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Article signat per 266 autors/es:S. Aiello, A. Albert, S. Alves Garre, Z. Aly, A. Ambrosone, F. Ameli, M. Andre, E. Androutsou, M. Anghinolfi, M. Anguita, L. Aphecetche, M. Ardid, S. Ardid, H. Atmani, J. Aublin, C. Bagatelas, L. Bailly-Salins, Z. Bardačová, B. Baret, S. Basegmez du Pree, Y. Becherini, M. Bendahman, F. Benfenati , M. Benhassi, D.M. Benoit, E. Berbee, V. Bertin, V. van Beveren, S. Biagi, M. Boettcher, J. Boumaaza, M. Bouta, M. Bouwhuis, C. Bozza, R.M. Bozza, H. Brânzaş, F. Bretaudeau, R. Bruijn, J. Brunner, R. Bruno, E. Buis, R. Buompane, J. Busto, B. Caiffi, D. Calvo, S. Campion, A. Capone, F. Carenini, V. Carretero, T. Cartraud, P. Castaldi, V. Cecchini, S. Celli, L. Cerisy, M. Chabab, M. Chadolias, A. Chen, S. Cherubini , T. Chiarusi, M. Circella, R. Cocimano, J.A.B. Coelho, A. Coleiro, R. Coniglione, P. Coyle, A. Creusot, A. Cruz, G. Cuttone, R. Dallier, Y. Darras, A. De Benedittis, B. De Martino, V. Decoene, R. Del Burgo, L.S. Di Mauro, I. Di Palma, A.F. Díaz, D. Diego-Tortosa, C. Distefano, A. Domi, C. Donzaud, D. Dornic, M. Dörr, E. Drakopoulou, D. Drouhin, R. Dvornický, T. Eberl, E. Eckerová, A. Eddymaoui, T. van Eeden, M. Eff, D. van Eijk, I. El Bojaddaini, S. El Hedri, A. Enzenhöfer, G. Ferrara, M.D. Filipović, F. Filippini, L.A. Fusco, O. Gabella, J. Gabriel, S. Gagliardini, T. Gal, J. García Méndez, A. Garcia Soto, C. Gatius Oliver, N. Geißelbrecht, H. Ghaddari, L. Gialanella, B.K. Gibson, E. Giorgio, A. Girardi, I. Goos, D. Goupilliere, S.R. Gozzini, R. Gracia, K. Graf, C. Guidi, B. Guillon, M. Gutiérrez , H. van Haren, A. Heijboer, A. Hekalo, L. Hennig, J.J. Hernández-Rey, F. Huang, W. Idrissi Ibnsalih, G. Illuminati, C.W. James, P. Jansweijer, M. de Jong, P. de Jong, B.J. Jung, P. Kalaczyński, O. Kalekin, U.F. Katz, N.R. Khan Chowdhury, A. Khatun, G. Kistauri, C. Kopper, A. Kouchner, V. Kulikovskiy, R. Kvatadze, M. Labalme, R. Lahmann, G. Larosa, C. Lastoria, A. Lazo, S. Le Stum, G. Lehaut, E. Leonora, N. Lessing, G. Levi, M. Lindsey Clark, F. Longhitano, J. Majumdar, L. Malerba, F. Mamedov, J. Mańczak, A. Manfreda, M. Marconi, A. Margiotta, A. Marinelli, C. Markou, L. Martin, J.A. Martínez-Mora, F. Marzaioli, M. Mastrodicasa, S. Mastroianni, S. Miccichè, G. Miele, P. Migliozzi, E. Migneco, S. Minutoli, M.L. Mitsou, C.M. Mollo, L. Morales-Gallegos, C. Morley-Wong, A. Mosbrugger, A. Moussa, I. Mozun Mateo, R. Muller, M.R. Musone, M. Musumeci, L. Nauta, S. Navas, A. Nayerhoda, C.A. Nicolau, B. Nkosi, B. Ó Fearraigh, V. Oliviero, A. Orlando, E. Oukacha, J. Palacios González, G. Papalashvili, E.J. Pastor Gomez, A.M. Păun, G.E. Păvălaş, S. Peña Martínez, M. Perrin-Terrin, J. Perronnel, V. Pestel, R. Pestes, P. Piattelli, C. Poirè, V. Popa, T. Pradier, S. Pulvirenti, G. Quéméner, C. Quiroz, U. Rahaman, N. Randazzo, S. Razzaque, I.C. Rea, D. Real, S. Reck, G. Riccobene, J. Robinson y, A. Romanov aq j, A. Saina c, F. Salesa Greus c, D.F.E. Samtleben at s, A. Sánchez Losa c ak, M. Sanguineti aq j, C. Santonastaso bb e, D. Santonocito x, P. Sapienza x, Y. Scarpetta J. Schnabel, M.F. Schneider, J. Schumann, H.M. Schutte, J. Seneca, B. Setter, I. Sgura, R. Shanidze, Y. Shitov, F. Šimkovic, A. Simonelli, A. Sinopoulou, M.V. Smirnov, B. Spisso, M. Spurio, D. Stavropoulos, I. Štekl, M. Taiuti, Y. Tayalati, H. Tedjditi, H. Thiersen I. Tosta e Melo, B. Trocme, S. Tsagkli, V. Tsourapis, E. Tzamariudaki, A. Vacheret, V. Valsecchi, V. Van Elewyck, G. Vannoye, G. Vasileiadis, F. Vazquez de Sola, C. Verilhac, A. Veutro, S. Viola, D. Vivolo, H. Warnhofer, J. Wilms, E. de Wolf, H. Yepes-Ramirez, G. Zarpapis, S. Zavatarelli, A. Zegarelli, D. Zito, J.D. Zornoza, J. Zúñiga, N. Zywucka The authors acknowledge the financial support of the funding agencies: Agence Nationale de la Recherche (contract ANR-15-CE31-0020), Centre National de la Recherche Scientifique (CNRS), Commission européenne (FEDER fund and Marie Curie Program), Labex UnivEarthS (ANR-10-LABX-0023 and ANR-18-IDEX-0001), Paris Île-de-France Region, France; Shota Rustaveli National Science Foundation of Georgia (SRNSFG, FR-22-13708), Georgia; The General Secretariat of Research and Innovation (GSRI), Greece Istituto Nazionale di Fisica Nucleare (INFN), Ministero dell'Università e della Ricerca (MIUR), PRIN 2017 program (Grant NAT-NET 2017W4HA7S) Italy; Ministry of Higher Education, Scientific Research and Innovation, Morocco, and the Arab Fund for Economic and Social Development, Kuwait; Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO), the Netherlands; The National Science Centre, Poland (2021/41/N/ST2/01177); The grant “AstroCeNT: Particle Astrophysics Science and Technology Centre”, carried out within the International Research Agendas programme of the Foundation for Polish Science financed by the European Union under the European Regional Development Fund; National Authority for Scientific Research (ANCS), Romania; Grants PID2021-124591NB-C41, -C42, -C43 funded by MCIN/AEI/ 10.13039/501100011033 and, as appropriate, by “ERDF A way of making Europe”, by the “European Union” or by the “European Union NextGenerationEU/PRTR”, Programa de Planes Complementarios I+D+I (refs. ASFAE/2022/023, ASFAE/2022/014), Programa Prometeo (PROMETEO/2020/019) and GenT (refs. CIDEGENT/2018/034, /2019/043, /2020/049. /2021/23) of the Generalitat Valenciana, Junta de Andalucía (ref. SOMM17/6104/UGR, P18-FR-5057), EU: MSC program (ref. 101025085), Programa María Zambrano (Spanish Ministry of Universities, funded by the European Union, NextGenerationEU), Spain; The European Union's Horizon 2020 Research and Innovation Programme (ChETEC-INFRA - Project no. 101008324). The KM3NeT Collaboration is building and operating two deep sea neutrino telescopes at the bottom of the Mediterranean Sea. The telescopes consist of latices of photomultiplier tubes housed in pressure-resistant glass spheres, called digital optical modules and arranged in vertical detection units. The two main scientific goals are the determination of the neutrino mass ordering and the discovery and observation of high-energy neutrino sources in the Universe. Neutrinos are detected via the Cherenkov light, which is induced by charged particles originated in neutrino interactions. The photomultiplier tubes convert the Cherenkov light into electrical signals that are acquired and timestamped by the acquisition electronics. Each optical module houses the acquisition electronics for collecting and timestamping the photomultiplier signals with one nanosecond accuracy. Once finished, the two telescopes will have installed more than six thousand optical acquisition nodes, completing one of the more complex networks in the world in terms of operation and synchronization. The embedded software running in the acquisition nodes has been designed to provide a framework that will operate with different hardware versions and functionalities. The hardware will not be accessible once in operation, which complicates the embedded software architecture. The embedded software provides a set of tools to facilitate remote manageability of the deployed hardware, including safe reconfiguration of the firmware. This paper presents the architecture and the techniques, methods and implementation of the embedded software running in the acquisition nodes of the KM3NeT neutrino telescopes. Peer Reviewed

Zetaproteobacteria have been reported in different marine and terrestrial environments all over the globe. They play an essential role in marine iron-rich microbial mats, as one of their autotrophic primary producers, oxidizing Fe(II) and producing Fe-oxyhydroxides with different morphologies. Here, we study and compare the Zetaproteobacterial communities of iron-rich microbial mats from six different sites of the Lucky Strike Hydrothermal Field through the use of the Zetaproteobacterial operational taxonomic unit (ZetaOTU) classification. We report for the first time the Zetaproteobacterial core microbiome of these iron-rich microbial mats, which is composed of four ZetaOTUs that are cosmopolitan and essential for the development of the mats. The study of the presence and abundance of different ZetaOTUs among sites reveals two clusters, which are related to the lithology and permeability of the substratum on which they develop. The Zetaproteobacterial communities of cluster 1 are characteristic of poorly permeable substrata, with little evidence of diffuse venting, while those of cluster 2 develop on hydrothermal slabs or deposits that allow the percolation and outflow of diffuse hydrothermal fluids. In addition, two NewZetaOTUs 1 and 2 were identified, which could be characteristic of anthropic iron and unsedimented basalt, respectively. We also report significant correlations between the abundance of certain ZetaOTUs and that of iron oxide morphologies, indicating that their formation could be taxonomically and/or environmentally driven. We identified a new morphology of Fe(III)-oxyhydroxides that we named “corals.” Overall, our work contributes to the knowledge of the biogeography of this bacterial class by providing additional data from the Atlantic Ocean, a lesser-studied ocean in terms of Zetaproteobacterial diversity. IMPORTANCE Up until now, Zetaproteobacterial diversity studies have revealed possible links between Zetaproteobacteria taxa, habitats, and niches. Here, we report for the first time the Zetaproteobacterial core microbiome of iron-rich mats from the Lucky Strike Hydrothermal Field (LSHF), as well as two new Zetaproteobacterial operational taxonomic units (NewZetaOTUs) that could be substratum specific. We highlight that the substratum on which iron-rich microbial mats develop, especially because of its permeability to diffuse hydrothermal venting, has an influence on their Zetaproteobacterial communities. Moreover, our work adds to the knowledge of the biogeography of this bacterial class by providing additional data from the hydrothermal vent sites along the Mid-Atlantic Ridge. In addition to the already described iron oxide morphologies, we identify in our iron-rich mats a new morphology that we named corals. Finally, we argue for significant correlations between the relative abundance of certain ZetaOTUs and that of iron oxide morphologies, contributing to the understanding of the drivers of iron oxide production in iron-oxidizing bacteria. International audience

Natural samples are characterized by surface roughness which is intrinsically multi-scale as depicted by the well known concept of fractal dimension. Nevertheless, surface asperities are barely taken into account in simulations and modelling where flat surfaces and sharp corners or edges are generally preferred for the sake of simplicity. In this context, we propose here a versatile Python program called Pyrough that aims at building virtual samples characterized by configurable surface roughness for numerical applications such as atomistic and finite-element simulations. The program is open source and relies on the classical roughness theory that integrates the concept of self-affine surface. Several basic shapes including basic blocks, spheres, grains and wires with self-affine surface asperities are implemented and the object-oriented structure of the program simplifies the implementation of more complex objects. Virtual sample design is improved using Pyrough, which enables more realistic simulations to be made. Several application examples including e.g., the design of wavy grain boundaries or nanoindentation testing using a roughened indenter tip are presented.

Abstract. Total alkalinity (AT) and dissolved inorganic carbon (CT) in the oceans are important properties with respect to understanding the ocean carbon cycle and its link to global change (ocean carbon sinks and sources, ocean acidification) and ultimately finding carbon-based solutions or mitigation procedures (marine carbon removal). We present a database of more than 44 400 AT and CT observations along with basic ancillary data (spatiotemporal location, depth, temperature and salinity) from various ocean regions obtained, mainly in the framework of French projects, since 1993. This includes both surface and water column data acquired in the open ocean, coastal zones and in the Mediterranean Sea and either from time series or dedicated one-off cruises. Most AT and CT data in this synthesis were measured from discrete samples using the same closed-cell potentiometric titration calibrated with Certified Reference Material, with an overall accuracy of ±4 µmol kg−1 for both AT and CT. The data are provided in two separate datasets – for the Global Ocean and the Mediterranean Sea (https://doi.org/10.17882/95414, Metzl et al., 2023), respectively – that offer a direct use for regional or global purposes, e.g., AT–salinity relationships, long-term CT estimates, and constraint and validation of diagnostic CT and AT reconstructed fields or ocean carbon and coupled climate–carbon models simulations as well as data derived from Biogeochemical-Argo (BGC-Argo) floats. When associated with other properties, these data can also be used to calculate pH, the fugacity of CO2 (fCO2) and other carbon system properties to derive ocean acidification rates or air–sea CO2 fluxes. International audience

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

Abstract Since 2011, the Caribbean coasts have been subject to episodic influxes of floating Sargassum seaweed of unprecedented magnitude originating from a new area “the Great Atlantic Sargassum Belt” (GASB), leading in episodic influxes and mass strandings of floating Sargassum. For the biofilm of both holopelagic and benthic Sargassum as well as in the surrounding waters, we characterized the main functional groups involved in the microbial nitrogen cycle. The abundance of genes representing nitrogen fixation (nifH), nitrification (amoA) and denitrification (nosZ) showed the predominance of diazotrophs, particularly within the GASB and the Sargasso Sea. In both location, the biofilm associated with holopelagic Sargassum harboured a more abundant proportion of diazotrophs than the surrounding water. The mean δ15N value of the GASB seaweed was very negative (−2.04‰), and lower than previously reported, reinforcing the hypothesis that the source of nitrogen comes from the nitrogen-fixing activity of diazotrophs within this new area of proliferation. Analysis of the diversity of diazotrophic communities revealed for the first time the predominance of heterotrophic diazotrophic bacteria belonging to the phylum Proteobacteria in holopelagic Sargassum biofilms. The nifH sequences belonging to Vibrio genus (Gammaproteobacteria) and Filomicrobium sp. (Alphaproteobacteria) were the most abundant and reached respectively up to 46.0% and 33.2% of the community. We highlighted the atmospheric origin of the nitrogen used during the growth of holopelagic Sargassum within the GASB and a contribution of heterotrophic nitrogen-fixing bacteria to a part of the Sargassum proliferation. International audience

International audience; On February 2nd 2021, a Cuvier's beaked whale (Ziphius cavirostris) stranded on the île de Ré (Northeast Atlantic, France). Preliminary analyses revealed that the death of the animal was probably caused by anthropogenic noise. Produced in the direct vicinity of an area where military tests were carried out by a vessel, this accident occurred within a marine protected area. This event became the starting point of an investigation aiming to trace its origin, and served as a basis for a broader collaborative work as part of the interdisciplinary research program of Esprit de Velox, Destination Ocean. At the confluence of several disciplines, our reflection highlights, through the lens of human-induced noise impacts on cetaceans, the complexity of the relationships between oceanic life and anthropic activities. In order to better understand and protect the ocean, we advocate for changes in the practices of ocean-related knowledge production, improvement of the legal norms governing the use and protection of the marine environment, and a transformation of our own anthropological relationship to the ocean.