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  • European Marine Science
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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: Ina M. Deutschmann; Erwan Delage; Caterina R. Giner; Marta Sebastián; +9 Authors

    Microbial interactions are vital in maintaining ocean ecosystem function, yet their dynamic nature and complexity remain largely unexplored. Here, we use association networks to investigate possible ecological interactions in the marine microbiome among archaea, bacteria, and picoeukaryotes throughout different depths and geographical regions of the tropical and subtropical global ocean. Our findings reveal that potential microbial interactions change with depth and geographical scale, exhibiting highly heterogeneous distributions. A few potential interactions were global, meaning they occurred across regions at the same depth, while 11-36% were regional within specific depths. The bathypelagic zone had the lowest proportion of global associations, and regional associations increased with depth. Moreover, we observed that most surface water associations do not persist in deeper ocean layers despite microbial vertical dispersal. Our work contributes to a deeper understanding of the tropical and subtropical global ocean interactome, which is essential for addressing the challenges posed by global change Sampling was carried out thanks to the Consolider-Ingenio program (project Malaspina 2010 Expedition, ref. CSD2008–00077, to C.M.D.) and HOTMIX project (CTM2011-30010/MAR, to J.A.), funded by the Spanish Ministry of Economy and Competitiveness Science and Innovation. [...] I.M.D., R.L., and R.M. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 675752 (SINGEK, http://www.singek.eu). R.L. was supported by a Ramón y Cajal fellowship (RYC-2013-12554, MINECO, Spain). This work was also supported by the projects INTERACTOMICS (CTM2015-69936-P, MINECO, Spain), MicroEcoSystems (240904, RCN, Norway), and MINIME (PID2019-105775RB-I00, AEI, Spain) to R.L. S.C. was supported by the CNRS MITI through the interdisciplinary program Modélisation du Vivant (GOBITMAP grant). S.C., D.E., and S.G.A. were funded by the H2020 project AtlantECO (award number 862923). We acknowledge funding of the Spanish government through the “Severo Ochoa Centre of Excellence” accreditation to the ICM-CSIC (CEX2019-000928-S) 17 pages, 6 figures, 2 tables, supplementary information https://doi.org/10.1038/s41467-023-44550-y.-- Data availability: DNA sequence data is publicly available at the European Nucleotide Archive (see details in Table 2). The accession numbers for the different datasets are: MalaSurf (PRJEB23913, PRJEB25224), MalaVP (PRJEB23771, PRJEB45015), MalaDeep (PRJEB45011, PRJEB45014), Hotmix (PRJEB44683, PRJEB44474). OTU tables and source data to generate the figures and tables are provided in GitHub (https://github.com/InaMariaDeutschmann/GlobalNetworkMalaspinaHotmix) and Zenodo: https://doi.org/10.5281/zenodo.1023007337. The following databases have been used: SILVA v13289, PR2 v4.11.190, and the World Ocean Database 201391.-- Code availability: The code for data analysis, including commands to run FlashWeave and EnDED (environmentally-driven-edge-detection and computing Jaccard index), is publicly available at GitHub (https://github.com/InaMariaDeutschmann/GlobalNetworkMalaspinaHotmix) and Zenodo37 Peer reviewed

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    Nature Communications
    Article . 2024 . Peer-reviewed
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    DIGITAL.CSIC
    Article . 2024 . Peer-reviewed
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      Nature Communications
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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: Mémin, Etienne; Li, Long; Lahaye, Noé; Tissot, Gilles; +1 Authors

    In this paper, we investigate the wave solutions of a stochastic rotating shallow water model. This approximate model provides an interesting simple description of the interplay between waves and random forcing ensuing either from the wind or coming as the feedback of the ocean on the atmosphere and leading in a very fast way to the selection of some wavelength. This interwoven, yet simple, mechanism explains the emergence of typical wavelength associated to near inertial waves. Ensemble-mean waves that are not in phase with the random forcing are damped at an exponential rate, whose magnitude depends on the random forcing variance. Geostrophic adjustment is also interpreted as a statistical homogenization process in which, in order to conserve potential vorticity, the small-scale component tends to align to the velocity fields to form a statistically homogeneous random field. Comment: Submitted for STUOD 2022 conference proceedings

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    https://doi.org/10.1007/978-3-...
    Part of book or chapter of book . 2023 . Peer-reviewed
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    https://doi.org/10.48550/arxiv...
    Article . 2023
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      https://doi.org/10.1007/978-3-...
      Part of book or chapter of book . 2023 . Peer-reviewed
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      https://doi.org/10.48550/arxiv...
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  • Authors: Téo Lemane; Nolan Lezzoche; Julien Lecubin; Eric Pelletier; +3 Authors

    AbstractPublic sequencing databases contain vast amounts of biological information, yet they are largely underutilized as one cannot efficiently search them for any sequence(s) of interest. We presentkmindex, an innovative approach that can index thousands of highly complex metagenomes and perform sequence searches in a fraction of a second. The index construction is an order of magnitude faster than previous methods, while search times are two orders of magnitude faster. With negligible false positive rates below 0.01%,kmindexoutperforms the precision of existing approaches by four orders of magnitude. We demonstrate the scalability ofkmindexby successfully indexing 1,393 complex marine seawater metagenome samples from theTaraOceans project. Additionally, we introduce the publicly accessible web server “Ocean Read Atlas” (ORA) athttps://ocean-read-atlas.mio.osupytheas.fr/, which enables real-time queries on theTaraOceans dataset. The open-sourcekmindexsoftware is available athttps://github.com/tlemane/kmindex.

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    Authors: Said Ouala; Bertrand Chapron; Fabrice Collard; Lucile Gaultier; +1 Authors

    Abstract Bernard O Koopman proposed an alternative view of dynamical systems based on linear operator theory, in which the time evolution of a dynamical system is analogous to the linear propagation of an infinite-dimensional vector of observables. In the last few years, several works have shown that finite-dimensional approximations of this operator can be extremely useful for several applications, such as prediction, control, and data assimilation. In particular, a Koopman representation of a dynamical system with a finite number of dimensions will avoid all the problems caused by nonlinearity in classical state-space models. In this work, the identification of finite-dimensional approximations of the Koopman operator and its associated observables is expressed through the inversion of an unknown augmented linear dynamical system. The proposed framework can be regarded as an extended dynamical mode decomposition that uses a collection of latent observables. The use of a latent dictionary applies to a large class of dynamical regimes, and it provides new means for deriving appropriate finite-dimensional linear approximations to high-dimensional nonlinear systems.

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    Machine Learning: Science and Technology
    Article . 2023 . Peer-reviewed
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    Article . 2023
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      Machine Learning: Science and Technology
      Article . 2023 . Peer-reviewed
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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: Dalibard, Anne-Laure; Guillod, Julien; Leblond, Antoine;

    The coupling between the transport equation for the density and the Stokes equation is considered in a periodic channel. More precisely, the density is advected by pure transport by a velocity field given by the Stokes equation with source force coming from the gravity due to differences in the density. Dirichlet boundary conditions are taken for the velocity field on the bottom and top of the channel, and periodic conditions in the horizontal variable. We prove that the affine stratified density profile is stable under small perturbations in Sobolev spaces and prove convergence of the density to another limiting stratified density profile for large time with an explicit algebraic decay rate. Moreover, we are able to precisely identify the limiting profile as the decreasing vertical rearrangement of the initial density. Finally, we study boundary layers formation to precisely characterize the long-time behavior beyond the constant limiting profile and enlighten the optimal decay rate. Comment: 69 pages

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    https://doi.org/10.48550/arxiv...
    Article . 2023
    License: arXiv Non-Exclusive Distribution
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      https://doi.org/10.48550/arxiv...
      Article . 2023
      License: arXiv Non-Exclusive Distribution
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    Authors: Platzer, Paul; Chapron, Bertrand; Tandeo, Pierre;

    AbstractLarge-scale weather can often be successfully described using a small amount of patterns. A statistical description of reanalysed pressure fields identifies these recurring patterns with clusters in state-space, also called “regimes”. Recently, these weather regimes have been described through instantaneous, local indicators of dimension and persistence, borrowed from dynamical systems theory and extreme value theory. Using similar indicators and going further, we focus here on weather regime transitions. We use 60 years of winter-time sea-level pressure reanalysis data centered on the North-Atlantic ocean and western Europe. These experiments reveal regime-dependent behaviours of dimension and persistence near transitions, although in average one observes an increase of dimension and a decrease of persistence near transitions. The effect of transition on persistence is stronger and lasts longer than on dimension. These findings confirm the relevance of such dynamical indicators for the study of large-scale weather regimes, and reveal their potential to be used for both the understanding and detection of weather regime transitions.

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    https://doi.org/10.1007/978-3-...
    Part of book or chapter of book . 2022 . Peer-reviewed
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    Authors: Udita Chandola; Camille Trottier; Marinna Gaudin; Louis Josselin Lavier Aydat; +10 Authors

    AbstractNon-cyanobacteria diazotrophs (NCDs) were shown to dominate in surface waters shifting the long-held paradigm of cyanobacteria dominance and raising fundamental questions on how these putative heterotrophic bacteria thrive in sunlit oceans. Here, we report an unprecedented finding in the widely used model diatomPhaeodactylum tricornutum(Pt) of NCDs sustaining diatom cells in the absence of bioavailable nitrogen. We identifiedPtNCDs using metagenomics sequencing and detected nitrogenase genesin silicoand/or by PCR. We demonstrated nitrogen fixation withinPtNCDs while establishing their genetic affiliation to NCDs found in the environment. We showed the wide occurrence of this type of interactions with the isolation of NCDs from other microalgae, their identification in the environment, and their predicted associations with photosynthetic microalgae. Our findings will help to understand the different players driving global marine nitrogen fixation. Overall, this study provides evidence for a hitherto unrecognized symbiosis that affects marine element cycling and primary production using a multidisciplinary model-based approach.

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    https://doi.org/10.21203/rs.3....
    Preprint . 2023
    License: CC BY
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    HAL-Rennes 1
    Preprint . 2022
    Data sources: HAL-Rennes 1
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    Authors: T. Uchida; J. Le Sommer; C. Stern; R. P. Abernathey; +26 Authors

    Abstract. With the increase in computational power, ocean models with kilometer-scale resolution have emerged over the last decade. These models have been used for quantifying the energetic exchanges between spatial scales, informing the design of eddy parametrizations, and preparing observing networks. The increase in resolution, however, has drastically increased the size of model outputs, making it difficult to transfer and analyze the data. It remains, nonetheless, of primary importance to assess more systematically the realism of these models. Here, we showcase a cloud-based analysis framework proposed by the Pangeo project that aims to tackle such distribution and analysis challenges. We analyze the output of eight submesoscale-permitting simulations, all on the cloud, for a crossover region of the upcoming Surface Water and Ocean Topography (SWOT) altimeter mission near the Gulf Stream separation. The cloud-based analysis framework (i) minimizes the cost of duplicating and storing ghost copies of data and (ii) allows for seamless sharing of analysis results amongst collaborators. We describe the framework and provide example analyses (e.g., sea-surface height variability, submesoscale vertical buoyancy fluxes, and comparison to predictions from the mixed-layer instability parametrization). Basin- to global-scale, submesoscale-permitting models are still at their early stage of development; their cost and carbon footprints are also rather large. It would, therefore, benefit the community to document the different model configurations for future best practices. We also argue that an emphasis on data analysis strategies would be crucial for improving the models themselves.

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    Authors: Armand Vic; Xavier Carton; Jonathan Gula;

    The stability of two superposed buoyancy vortices is studied linearly in a two-level Surface Quasi-Geostrophic (SQG) model. The basic flow is chosen as two circular vortices with uniform buoyancy, coaxial, and the same radius. A perturbation with a single angular mode is added to this mean flow. The SQG equations linearized in perturbation around this basic flow form a two-dimensional ODE for which the normal and singular mode solutions are numerically computed. The instability of these two vortices depends on several parameters. The parameters varied here are: the vertical distance between the two levels and the two values of the vortex buoyancies (called vortex intensity hereafter); the other parameters remain fixed. For normal modes, the system is stable if the levels are sufficiently far from each other vertically, to prevent vertical interactions of the buoyancy patches. Stability is also reached if the layers are close to each other, but if the vortices have very different intensities, again preventing the resonance of Rossby waves around their contours. The system is unstable if the vortex intensities are similar and if the two levels are close to each other. The growth rates of the normal modes increase with the angular wave-number, also corresponding to shorter vertical distances. The growth rates of the singular modes depend more on the distance between the levels than on the ratio of the vortex intensities, at a short time; as expected, they converge towards the growth rates of the normal modes. This study remaining linear does not predict the final evolution of such unstable vortices. This nonlinear evolution will be studied in a sequel of this work.

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    Symmetry
    Other literature type . Article . 2022 . Peer-reviewed
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    Authors: Tara Ocean Foundation; Abreu, Andre; Bourgois, Etienne; Gristwood, Adam; +45 Authors

    Microbial communities have essential roles in ocean ecology and planetary health. Microbes participate in nutrient cycles, remove huge quantities of carbon dioxide from the air and support ocean food webs. The taxonomic and functional diversity of the global ocean microbiome has been revealed by technological advances in sampling, DNA sequencing and bioinformatics. A better understanding of the ocean microbiome could underpin strategies to address environmental and societal challenges, including achievement of multiple Sustainable Development Goals way beyond SDG 14 ‘life below water’. We propose a set of priorities for understanding and protecting the ocean microbiome, which include delineating interactions between microbiota, sustainably applying resources from oceanic microorganisms and creating policy- and funder-friendly ocean education resources, and discuss how to achieve these ambitious goals We thank R. Zaayman-Gallant, T. Rauscher and F. Ibarbalz for preparation of the figures, and the European Union’s Horizon 2020 research and innovation project AtlantECO, under grant agreement no. 862923 With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S) This article is contribution number 131 of Tara Oceans.-- 11 pages, 5 figures, 1 table, 1 box Peer reviewed

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    Nature Microbiology
    Other literature type . Article . 2022 . Peer-reviewed
    License: Springer TDM
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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: Ina M. Deutschmann; Erwan Delage; Caterina R. Giner; Marta Sebastián; +9 Authors

    Microbial interactions are vital in maintaining ocean ecosystem function, yet their dynamic nature and complexity remain largely unexplored. Here, we use association networks to investigate possible ecological interactions in the marine microbiome among archaea, bacteria, and picoeukaryotes throughout different depths and geographical regions of the tropical and subtropical global ocean. Our findings reveal that potential microbial interactions change with depth and geographical scale, exhibiting highly heterogeneous distributions. A few potential interactions were global, meaning they occurred across regions at the same depth, while 11-36% were regional within specific depths. The bathypelagic zone had the lowest proportion of global associations, and regional associations increased with depth. Moreover, we observed that most surface water associations do not persist in deeper ocean layers despite microbial vertical dispersal. Our work contributes to a deeper understanding of the tropical and subtropical global ocean interactome, which is essential for addressing the challenges posed by global change Sampling was carried out thanks to the Consolider-Ingenio program (project Malaspina 2010 Expedition, ref. CSD2008–00077, to C.M.D.) and HOTMIX project (CTM2011-30010/MAR, to J.A.), funded by the Spanish Ministry of Economy and Competitiveness Science and Innovation. [...] I.M.D., R.L., and R.M. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 675752 (SINGEK, http://www.singek.eu). R.L. was supported by a Ramón y Cajal fellowship (RYC-2013-12554, MINECO, Spain). This work was also supported by the projects INTERACTOMICS (CTM2015-69936-P, MINECO, Spain), MicroEcoSystems (240904, RCN, Norway), and MINIME (PID2019-105775RB-I00, AEI, Spain) to R.L. S.C. was supported by the CNRS MITI through the interdisciplinary program Modélisation du Vivant (GOBITMAP grant). S.C., D.E., and S.G.A. were funded by the H2020 project AtlantECO (award number 862923). We acknowledge funding of the Spanish government through the “Severo Ochoa Centre of Excellence” accreditation to the ICM-CSIC (CEX2019-000928-S) 17 pages, 6 figures, 2 tables, supplementary information https://doi.org/10.1038/s41467-023-44550-y.-- Data availability: DNA sequence data is publicly available at the European Nucleotide Archive (see details in Table 2). The accession numbers for the different datasets are: MalaSurf (PRJEB23913, PRJEB25224), MalaVP (PRJEB23771, PRJEB45015), MalaDeep (PRJEB45011, PRJEB45014), Hotmix (PRJEB44683, PRJEB44474). OTU tables and source data to generate the figures and tables are provided in GitHub (https://github.com/InaMariaDeutschmann/GlobalNetworkMalaspinaHotmix) and Zenodo: https://doi.org/10.5281/zenodo.1023007337. The following databases have been used: SILVA v13289, PR2 v4.11.190, and the World Ocean Database 201391.-- Code availability: The code for data analysis, including commands to run FlashWeave and EnDED (environmentally-driven-edge-detection and computing Jaccard index), is publicly available at GitHub (https://github.com/InaMariaDeutschmann/GlobalNetworkMalaspinaHotmix) and Zenodo37 Peer reviewed

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    Nature Communications
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    Authors: Mémin, Etienne; Li, Long; Lahaye, Noé; Tissot, Gilles; +1 Authors

    In this paper, we investigate the wave solutions of a stochastic rotating shallow water model. This approximate model provides an interesting simple description of the interplay between waves and random forcing ensuing either from the wind or coming as the feedback of the ocean on the atmosphere and leading in a very fast way to the selection of some wavelength. This interwoven, yet simple, mechanism explains the emergence of typical wavelength associated to near inertial waves. Ensemble-mean waves that are not in phase with the random forcing are damped at an exponential rate, whose magnitude depends on the random forcing variance. Geostrophic adjustment is also interpreted as a statistical homogenization process in which, in order to conserve potential vorticity, the small-scale component tends to align to the velocity fields to form a statistically homogeneous random field. Comment: Submitted for STUOD 2022 conference proceedings

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    https://doi.org/10.1007/978-3-...
    Part of book or chapter of book . 2023 . Peer-reviewed
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    https://doi.org/10.48550/arxiv...
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      https://doi.org/10.1007/978-3-...
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  • Authors: Téo Lemane; Nolan Lezzoche; Julien Lecubin; Eric Pelletier; +3 Authors

    AbstractPublic sequencing databases contain vast amounts of biological information, yet they are largely underutilized as one cannot efficiently search them for any sequence(s) of interest. We presentkmindex, an innovative approach that can index thousands of highly complex metagenomes and perform sequence searches in a fraction of a second. The index construction is an order of magnitude faster than previous methods, while search times are two orders of magnitude faster. With negligible false positive rates below 0.01%,kmindexoutperforms the precision of existing approaches by four orders of magnitude. We demonstrate the scalability ofkmindexby successfully indexing 1,393 complex marine seawater metagenome samples from theTaraOceans project. Additionally, we introduce the publicly accessible web server “Ocean Read Atlas” (ORA) athttps://ocean-read-atlas.mio.osupytheas.fr/, which enables real-time queries on theTaraOceans dataset. The open-sourcekmindexsoftware is available athttps://github.com/tlemane/kmindex.

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    Authors: Said Ouala; Bertrand Chapron; Fabrice Collard; Lucile Gaultier; +1 Authors

    Abstract Bernard O Koopman proposed an alternative view of dynamical systems based on linear operator theory, in which the time evolution of a dynamical system is analogous to the linear propagation of an infinite-dimensional vector of observables. In the last few years, several works have shown that finite-dimensional approximations of this operator can be extremely useful for several applications, such as prediction, control, and data assimilation. In particular, a Koopman representation of a dynamical system with a finite number of dimensions will avoid all the problems caused by nonlinearity in classical state-space models. In this work, the identification of finite-dimensional approximations of the Koopman operator and its associated observables is expressed through the inversion of an unknown augmented linear dynamical system. The proposed framework can be regarded as an extended dynamical mode decomposition that uses a collection of latent observables. The use of a latent dictionary applies to a large class of dynamical regimes, and it provides new means for deriving appropriate finite-dimensional linear approximations to high-dimensional nonlinear systems.

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    Machine Learning: Science and Technology
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    Authors: Dalibard, Anne-Laure; Guillod, Julien; Leblond, Antoine;

    The coupling between the transport equation for the density and the Stokes equation is considered in a periodic channel. More precisely, the density is advected by pure transport by a velocity field given by the Stokes equation with source force coming from the gravity due to differences in the density. Dirichlet boundary conditions are taken for the velocity field on the bottom and top of the channel, and periodic conditions in the horizontal variable. We prove that the affine stratified density profile is stable under small perturbations in Sobolev spaces and prove convergence of the density to another limiting stratified density profile for large time with an explicit algebraic decay rate. Moreover, we are able to precisely identify the limiting profile as the decreasing vertical rearrangement of the initial density. Finally, we study boundary layers formation to precisely characterize the long-time behavior beyond the constant limiting profile and enlighten the optimal decay rate. Comment: 69 pages

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    https://doi.org/10.48550/arxiv...
    Article . 2023
    License: arXiv Non-Exclusive Distribution
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      https://doi.org/10.48550/arxiv...
      Article . 2023
      License: arXiv Non-Exclusive Distribution
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    Authors: Platzer, Paul; Chapron, Bertrand; Tandeo, Pierre;

    AbstractLarge-scale weather can often be successfully described using a small amount of patterns. A statistical description of reanalysed pressure fields identifies these recurring patterns with clusters in state-space, also called “regimes”. Recently, these weather regimes have been described through instantaneous, local indicators of dimension and persistence, borrowed from dynamical systems theory and extreme value theory. Using similar indicators and going further, we focus here on weather regime transitions. We use 60 years of winter-time sea-level pressure reanalysis data centered on the North-Atlantic ocean and western Europe. These experiments reveal regime-dependent behaviours of dimension and persistence near transitions, although in average one observes an increase of dimension and a decrease of persistence near transitions. The effect of transition on persistence is stronger and lasts longer than on dimension. These findings confirm the relevance of such dynamical indicators for the study of large-scale weather regimes, and reveal their potential to be used for both the understanding and detection of weather regime transitions.

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    https://doi.org/10.1007/978-3-...
    Part of book or chapter of book . 2022 . Peer-reviewed
    License: CC BY
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    Authors: Udita Chandola; Camille Trottier; Marinna Gaudin; Louis Josselin Lavier Aydat; +10 Authors

    AbstractNon-cyanobacteria diazotrophs (NCDs) were shown to dominate in surface waters shifting the long-held paradigm of cyanobacteria dominance and raising fundamental questions on how these putative heterotrophic bacteria thrive in sunlit oceans. Here, we report an unprecedented finding in the widely used model diatomPhaeodactylum tricornutum(Pt) of NCDs sustaining diatom cells in the absence of bioavailable nitrogen. We identifiedPtNCDs using metagenomics sequencing and detected nitrogenase genesin silicoand/or by PCR. We demonstrated nitrogen fixation withinPtNCDs while establishing their genetic affiliation to NCDs found in the environment. We showed the wide occurrence of this type of interactions with the isolation of NCDs from other microalgae, their identification in the environment, and their predicted associations with photosynthetic microalgae. Our findings will help to understand the different players driving global marine nitrogen fixation. Overall, this study provides evidence for a hitherto unrecognized symbiosis that affects marine element cycling and primary production using a multidisciplinary model-based approach.

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    https://doi.org/10.21203/rs.3....
    Preprint . 2023
    License: CC BY
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    HAL-Rennes 1
    Preprint . 2022
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    Authors: T. Uchida; J. Le Sommer; C. Stern; R. P. Abernathey; +26 Authors

    Abstract. With the increase in computational power, ocean models with kilometer-scale resolution have emerged over the last decade. These models have been used for quantifying the energetic exchanges between spatial scales, informing the design of eddy parametrizations, and preparing observing networks. The increase in resolution, however, has drastically increased the size of model outputs, making it difficult to transfer and analyze the data. It remains, nonetheless, of primary importance to assess more systematically the realism of these models. Here, we showcase a cloud-based analysis framework proposed by the Pangeo project that aims to tackle such distribution and analysis challenges. We analyze the output of eight submesoscale-permitting simulations, all on the cloud, for a crossover region of the upcoming Surface Water and Ocean Topography (SWOT) altimeter mission near the Gulf Stream separation. The cloud-based analysis framework (i) minimizes the cost of duplicating and storing ghost copies of data and (ii) allows for seamless sharing of analysis results amongst collaborators. We describe the framework and provide example analyses (e.g., sea-surface height variability, submesoscale vertical buoyancy fluxes, and comparison to predictions from the mixed-layer instability parametrization). Basin- to global-scale, submesoscale-permitting models are still at their early stage of development; their cost and carbon footprints are also rather large. It would, therefore, benefit the community to document the different model configurations for future best practices. We also argue that an emphasis on data analysis strategies would be crucial for improving the models themselves.

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    DOAJ
    Article . 2022
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    Authors: Armand Vic; Xavier Carton; Jonathan Gula;

    The stability of two superposed buoyancy vortices is studied linearly in a two-level Surface Quasi-Geostrophic (SQG) model. The basic flow is chosen as two circular vortices with uniform buoyancy, coaxial, and the same radius. A perturbation with a single angular mode is added to this mean flow. The SQG equations linearized in perturbation around this basic flow form a two-dimensional ODE for which the normal and singular mode solutions are numerically computed. The instability of these two vortices depends on several parameters. The parameters varied here are: the vertical distance between the two levels and the two values of the vortex buoyancies (called vortex intensity hereafter); the other parameters remain fixed. For normal modes, the system is stable if the levels are sufficiently far from each other vertically, to prevent vertical interactions of the buoyancy patches. Stability is also reached if the layers are close to each other, but if the vortices have very different intensities, again preventing the resonance of Rossby waves around their contours. The system is unstable if the vortex intensities are similar and if the two levels are close to each other. The growth rates of the normal modes increase with the angular wave-number, also corresponding to shorter vertical distances. The growth rates of the singular modes depend more on the distance between the levels than on the ratio of the vortex intensities, at a short time; as expected, they converge towards the growth rates of the normal modes. This study remaining linear does not predict the final evolution of such unstable vortices. This nonlinear evolution will be studied in a sequel of this work.

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    Symmetry
    Other literature type . Article . 2022 . Peer-reviewed
    License: CC BY
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    Authors: Tara Ocean Foundation; Abreu, Andre; Bourgois, Etienne; Gristwood, Adam; +45 Authors

    Microbial communities have essential roles in ocean ecology and planetary health. Microbes participate in nutrient cycles, remove huge quantities of carbon dioxide from the air and support ocean food webs. The taxonomic and functional diversity of the global ocean microbiome has been revealed by technological advances in sampling, DNA sequencing and bioinformatics. A better understanding of the ocean microbiome could underpin strategies to address environmental and societal challenges, including achievement of multiple Sustainable Development Goals way beyond SDG 14 ‘life below water’. We propose a set of priorities for understanding and protecting the ocean microbiome, which include delineating interactions between microbiota, sustainably applying resources from oceanic microorganisms and creating policy- and funder-friendly ocean education resources, and discuss how to achieve these ambitious goals We thank R. Zaayman-Gallant, T. Rauscher and F. Ibarbalz for preparation of the figures, and the European Union’s Horizon 2020 research and innovation project AtlantECO, under grant agreement no. 862923 With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S) This article is contribution number 131 of Tara Oceans.-- 11 pages, 5 figures, 1 table, 1 box Peer reviewed

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    Nature Microbiology
    Other literature type . Article . 2022 . Peer-reviewed
    License: Springer TDM
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