J. (1965). Production of organic matter in primary stages of themarine food chain. In: Chemical Oceanography, Academic Press, London, edited by: J. P. Riley and G. Skirrow. Chemical Oceanography, Academic Press: 477-610.", "Taupier-Letage, Millot, C. (1988). Surface circulation in the Algerian basin during 1984. Oceanologia Acta, 9: 79-85. https://archimer.ifremer.fr/doc/00267/37811"]} NASA (National Aeronautics and Space Administration) has acquired to the present-day data on the temporal and spatial distribution of chlorophyll-a (Chl-a) biomass from the Moderate-Resolution Imaging Spectroradiometer (MODIS) Aqua sensor for ocean color. In our work, the daily Chl-a biomass was estimated from the MODIS product OC3M bio-optical standard algorithm. The Seasonal-Trend decomposition of time series based on Loess (STL) identified the temporal variability of the dynamical features in the MODIS products for Chl-a concentration time series in the Algerian Basin (AB) surface waters. The STL has the specificity to identify seasonal components changing over the time series composition, perfectly detects the presence of outliers, and is responsive to nonlinear trends. In the current work, this method was applied to a time series of 16 years in AB (Southwestern Mediterranean Sea) at 120 km offshore [0 to 120 km]. Decomposing the MODIS products into a trend, seasonal, and remainder components, the Chl-a indicated the dominance of the seasonal components with 108.7% from 2003 to 2018. Furthermore, interannual seasonal variation for Chl-a biomass showed the influence of the same sources of enrichment each year in the Algerian Basin.

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    Authors: Dorrell, Richard; Liang, Yue; Gueguen, Nolwenn; Nonoyama, Tomomi; +11 Authors

    Abstract Organic carbon fixed through the Calvin Cycle can be diverted towards different metabolic fates within and beyond the plastids of photosynthetic eukaryotes. These include export to the cytoplasm and mitochondrial respiration; gluconeogenesis of storage compounds; and the anabolic synthesis of lipids, amino acids and cofactors via the plastidial pyruvate hub. In plants, pyruvate is principally synthesised via the lower half of glycolysis-gluconeogenesis in the cytoplasm, although a secondary plastid-targeted pathway in non-photosynthetic tissue directly links glyceraldehyde-3-phosphate to the pyruvate hub. Here, we characterize a complete plastidial lower half glycolytic-gluconeogenic pathway in the photosynthetic plastids of diatoms, obligately photosynthetic eukaryotic algae that are important contributors to marine primary production. We show that the two enzymes required to complete plastidial glycolysis-gluconeogenesis, plastidial Enolase and PGAM ( bis -phospho-glycerate mutase), originated through recent duplications of mitochondria-targeted respiratory glycolytic isoforms. Through CRISPR-Cas9 mutagenesis and integrative ‘omic analyses in the diatom Phaeodactylum tricornutum , we present evidence that this pathway functions to divert excess plastidial glyceraldehyde-3-phosphate into diverse fates accessed from the pyruvate hub, and may potentially also function in the gluconeogenic direction to permit more efficient management of cellular carbon. Considering meta-genomic data, we show that this pathway is of greater importance in polar and sub-polar oceans, in which diatoms dominate primary production; and considering experimental data, we show that this principally relates to the elongated photoperiods present at high latitudes. Our data provide insights into the functions of a poorly understood yet evolutionarily recurrent plastidial metabolic pathway, and a further explanation for the success of diatoms in the contemporary ocean.

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    Authors: Briottet, Xavier; Bajjouk, Touria; Chami, Malik; Delacourt, Christophe; +12 Authors

    L'imagerie hyperspectrale a démontré son intérêt pour la caractérisation des propriétés biochimiques, biophysiques et structurelles de la végétation, des sols naturels et agricoles ainsi que des surfaces artificialisées. A la suite de la mission Hyperion, de nouvelles missions spatiales ont vu le jour (PRISMA, EnMAP), ou sont en phase d'étude (SBG, CHIME). Ces spectro-imageurs ont une résolution spatiale au sol de l'ordre de 30 m, un large champ de vue et peuvent couvrir de vastes zones du globe terrestre afin de caractériser les écosystèmes terrestres et océaniques avec un temps de revisite variant de 4 à 16 jours. Néanmoins, leur résolution spatiale est limitée ce qui induit un nombre important de pixels mixtes réduisant leur potentiel de discrimination pour des zones hétérogènes. La mission BIODIVERSITY a pour objectif de compléter ces missions par des acquisitions de meilleure résolution spatiale (typiquement 8-10 m) avec une revisite de l'ordre de 5 jours sur des sites de référence ciblés possédant des caractéristiques identifiées et bien localisées. Elle permettra ainsi de répondre à deux problématiques scientifiques qui vont dimensionner l'instrument. La première problématique porte sur la distribution spatiale et temporelle des traits de la végétation dans les assemblages d'espèces ; ces traits sont associés à la résilience des écosystèmes terrestres, aux influences anthropiques et à la biodiversité des écosystèmes en termes de composition et d'assemblages en espèces. La seconde problématique porte sur l'amélioration de nos connaissances des zones côtières et des eaux continentales en termes de biodiversité, de qualité des eaux et de bathymétrie, pour ensuite évaluer l'impact de l'activité anthropique sur leurs écosystèmes. Enfin, ces deux applications qui déterminent les spécifications de l'instrument seront complétées par l'étude, à fine résolution spatiale, de l'impact des pratiques de gestion des sols dans un processus environnemental tels que le stockage du carbone dans les sols, l'infiltration et la rétention d'eau en surface ou l'érosion des sols. Elles ouvrent également de nouvelles voies pour évaluer comment les matériaux urbains influencent notre environnement proche et pour caractériser les pollutions urbaine et industrielle. Les défis scientifiques ainsi que les exigences-utilisateurs pour une telle mission sont présentés pour chaque application. Imaging spectroscopy has demonstrated its interest in characterizing the biochemical, biophysical and structural properties of vegetation, natural and agricultural soils, as well as artificial surfaces. Following the Hyperion mission, new space missions have emerged (PRISMA, EnMap), or are under study (CHIME, SBG). However, one of their main limitations lies in their spatial resolution that induces a large number of mixed pixels reducing their potential for discrimination for very heterogeneous areas. The BIODIVERSITY mission aims to complement these space missions with better GSD acquisitions (typically 8-10 m) with a 5-day revisit on targeted reference sites with identified and well-located characteristics. It will thus make it possible, in particular, to answer two scientific issues that will design the instrument. The first issue concerns the spatial and temporal distribution of vegetation traits in species assemblages; these traits are associated with the resilience of terrestrial ecosystems, anthropogenic influences, and the biodiversity of ecosystems in terms of species composition and assemblages. The second issue relates to improving our knowledge of coastal areas and inland waters in terms of biodiversity, water quality and bathymetry, in order to assess the impact of human activity on their ecosytems. The scientific challenges as well as the user requirements for such a mission are presented for each application. International audience

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    Authors: Manca, Eleonora;

    This report details the collaborative effort between partners from Europe and China to deliver the first broad-scale habitat map for a Chinese sea basin, using the EUNIS (European Nature Information System) approach, as part of Task 4.1 of the joint EMOD-PACE/CEMDNET project. Broad-scale habitat models can be useful in data poor regions and, provide a full spatial coverage dataset on the distribution of habitat types, for very large areas (basin wide, national water, European waters) for application such as marine spatial planning or marine protected sites network assessments. EUNIS (European Nature Information System) broad-scale habitat map provide a first general picture of the variety and general types of physical habitats at the seabed and should be based on good understanding of key physical variables that drive the distribution of characteristics benthic communities. The present report introduces the first broad-scale habitat map in an Asian sea basin, based on the EMODnet habitat mapping approach, and associated confidence datasets. The case study site selected for this work covers part of the Beibu Gulf, located in the north-western parts of the South China Sea. We include a summary of the methodology used, as well as a presentation the habitat map, its input layers and associated confidence assessments. Furthermore, we discuss limitations of the approach, applicability to Chinese sea basins and propose the next steps to improve in this work.

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    Authors: Schwab, Romain; Le Roy, Ronan; Marion, Claire; Debese, Nathalie; +1 Authors

    Jedes Jahr schließen rund 60 hochqualifizierte Hydrographen ihre Ausbildung an den französischen Institutionen ENSTA Bretagne, Cnam Intechmer und Shom/UBO ab. Diese sich ergänzenden Ausbildungen decken sowohl den zivilen als auch den militärischen Bedarf ab. Die Vermessungspraxis ist ein zentraler Bestandteil der Ausbildung, um die Studierenden schnell in der Berufswelt einsetzen zu können. In diesem Paper werden die wichtigsten von den einzelnen Schulen durchgeführten Feldarbeiten beschrieben, bei denen die Studierenden technische Fähigkeiten erwerben. Um den hohen Bedarf an Personal und Ausrüstung zu decken, arbeiten die französischen Einrichtungen aktiv zusammen. Insbesondere gibt es einige Brücken zwischen Bildungsprogrammen und auch einen globaleren Austausch von Fachwissen und Materialien. Les établissements français à savoir l’ENSTA Bretagne, Cnam Intechmer et le Shom/UBO forment chaque année une soixantaine d’hydrographes. Ces formations complémentaires répondent à la fois aux besoins civils et militaires. La composante pratique de la formation est fondamentale pour rendre ces futurs diplômés rapidement opérationnels dans le monde du travail. Ce papier présente un projet terrain d’envergure propre à chaque école dans lequel les étudiants développent leurs expertises techniques. Pour faire face aux besoins importants tant en termes d’encadrement que de matériel, les instituts collaborent activement entre eux. Il existe ainsi des passerelles inter-établissements sur la formation, et des partages de compétence sur les enjeux actuels et futurs de l’hydrographie Every year, around 60 highly-qualified hydrographers graduate from the French institutions ENSTA Bretagne, Cnam Intechmer and Shom/UBO. These complementary teachings address both civilian and military demands. The survey practice is a key part of the training which ensure students’ ability to be quickly operational in the professional world. This paper outlines major fieldwork conducted by each school, where trainees acquire technical skills. To face these growing needs in terms of staff and equipment, French facilities actively cooperate. In particular, there are some bridges between educational programmes and also more global expertise and materials sharing.

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    Authors: Lemane, Téo;

    Le 21ème siècle subit un tsunami de données dans de nombreux domaines, notamment en bio-informatique. Ce changement de paradigme nécessite le développement de nouvelles méthodes de traitement capables de passer à l’échelle sur de telles données. Ce travail consiste principalement à considérer des jeux de données massifs provenant du séquençage génomique. Une façon courante de traiter ces données est de les représenter comme un ensemble de mots de taille fixe, appelés k-mers. Les k-mers sont très largement utilisés comme éléments de bases par de nombreuses méthodes d’analyses de données de séquençages. L’enjeu est de pouvoir représenter les k-mers et leurs abondances dans un grand nombre de jeux de données. Une possibilité est la matrice de k-mers, où chaque ligne est un k-mer associé à un vecteur d’abondances. Ces k-mers sont erronées en raison des erreurs de séquençage et doivent être filtrés. La technique habituelle consiste à écarter les k-mers peu abondants. Sur des ensembles de données complexes comme les métagénomes, un tel filtre n’est pas efficace et élimine un trop grand nombre de k-mers. La vision des abondances à travers les échantillons permise par la représentation matricielle permet également une nouvelle procédure de détection des erreurs dans les jeux de données complexes. En résumé, nous explorons le concept de matrice de k-mer et montrons ses capacités en termes de passage à l’échelle au travers de diverses applications, de l’indexation à l’analyse, et proposons différents outils à cette fin. Sur le plan de l’indexation, nos outils ont permis d’indexer un grand ensemble métagénomique du projet Tara Ocean tout en conservant des k-mers rares, habituellement écartés par les techniques de filtrage classiques. En matière d’analyse, notre technique de construction de matrices permet d’accélérer d’un ordre de grandeur l’analyse différentielle de k-mers. The 21st century is bringing a tsunami of data in many fields, especially in bioinformatics. This paradigm shift requires the development of new processing methods capable of scaling up on such data. This work consists mainly in considering massive tera-scaled datasets from genomic sequencing. A common way to process these data is to represent them as a set of words of a fixed size, called k-mers. The k-mers are widely used as building blocks by many sequencing data analysis techniques. The challenge is to be able to represent the k-mers and their abundances in a large number of datasets. One possibility is the k-mer matrix, where each row is a k-mer associated with a vector of abundances and each column corresponds to a sample. Some k-mers are erroneous due to sequencing errors and must be discarded. The usual technique consists in discarding low-abundant k-mers. On complex datasets such as metagenomes, such a filter is not efficient and discards too many k-mers. The holistic view of abundances across samples allowed by the matrix representation also enables a new procedure for error detection on such datasets. In summary, we explore the concept of k-mer matrix and show its scalability in various applications, from indexing to analysis, and propose different tools for this purpose. On the indexing side, our tools have allowed indexing a large metagenomic dataset from the Tara Ocean project while keeping additional k-mers, usually discarded by the classical k-mer filtering technique. The next and important step is to make the index publicly available. On the analysis side, our matrix construction technique enables to speed up a differential k-mer analysis of a state-of-the-art tool by an order of magnitude.

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    Authors: Gnede, Shade; Dayoub, Amal; Hassan, Mohamad;

    The present study aimed at isolating ectoparasite species and blood-sucking parasite- affecting wild Mugil cephalus and Scomber scombrus, and evaluating the impact of infection on the chemical composition of their muscles. A total of 238 individuals of M. cephalus and 224 of S. scombrus were captured from Syrian marine waters (Eastern Mediterranean) through two years, from April 2020 to April 2022. Fish samples were examined for infection, and parasites were isolated according to the wet smears method and identified at species level. Chemical composition: proteins, fats, moisture and ash contents of muscle of two species studied were determined. Variations of these different components in the infected and non-infected samples, and according to months or season, age and sex were assessed. Results showed the infection of M. cephalus by Ligophorus mediterraneus, Ergenstrema sp. (Monogenea) and Caligus pageti (Copepoda), whereas, only one ectoparasite species: Kuhnia scombri (Monogenea) was identified from S. scombrus. This is actually the first record of Ergenstrema sp; C. pageti and K. scombri in the two species studied in Syrian marine waters. This is also the first record of Ergenstrema sp. in wild M. cephalus in the world. No significant differences in the content of moisture, protein and ash were observed between the infected and non-infected fish. Nevertheless, fat content has showed a significant (P-value <0.05) decrease in the samples infected by the blood-sucking parasites- (i.e. C. pageti and K. scombri) in both species studied. In addition, significant differences of the chemical composition according to season and age were also found, but not between females and males.

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