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AbstractThe impact of climate change on diversity, functioning and biogeography of marine plankton remains a major unresolved issue. Here, niche theory is applied to plankton metagenomes of 6 size fractions, from viruses to meso-zooplankton, sampled during the Tara Oceans expedition. Niches are used to derive plankton size-dependent structuring of the oceans south of 60°N in climato-genomic provinces characterized by signature genomes. By 2090, assuming the RCP8.5 high warming scenario, provinces would be reorganized over half of the considered ocean area and quasi-systematically displaced poleward. Particularly, tropical provinces would expand at the expense of temperate ones. Sea surface temperature is identified as the main driver of changes (50%) followed by phosphate (11%) and salinity (10%). Compositional shifts among key planktonic groups suggest impacts on the nitrogen and carbon cycles. Provinces are linked to estimates of carbon export fluxes which are projected to decrease on average by 4% in response to biogeographical restructuring.

These slides of one of the keynote presentations at the Kick-off event of the AtlantECO project give an overview of the concepts of seascape and connectivity, focussing on the question 'how ocean currents move stuff around'. In this presentation, I show how trajectories of drifting buoys van be used to cluster the ocean surface into connected regions, and how these regions are related to biogeography of planktonic organisms. I discuss how these clusterings can be used for marine spatial planning and management, and touch upon the challenges of extending these methods to the full three-dimensional (including depth) ocean. Keynote presentation at the Kick-off event of the AtlantECO project

Stéphane Pesant gave this presentation as invited speaker during the Open Science clinic of the second JPI-Oceans conference in Lisbonne (26th October 2017). It provides an overview of the OpenAIRE-Connect initiative and shares community experience from the Tara Oceans initiative, the H2020 project ATLAS, and the EuroMarine network of marine research.

The Open Science movement is promising to revolutionise the way science is conducted with the goal to make it more fair, solid and democratic. This revolution is destined to remain just a wish if it is not supported by changes in culture and practices as well as in enabling technologies. This paper describes the gCube offering to enact Open Science-friendly Virtual Research Environments. In particular, the paper describes how a complete solution suitable for realising Open Science practices is achieved by a social networking collaborative environment in conjunction with a shared workspace, an open data analytics platform, and a catalogue enabling FAIR principles on every research artefact.

The ambition of AtlantECO is to develop and apply a novel, unifying framework that provides knowledge-based resources to design policies, support decisions making and engage with citizens to encourage responsible behaviour to manage the Atlantic system and protect its Ecosystem Services (ES) provision. The aim of AtlantECO is to determine the structure and function of Atlantic microbiome in the context of ocean circulation and presence of pollutants, e.g., plastics, to assess its role in driving the dynamics of Atlantic ecosystems at basin and regional scales; its potential of being used as a sensor of ecosystem state and the mechanisms by which it drives the provision of five ES. This is key to improve our predictions on future provision of ES in the basin and to favour the establishment of a sustainable Blue Growth strategy for an All-Atlantic community. To realise this vision, AtlantECO has four objectives which are to 1) Assess dynamics of Atlantic marine ecosystems, their ES provision and the interplay of both with socio-economic activities; 2 increase knowledge and data on microbiomes, plastics, the plastisphere and carbon fluxes that support ecosystems at basin scale using best practices and integrative sampling strategies, novel genomics, imaging and biogeochemical methods, bioinformatics and modelling approaches; 3) Assess and predict the cumulative impacts of multiple stressors on ecosystem status and dynamics and ES provision, identifying their drivers and role on tipping points, assessing their changes in recovery of ecosystem structures, functions and services, and developing eco-socio-economic models to predict future trajectories and 4) Deploy a systemic strategy to build capacity and transfer knowledge for a seamless engagement between science, industry, policy, and society. To achieve these objectives AtlantECO brings together experts and pioneers from Europe, South America and South Africa with the relevant resources, knowledge and experience.

The role of the Arctic Ocean ecosystem in climate regulation may depend on the responses of marine microorganisms to environmental change. We applied genome-resolved metagenomics to 41 Arctic seawater samples, collected at various depths in different seasons during the Tara Oceans Polar Circle expedition, to evaluate the ecology, metabolic potential and activity of resident bacteria and archaea. We assembled 530 metagenome-assembled genomes (MAGs) to form the Arctic MAGs catalogue comprising 526 species. A total of 441 MAGs belonged to species that have not previously been reported and 299 genomes showed an exclusively polar distribution. Most Arctic MAGs have large genomes and the potential for fast generation times, both of which may enable adaptation to a copiotrophic lifestyle in nutrient-rich waters. We identified 38 habitat generalists and 111 specialists in the Arctic Ocean. We also found a general prevalence of 14 mixotrophs, while chemolithoautotrophs were mostly present in the mesopelagic layer during spring and autumn. We revealed 62 MAGs classified as key Arctic species, found only in the Arctic Ocean, showing the highest gene expression values and predicted to have habitat-specific traits. The Artic MAGs catalogue will inform our understanding of polar microorganisms that drive global biogeochemical cycles This work acknowledges the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S). We thank the commitment of the following sponsors and research funding agencies: the Spanish Ministry of Economy and Competitiveness (project MAGGY, grant no. CTM2017-87736-R and Polar EcoGen PID2020-116489RB-I00), Horizon 2020-Research and Innovation Framework Programme (Atlantic ECOsystems assessment, forecasting & sustainability, grant no. H2020-BG-2019-2), Centre National de la Recherche Scientifique (in particular Groupement de Recherche GDR3280 and the Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE), European Molecular Biology Laboratory, Genoscope/Commissariat à l’Énergie Atomique et aux Énergies Alternatives, the French Ministry of Research and the French Government’s ‘Investissements d’Avenir’ programmes OCEANOMICS (project no. ANR-11-BTBR-0008), FRANCE GENOMIQUE (project no. ANR-10-INBS-09-08), MEMO LIFE (project no. ANR-10-LABX-54), Paris Sciences et Lettres University (project no. ANR-11-IDEX-0001-02), Eidgenössische Technische Hochschule Zürich and Helmut Horten Foundation, the Swiss National Foundation (project no. 205321_184955), MEXT/JSPS/KAKENHI (project nos. 16H06429, 16K21723, 16H06437 and 18H02279) 14 pages, 6 figures, additional information https://doi.org/10.1038/s41564-021-00979-9.-- Data availability: Accession numbers for the data used and generated in this study can be found in Supplementary Table 12, which includes the Arctic MAGs Catalogue and their functional annotation (European Bioinformatics Institute BioStudies ID: S-BSST451) and the co-assembly of metagenomic samples used to generate the metagenomic bins (European Nucleotide Archive PRJEB41575). Accession numbers for the metagenomic and metatranscriptomic samples used in the fragment recruitment analyses can be found in Supplementary Table 13. Publicly available datasets used in this study include the following: CheckM v.1.0.11 (https://github.com/Ecogenomics/CheckM/releases/tag/v1.1.0), GTDB release 89 (https://data.gtdb.ecogenomic.org/releases/release89/), SILVA 132 (https://www.arb-silva.de/documentation/release-132/), KEGG release 89.1 (https://www.genome.jp/kegg/docs/relnote.html) and Pfam database release 31.0 (http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam31.0/). Source data are provided with this paper Peer reviewed

The ambition of AtlantECO is to develop and apply a novel, unifying framework that provides knowledge-based resources to design policies, support decisions making and engage with citizens to encourage responsible behaviour to manage the Atlantic system and protect its Ecosystem Services (ES) provision. The aim of AtlantECO is to determine the structure and function of Atlantic microbiome in the context of ocean circulation and presence of pollutants, e.g., plastics, to assess its role in driving the dynamics of Atlantic ecosystems at basin and regional scales; its potential of being used as a sensor of ecosystem state and the mechanisms by which it drives the provision of five ES. This is key to improve our predictions on future provision of ES in the basin and to favour the establishment of a sustainable Blue Growth strategy for an All-Atlantic community. To realise this vision, AtlantECO has four objectives which are to 1) Assess dynamics of Atlantic marine ecosystems, their ES provision and the interplay of both with socio-economic activities; 2 increase knowledge and data on microbiomes, plastics, the plastisphere and carbon fluxes that support ecosystems at basin scale using best practices and integrative sampling strategies, novel genomics, imaging and biogeochemical methods, bioinformatics and modelling approaches; 3) Assess and predict the cumulative impacts of multiple stressors on ecosystem status and dynamics and ES provision, identifying their drivers and role on tipping points, assessing their changes in recovery of ecosystem structures, functions and services, and developing eco-socio-economic models to predict future trajectories and 4) Deploy a systemic strategy to build capacity and transfer knowledge for a seamless engagement between science, industry, policy, and society. To achieve these objectives AtlantECO brings together experts and pioneers from Europe, South America and South Africa with the relevant resources, knowledge and experience.

Cold-water corals form substantial biogenic habitats on continental shelves and in deep-sea areas with topographic highs, such as banks and seamounts. In the Atlantic, many reef and mound complexes are engineered by Lophelia pertusa, the dominant framework-forming coral. In this study, a variety of mapping approaches were used at a range of scales to map the distribution of both cold-water coral habitats and individual coral colonies at the Mingulay Reef Complex (west Scotland). The new ArcGIS-based British Geological Survey (BGS) seabed mapping toolbox semi-automatically delineated over 500 Lophelia reef ‘mini-mounds’ from bathymetry data with 2-m resolution. The morphometric and acoustic characteristics of the mini-mounds were also automatically quantified and captured using this toolbox. Coral presence data were derived from high-definition remotely operated vehicle (ROV) records and high-resolution microbathymetry collected by a ROV-mounted multibeam echosounder. With a resolution of 0.35 × 0.35 m, the microbathymetry covers 0.6 km2 in the centre of the study area and allowed identification of individual live coral colonies in acoustic data for the first time. Maximum water depth, maximum rugosity, mean rugosity, bathymetric positioning index and maximum current speed were identified as the environmental variables that contributed most to the prediction of live coral presence. These variables were used to create a predictive map of the likelihood of presence of live cold-water coral colonies in the area of the Mingulay Reef Complex covered by the 2-m resolution data set. Predictive maps of live corals across the reef will be especially valuable for future long-term monitoring surveys, including those needed to understand the impacts of global climate change. This is the first study using the newly developed BGS seabed mapping toolbox and an ROV-based microbathymetric grid to explore the environmental variables that control coral growth on cold-water coral reefs.