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This paper presents two metazoan zooplankton datasets obtained by imaging samples collected on the Bay of Biscay continental shelf in spring during the PELGAS integrated surveys, over the 2004–2019 period. The samples were collected at night, with a WP2 200 µm mesh size fitted with a Hydrobios (back-run stop) mechanical flowmeter, hauled vertically from the sea floor to the surface with a maximum depth set at 100 m when the bathymetry is deeper. The first dataset originates from samples collected from 2004 to 2016, imaged on land with the ZooScan and is composed of 1,153,507 imaged and measured objects. The second dataset originates from samples collected from 2016 to 2019, imaged on board the R/V Thalassa with the ZooCAM and is composed of 702,111 imaged and measured objects. The imaged objects is composed of zooplankton individuals, zooplankton pieces, non-living particles and imaging artefacts, ranging from 300 µm to 3.39 mm Equivalent Spherical Diameter, individually imaged, measured and identified. Each imaged object is geolocated, associated to a station, a survey, a year and other metadata. Each object is described by a set of morphological and grey level based features (8 bits encoding, 0 = black, 255 = white), including size, automatically extracted on each individual image. Each object was taxonomically identified using the web based application Ecotaxa with built-in, random forest and CNN based, semi-automatic sorting tools followed by expert validation or correction. The objects were sorted in 172 taxonomic and morphological groups. Each dataset features a table combining metadata and data, at the individual object granularity, from which one can easily derive quantitative population and communities descriptors such as abundances, mean sizes, biovolumes, biomasses, and size structure. Each object’s individual image is provided along with the data. These two datasets can be used combined together for ecological studies as the two instruments are interoperable, or as training sets for ZooScan and ZooCAM users.

The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions., Scientific Data, 10 (1), ISSN:2052-4463

Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump, This article is contribution number 121 of Tara Oceans.-- 19 pages, 6 figures, 2 tables, supplementary information https://doi.org/10.1038/s41598-021-94615-5.-- Data availability: Median ESD and abundance values by zooplankton groups are available at https://doi.org/10.17632/nwvjwccgvh.1. Zooplankton imaging datasets from the Tara Oceans expeditions are available through the collaborative web Ecotaxa application and repository under the addresses: https://ecotaxa.obs-vlfr.fr/prj/377, https://ecotaxa.obs-vlfr.fr/prj/2245, https://ecotaxa.obs-vlfr.fr/prj/378 for the WP2 net; https://ecotaxa.obs-vlfr.fr/prj/397, https://ecotaxa.obs-vlfr.fr/prj/398, https://ecotaxa.obs-vlfr.fr/prj/395 for the Bongo net; https://ecotaxa.obs-vlfr.fr/prj/415, https://ecotaxa.obs-vlfr.fr/prj/409, https://ecotaxa.obs-vlfr.fr/prj/408, https://ecotaxa.obs-vlfr.fr/prj/411, https://ecotaxa.obs-vlfr.fr/prj/412 for the Régent net. Contextual data from the Tara Oceans expedition, including those that are newly released from the Arctic Ocean, are available at https://doi.org/10.1594/PANGAEA.875582, Tara Oceans (which includes both the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Expeditions Foundation and the continuous support of 23 institutes (http://oceans.taraexpeditions.org). We further thank the commitment of the following sponsors: CNRS (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 (EMBL), Genoscope/CEA, The French Ministry of Research, and the French Government ‘Investissements d’Avenir’ programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), and PSL Research University (ANR-11-IDEX-0001-02). M.C.B. acknowledges postdoc fellowships from the Coordination for the Improvement of Higher Education Personnel of Brazil (CAPES) (99999.000487/2016-03) and the Fonds Français pour l'Environnement Mondial (FFEM). F.B. received support from ETH Zürich and from the European Union’s Horizon 2020 research and innovation program under grant agreement n°SEP-210591007, With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)

Tara expeditions (2009-2013) sampled the world’s oceans with standardized protocols, putting an exceptional effort into sampling plankton diversity across a large size range, using a combination of water samples and net tows. The efforts to explore the genomic diversity of plankton, through metabarcoding and metagenomics, have led to well publicized papers and have made the renown of Tara. While a similar extensive effort has been put on imaging, the datasets are not public yet. In a limited number of stations, in addition to the usual 5μm -> ~5cm Tara sampling strategy, multinet trawls allowed to sample the vertical distribution of plankton; this is the content of this dataset. Using a 300µm mesh net, it cover organisms from 300µm to ~3cm.

Tara expeditions sampled the world’s oceans with standardized protocols, putting an exceptional effort into sampling plankton diversity across a large size range, using a combination of water samples and net tows. The efforts to explore the genomic diversity of plankton, through metabarcoding and metagenomics, have led to well publicized papers and have made the renown of Tara. While a similar extensive effort has been put on imaging, the datasets are not public yet. In a limited number of stations, in addition to the usual 5μm -> ~5cm Tara sampling strategy, Bongo net samples were taken during the day and during the night, at the same station; this is the content of this dataset. Using a 300µm mesh net, it cover organisms from 300µm to ~3cm, Bongo net (300μm mesh) hauled vertically from 500m depth to the surface, once during the day, and once during the night. Sample preserved in 4% buffered formalin and stored over the long term at the Centre de Collections Planctoniques de Villefranche (CCPv). Sample scanned on a ZooScan, images processed with ZooProcess and sorted taxonomically on EcoTaxa, within the Plateforme d'Imagerie Quantitative de Villefranche (PIQv). The PIQv and CCPv platforms are part of EMBRC-France, a national Research Infrastructure supported by ANR, under the reference ANR-10-INSB-02.

The Tara Oceans project sampled contrasting ecosystems of the world oceans during a three-year expedition (2009-2013), collecting environmental data and plankton, from viruses to metazoans, on board the 36-metre Tara Schooner. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. Samples were later analysed using modern sequencing and state-of-the-art imaging technologies., We are keen to thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS, EMBL, Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects POSEIDON, BIOMARKS, PROMETHEUS, and TARA-GIRUS), FWO, BIO5, Biosphere 2, agnès b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L'Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner and its captain and crew. Tara Oceans would not exist without the continuous support of the participating 23 institutes

The Tara Oceans project sampled contrasting ecosystems of the world oceans during a three-year expedition (2009-2013), collecting environmental data and plankton, from viruses to metazoans, on board the 36-metre Tara Schooner. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. Samples were later analysed using modern sequencing and state-of-the-art imaging technologies., We are keen to thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS, EMBL, Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects POSEIDON, BIOMARKS, PROMETHEUS, and TARA-GIRUS), FWO, BIO5, Biosphere 2, agnès b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L'Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner and its captain and crew. Tara Oceans would not exist without the continuous support of the participating 23 institutes (see http://oceans.taraexpeditions.org).