French Research Institute for Exploitation of the Sea
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Energetically consistent localised APE budgets for local and regional studies of stratified flow energetics
No full textBecause it allows a rigorous separation between reversible and irreversible processes, the concept of available potential energy (APE) has become central to the study of turbulent stratified fluids. In ocean modelling, it is fundamental to the parameterisation of meso-scale ocean eddies and of the turbulent mixing of heat and salt. However, how to apply APE theory consistently to local or regional subdomains has been a longstanding source of confusion due to the globally defined Lorenz reference state entering the definition of APE and of buoyancy forces being generally thought to be meaningless in those cases. In practice, this is often remedied by introducing heuristic `localised' forms of APE density depending uniquely on region-specific reference states, possibly diverging significantly from the global Lorenz reference state. In this paper, we argue that this practice is problematic because it cannot consistently describes the turbulent APE cascades associated with the inter-scale energy transfers between the APE produced at large scales -- which depends on the global Lorenz reference state -- and the APE of smaller scales. To avoid this difficulty, we argue that localised forms of APE density should be defined as the eddy APE component of an exact mean/eddy decomposition of the APE density. The eddy APE density thus defined exhibits a much weaker dependency on the global Lorenz reference state than the mean APE, in agreement with physical intuition, but with a different structure than that of existing heuristic localised APE forms. The results are important, because they establish a rigorous physical basis for linking parameterised energy transfers to observable viscous and diffusive dissipation rates, which is a pivotal goal of energetically consistent ocean models
Depositional environmental, provenance and climatic signatures of textural characteristics and heavy mineral distribution of the Vaigai river channel bed sediments, Southern India
No full textSurface sediments of the river channels provide a proxy to understand contemporary-paleoconditions of sedimentary environments, climate, provenance, etc. Systematic field mapping, and delineation of geological and geomorphic features was conducted, followed by collection of surface sediments from river channels. Laboratory analyses included granulometry, textural statistical parameters, and heavy mineral analysis of 53 sediment samples collected from the entire reach of the Vaigai River from upstream to downstream, the majority of them were coarse sand, moderately sorted, finely skewed and platykurtic. Barring a few aberrations, a gradual increase in roundness of the grains from the headwaters to the basin outlet is recorded in the present study. The transportation of sediments is characterized by suspension with rolling. Discriminant plots of environmental and energy conditions affiliate the studied sediments to the riverine environment and unidirectional flow except few. Recycling of valley?fill sediments and negligible?noticeable sorting, weak transport characteristics during normal flow and effective exhumation?erosion?deposition during significant flow conditions were interpreted. Among the heavy minerals, the ubiquitous occurrence of hornblende followed by garnet, magnetite, epidote, rutile, zircon, and monazite in the decreasing proportion is documented. Elemental abundances in the heavy minerals of samples from the upper part of the basin show no significant/noticeable enrichment/depletion characteristics, whereas the samples of the lower part of the basin show uniformly abundant Si. These data and interpretations suggests that the channel bed sediments are mostly reworked and recycled, probably influenced by the river?s flow on an antecedent valley and valley?fill. Within this general nature, aberrations are introduced by land use and other anthropogenic factors?imposed changes in sediment size, shape, sorting and heavy mineral occurrence and relative proportions
A summer in the greater Paris: trophic status of peri-urban lakes shapes prokaryotic community structure and functional potential
No full textWith more than 12 million inhabitants, the Greater Paris offers a “natural laboratory” to explore the effects of eutrophication on freshwater lake’s microbiomes within a relative restricted area (~ 70 km radius). Here, a 4-months survey was carried out during summertime to monitor planktonic microbial communities of nine lakes located around Paris (Île-de-France, France) of comparable morphologies, yet distinct trophic statuses from mesotrophic to hypereutrophic. By thus minimizing the confounding factors, we investigated how trophic status could influence prokaryotic community structures (16S rRNA gene sequencing) and functions (shotgun metagenomics). These freshwater lakes harbored highly distinct and diverse prokaryotic communities, and their trophic status appears as the main driver explaining both differences in community structure and functional potential. Although their gene pool was quite stable and shared among lakes, taxonomical and functional changes were correlated. According to trophic status, differences in phosphorus metabolism-related genes were highlighted among the relevant functions involved in the biogeochemical cycles. Overall, hypereutrophic lakes microbiomes displayed the highest contrast and heterogeneity over time, suggesting a specific microbial regime shift compared to eutrophic and mesotrophic lakes
Genèse d’un suivi scientifique à long terme pour documenter les transitions écologiques et territoriales accompagnant l’effacement de grands barrages en France
No full textLes politiques internationales encouragent la restauration des écosystèmes aquatiques, notamment par l'effacement de barrages, une méthode perçue comme bénéfique pour la biodiversité et les continuités écologiques des cours d’eau. Peu d'études scientifiques complètes ont jusqu’à présent réussi à documenter ce type d’opérations afin d’en analyser les impacts écologiques, hydrologiques et territoriaux. C’est l’ambition du programme scientifique Sélune qui suit depuis 2012 l’effacement de deux grands barrages hydroélectriques en Normandie : les barrages de Vezins et de La-Roche-Qui-Boit. L'effacement des barrages, décidé pour des raisons économiques et écologiques (obsolescence, qualité de l'eau, protection des poissons migrateurs), a ainsi permis de reconnecter 1000 km de cours d'eau à l'océan en 2022. Le programme scientifique étudie la restauration de la vallée de la Sélune, en comparant l’état de la vallée avant et après les barrages. Impliquant plusieurs équipes de recherche, ce suivi multidisciplinaire explore les dynamiques fluviales, la biodiversité et les dynamiques territoriales jusqu'en 2027. Les premiers résultats montrent que la Sélune retrouve sa dynamique naturelle, bien que le territoire reste encore instable. A terme, ces résultats permettront de fournir un retour d’expérience essentiel pour approfondir la compréhension de la résilience des écosystèmes et pour soutenir les politiques de restauration de la nature
Qualité du Milieu Marin Littoral. Bulletin de la surveillance 2023. Départements d'Ille-et-Vilaine et des Côtes d'Armor
No full textL’Ifremer coordonne, sur l’ensemble du littoral métropolitain, la mise en oeuvre des réseaux d’observation et de surveillance de la mer côtière. Ce bulletin contient une synthèse et une analyse des données collectées par l’ensemble des réseaux pour les départements d’Ille‐et‐Vilaine et des Côtes d’Armor. Des représentations graphiques homogènes, assorties de commentaires, donnent des indications sur les niveaux et les tendances des paramètres mesurés
Navigating the Future VI: The Ocean's role in addressing global crises
No full textEMB Policy Brief 13 on "Navigating the Future VI: The Ocean’s role in addressing global crises" summarises the main messages of EMB Position Paper 28 "Navigating the Future VI: Placing the Ocean within the wider Earth system". The flagship EMB Navigating the Future foresight series provides periodic reviews of the current state of knowledge in marine science and gives strategic direction regarding the upcoming challenges and needs in marine science and policy. Navigating the Future VI considers the natural and social marine science needed to help us address the challenges facing the planet and the collaborations needed to co-construct solutions.
Characterization of coastal habitats and marine benthic communities of the sub-Antarctic Crozet archipelago using underwater imagery
No full textSub-Antarctic marine life exhibits unique ecological traits and pronounced endemicity levels. Despite their ecological uniqueness and high conservation value, studies on sub-Antarctic benthic communities are scarce. Using underwater video imagery, we assessed the nearshore diversity and structure of faunal and algal communities of the Crozet archipelago along 12 scuba and remotely operated vehicle transects performed at Baie du Marin and Crique du Sphinx (Ile de la Possession). The influence of habitat types on species distribution was evaluated in relation to the setting up of submarine cables. A total of 51 faunal (mainly represented by Echinodermata and Porifera) and 14 algal (mainly represented by Rhodophyta) taxa were identified. The high habitat heterogeneity found in shallow waters (from 0 to 20 m depth) enhances the species richness and diversity, whereas deeper (> 20 m depth) areas were dominated by large sandy stretches and a lower diversity. Rocky habitats had the highest richness and diversity values, promoting local diversity. Submarine cables act as a hard substrate for species, whose suspended sections influence the composition and structure of benthic communities. This study improves our limited knowledge of benthic habitats and diversity from Crozet and constitutes a baseline for further monitoring of marine communities for conservation strategies related to this part of the French Southern Territories National Nature Reserve
Multiple, diverse endogenous giant virus elements within the genome of a brown alga
No full textEndogenous viral elements (EVEs) have been found in diverse eukaryotic genomes. These elements are particularly frequent in the genomes of brown algae (Phaeophyceae) because these seaweeds are infected by viruses (Phaeovirus) of the phylum Nucleocytoviricota (NCV) that are capable of inserting into their host’s genome as part of their infective cycle. A search for inserted viral sequences in the genome of the freshwater brown alga Porterinema fluviatile identified seven large EVEs, including four complete or near-complete proviruses. The EVEs, which all appear to have been derived from independent insertion events, correspond to phylogenetically diverse members of the Phaeovirus genus and include members of both the A and B subgroups of this genus. This latter observation is surprising because the two subgroups were thought to have different evolutionary strategies and were therefore not expected to be found in the same host. The EVEs contain a number of novel genes including a H4 histone-like sequence but only one of the EVEs possesses a full set of NCV core genes, indicating that the other six probably correspond to non-functional, degenerated viral genomes. The majority of the genes within the EVEs were transcriptionally silent and most of the small number of genes that showed some transcriptional activity were of unknown function. However, the existence of some transcriptionally active-genes and several genes containing introns in some EVEs, suggests that these elements may be undergoing some degree of endogenisation within the host genome over time
Rapport d’expertise de l’Ifremer sur le dossier de demande d’autorisation environnementale relatif au projet de raccordement mutualisé des parcs éoliens en mer de Bretagne Sud
No full textCe rapport d’expertise présente les observations de l’Ifremer sur le dossier de demande d’autorisation environnementale relatif au projet de raccordement mutualisé des parcs éoliens en mer de Bretagne Sud déposé par RTE, en réponse à une demande de la DDTM56. Les compartiments expertisés par l’Ifremer sont les suivants : Qualité de l’eau et des sédiments, Habitats et peuplements benthiques, Zooplancton, Ressources halieutique
Reconstructing the dynamics of past coral endosymbiotic algae communities using coral ancient DNA (coraDNA)
No full textMost scleractinian corals are under threat from global warming, yet some exhibit remarkable resistance to heat stress. Coral thermal tolerance depends on both the intrinsic properties of the cnidarian host and the physiology of their symbiotic algae (Symbiodiniaceae). Some corals adapt to heat stress by altering their Symbiodiniaceae communities, but these shifts are primarily observed over very short evolutionary timescales, leaving a gap in our understanding of coral holobiont evolution over longer periods. In this study, we combined ancient DNA analysis from a coral core with a metabarcoding approach to reconstruct past Symbiodiniaceae communities associated with a living colony of Porites lobata from New Caledonia over the last century. Using the SymPortal analytical pipeline, we identified 53 ‘defining intragenomic variants’ (DIVs) related to Symbiodiniaceae. The number of Symbiodiniaceae DIVs per sample ranged from 5 to 22 and showed no correlation with the age of the coraDNA sample or the total number of sequences obtained. Our results reveal a generally stable Symbiodiniaceae community associated with P. lobata, dominated by the C15 clade, though substantial shifts in community composition coincided with an extreme warm winter event. Additionally, we detected the presence of Azadinium spinosum (Dinophyceae) in two coraDNA replicates from the same position in the coral core, and sequences of the host P. lobata in a subset of samples. This study lays the groundwork for future research into the evolutionary dynamics of coral holobionts at the colony level across extensive temporal scales