biodiversity
Global scale surface meso-plankton dataset collected with High-Speed Net and imaged with ZooScan during the Tara Pacific Expedition
The Tara Pacific expedition sampled differents ecosystems of the oceans during a two-year expedition (2016-2018), collecting environmental data and surface plankton of Atlantic and Pacific Ocean, from viruses to metazoans, on board the 36-metre Tara Schooner. Mesoplankton was sampled using the High-Speed Net (330-micron mesh size), a net designed to collect plankton while sailing at high speed. See https://doi.org/10.17882/102336 for more details.
Darwin Core Archive of Global scale surface meso-plankton dataset collected with High-Speed Net and imaged with ZooScan during the Tara Pacific Expedition
Long-term monitoring of the phytoplankton at the SOMLIT-Astan Station in the Western English Channel from 2000 to present
The monitoring at the SOMLIT-Astan station (north of Roscoff - France, Western English Channel) was designed to study long term changes in phytoplankton communities in a global change context (diversity, phenology). Phytoplankton communities are monitored twice a month according to the SOMLIT monitoring program (Service d'Observation en Milieu Littoral : http://somlit.epoc.u-bordeaux1.fr/fr/), national network performing measurements of hydrological parameters. SOMLIT-Astan phytoplankton monitoring contains :1/ Microphytoplankton - Species abundances (according to Utermöhl method microphytoplankton abundances - number of cells per liter) ; 2/ Microphytoplankton - Species semi-quantitative occurrences (20µm net haul, occurrence code : "1" present, "2" numerous, "3"dominant) ; 3/ Fonctionnal groups abundances (Flowcytometry - number of cells per milliliter) : pico-, nano-phytoplankton, heterotrophic and autotrophic bacteria. The datasets that are provided include only occurrence data determined through methods 1 and 2. Flow cytometry is thus not included.
Darwin Core Archive of Long-term monitoring of the phytoplankton at the SOMLIT-Astan Station in the Western English Channel from 2000 to present
RiOMar SeineMO-2 - Phytoplankton diversity at high spatial and temporal resolution (IFCB)
The RiOMar SeineMO-2 oceanographic campaign (17 - 31 July 2024) was coordinated by the Laboratoire d'Océanologie et Géosciences (CNRS UMR 8187 LOG) on the "Côtes de la Manche" R.V. (French Oceanographic Fleet). Phytoplankton was sampled in French waters of the Eastern English Channel. The Imaging FlowCytoBot enabled imaging of nano- and microphytoplankton (10 µm to 150 µm), every 30 minutes from underwater continuous pumping in surface waters (5m), as well as in surface samples collected by Niskin bottles. Images and metadata were acquired, retrieved from IFCB using the ROI viewer software and the SYKEPIC tool, processed and identified at the Laboratoire d'Océanologie et Géosciences (CNRS UMR 8187 LOG). The discrete dataset corresponds to the 53 stations sampled during the campaign. There are two samples per station to process a total of 10 mL of sampled seawater.
Darwin Core Archive of RiOMar SeineMO-2 - Phytoplankton diversity at high spatial and temporal resolution (IFCB)
Occurrences of planktonic organisms imaged by an Underwater Vision Profiler 6 on a SeaExplorer glider during the 2021 spring bloom in the North Western Mediterranean Sea
Regular glider surveys are conducted in the Ligurian Sea (North Western Mediterranean), between Nice and the DYFAMED sampling point. Between February and June 2021, i.e. during the spring bloom, the glider was equipped with an Underwater Vision Profiler: an intelligent camera system that records and process images, yielding images of all objects larger than ~600µm in Equivalent Spherical Diameter. These objects where then taxinomically assigned. For more details on the method see https://doi.org/10.1002/lno.12566.
Darwin Core Archive of Occurrences of planktonic organisms imaged by an Underwater Vision Profiler 6 on a SeaExplorer glider during the 2021 spring bloom in the North Western Mediterranean Sea
International Bottom Trawl Survey 2023 - Phytoplankton diversity at high spatial and temporal resolution (IFCB)
The IBTS 2023 fisheries campaign (January 25 - February 13, 2023) was coordinated by IFREMER on the "Thalassa" R.V. (French Oceanographic Fleet). Plankton was sampled in the Eastern English Channel and the North Sea. The Imaging FlowCytoBot enabled imaging of nano- and microphytoplankton (10 µm to 150 µm), every 30 minutes from underwater continuous pumping in surface waters (5m), as well as in surface samples collected by Niskin bottles. Images and metadata were acquired, retrieved from IFCB using the ROI viewer software and the SYKEPIC tool, processed and identified at the Laboratoire d'Océanologie et Géosciences (CNRS UMR 8187 LOG). The discrete dataset corresponds to the 143 stations sampled during the campaign. There are two samples per station to process a total of 10 mL of sampled seawater.
Darwin Core Archive of International Bottom Trawl Survey 2023 - Phytoplankton diversity at high spatial and temporal resolution (IFCB)
International Bottom Trawl Survey 2024 - Phytoplankton diversity at high spatial and temporal resolution (IFCB)
The IBTS 2024 fisheries campaign (January 20 - February 8, 2024) was coordinated by IFREMER on the "Thalassa" R.V. (French Oceanographic Fleet). Phytoplankton was sampled in the eastern English Channel and the southern North Sea. The Imaging FlowCytoBot enabled imaging of nano- and microphytoplankton (10 µm to 150 µm), every 30 minutes from underwater continuous pumping in surface waters (5m), as well as in surface samples collected by Niskin bottles. Images and metadata were acquired, retrieved from IFCB using the ROI viewer software and the SYKEPIC tool, processed and identified at the Laboratoire d'Océanologie et Géosciences (CNRS UMR 8187 LOG). The discrete dataset corresponds to the 108 stations sampled during the campaign. There are two samples per station to process a total of 10 mL of seawater.
Darwin Core Archive of International Bottom Trawl Survey 2024 - Phytoplankton diversity at high spatial and temporal resolution (IFCB)
Global scale surface meso-plankton dataset collected with Deck Net and imaged with Flowcam during the Tara Pacific Expedition
The Tara Pacific expedition sampled differents ecosystems of the oceans during a two-year expedition (2016-2018), collecting environmental data and surface plankton of Atlantic and Pacific Ocean, from viruses to metazoans, on board the 36-metre Tara Schooner. Surface microplankton were collected using a custom-built water pumping system called the Dolphin, designed for use while sailing at high speed. The pumped water was filtered through a 20 µm mesh net (Deck-Net) installed on the deck of the schooner Tara. See https://doi.org/10.17882/102697 for more details.
Darwin Core Archive of Global scale surface meso-plankton dataset collected with Deck Net and imaged with Flowcam during the Tara Pacific Expedition
Plankton community sampled during the Tara Europa expedition with a WP2 net (20µm) and analysed with a Flowcam.
The Tara EUROPA expedition (April 2023 – July 2024) sampled plankton – from microplankton (20 µm) to macroplankton (a few centimeters) along European coasts. Meso- and macroplankton were sampled using a 20 µm WP2 net yielding FCAM20 samples for Flowcam analysis. Images were acquired and processed at sea then identified at the Quantitative Imaging Platform of Villefranche (PIQv).
Darwin Core Archive of Plankton community sampled during the Tara Europa expedition with a WP2 net (20µm) and analysed with a Flowcam.
RiOMar SeineMO-1 - Phytoplankton diversity at high spatial and temporal resolution (IFCB)
The RiOMar SeineMO-I oceanographic campaign (3 - 8 may 2024) was coordinated by the Laboratoire d'Océanologie et Géosciences (CNRS UMR 8187 LOG) on the "Côtes de la Manche" R.V. (French Oceanographic Fleet). Phytoplankton was sampled in French waters of the Eastern English Channel. The Imaging FlowCytoBot enabled imaging nano and microphytoplankton (10 µm to 150 µm), every 30 minutes from underwater continuous pumping in surface waters (3m), as well as in surface samples collected by Niskin bottles. Images and metadata were acquired, retrieved from IFCB using the ROI viewer software and the SYKEPIC tool, processed and identified at the Laboratoire d'Océanologie et Géosciences (CNRS UMR 8187 LOG). The discrete dataset corresponds to the 20 stations sampled during the campaign. There are two samples per station to process a total of 10 mL of sampled seawater.
Darwin Core Archive of RiOMar SeineMO-1 - Phytoplankton diversity at high spatial and temporal resolution (IFCB)
Specific diversity data of macrobenthic communities in the "Pierre Noire" study site in the English Channel from 1977 on
The experiment was designed to study long-term changes in communities strucutre in response to global change (climatic change) and local anthropogenis pressures (e.g. eutrophication). Fine sand macrobenthic communities are monitored two to five times a year at the "Pierre Noire" site. The different parameters wich are measured are (1) total and specific abundances, (2) specific richness
Darwin Core Archive of Specific diversity data of macrobenthic communities in the "Pierre Noire" study site in the English Channel from 1977 on
Biological samples from the french oceanographic fleet's deep-sea cruises
Description of biological samples collected during deep-sea campaigns operated by the French oceanographic fleet since 2011. These data are acquired by underwater devices during the campaigns and then stored by Ifremer's CNDO (Centre National de Donnees Oceanographiques) Sismer. These data are mainly located in the Mid-Atlantic Ridge and around mainland France.
Darwin Core Archive of Biological samples from the french oceanographic fleet's deep-sea cruises
Global scale surface meso-plankton dataset collected with Manta Net and imaged with ZooScan during the Tara Pacific Expedition
The Tara Pacific expedition sampled differents ecosystems of the oceans during a two-year expedition (2016-2018), collecting environmental data and surface plankton of Atlantic and Pacific Ocean, from viruses to metazoans, on board the 36-metre Tara Schooner. Mesoplankton and plastics were sampled using the Manta (300-micron mesh size) at sea surface. See https://doi.org/10.17882/102537 for more details.
Darwin Core Archive of Global scale surface meso-plankton dataset collected with Manta Net and imaged with ZooScan during the Tara Pacific Expedition
Metabarcoding dataset of plankton, in the northwestern Mediterranean, from MOOSE-GE campaigns (2017-2019).
MOOSE GE is a yearly ocean-monitoring cruise which is part of the MOOSE program https://www.moose-network.fr, within the Research Infrastructure ILICO, the aim of which is to monitor the North-Western Mediterranean (considered to act as a model system for larger ocean basins).This dataset contains the taxonomic occurrence from metabarcoding collected by triple net (64, 200 to 500µm mesh) and niskin bottle.
Darwin Core Archive of Metabarcoding dataset of plankton, in the northwestern Mediterranean, from MOOSE-GE campaigns (2017-2019).
Phytoplankton monitoring at the Château du Taureau Station in the Western English Channel, from 2009 to 2011
The monitoring at the Château du Taureau station (north Brittany - France, Western English Channel) was designed to study the influence of trophic conditions on larval development of the invasive species Crepidula fornicata. From 2009 to 2011, phytoplankton communities were monitored twice a month in the frame of a research work on Crepidula fornicata larvae. :1/ Microphytoplankton - Species abundances (according to Utermöhl method microphytoplankton abundances - number of cells per liter) ; 2/ Microphytoplankton - Species occurrences (20µm net haul, occurrence code : "1" for present).
Darwin Core Archive of Phytoplankton monitoring at the Château du Taureau Station in the Western English Channel, from 2009 to 2011
Roscoff inventories: marine fauna and flora since 1800
" Inventories list marine species observations performed in Roscoff area since 1800. Observations result from a review of historical literature and observations made by voluntary contributors and the scientific teams of the Roscoff Marine Station. Taxonomic groups documenting in the inventories are macroalgae, marine benthic macroinvertebrates and fish. Inventories provide information (when known) about location, collection date, collection type, collector, and species biology (habitat, reproduction period, …).
Darwin Core Archive of Roscoff inventories: marine fauna and flora since 1800
Separating faces in ARMS metabarcoding improves marine biodiversity monitoring
Monitoring marine biodiversity requires approaches that capture its full complexity through space and time. DNA metabarcoding coupled with Autonomous Reef Monitoring Structures (ARMS) is increasingly used for this purpose, yet most applications still pool all sessile fractions and rarely benchmark molecular ouputs against photographic observations. Here, we combined photographic analysis with cytochrome c oxidase I (COI) metabarcoding across ten north-western Mediterranean sites to test, compare, and refine ARMS-based monitoring protocols. We first optimized laboratory procedures (DNA extraction and polymerase choice) and applied the control-driven, replicate-aware VTAM pipeline to minimize false positives and ensure full traceability. We then conducted the first face-by-face comparison of α- and β-diversity between imaging and eDNA in which each individual ARMS face was metabarcoded separately rather than pooled.
Darwin Core Archive of Separating faces in ARMS metabarcoding improves marine biodiversity monitoring
Plankton community in Juday-Bogorov net (330µm) (since 1966) Point B, Villefranche-sur-Mer, France
This series is part of the long term planktonic monitoring of Villefranche-sur-mer, which is one of the oldest and richest in the world, running from 1966. It aims at describing the dynamics of the mesozooplankton community. The data collection and processing has been funded by several projects over its lifetime. It is currently supported directly by the Institut de la Mer de Villefranche (IMEV), as part of its long term monitoring effort. This dataset contains the planktonic organisms collected by a Juday-Bogorov net (330µm mesh) and therefore cover organisms from ~300µm to ~2cm.
Darwin Core Archive of Plankton community in Juday-Bogorov net (330µm) (since 1966) Point B, Villefranche-sur-Mer, France
Pour gérer les données de la surveillance du littoral, l'Ifremer a développé le système d'information Quadrige , qui associe à une base de données une panoplie d'outils d'interprétation et d'élaboration de produits d'information. Quadrige constitue un élément du Système d'Information sur l'Eau (SIE) http://www.eaufrance.fr, et à ce titre, contribue aux travaux du Secrétariat d'Administration National des Données Relatives à l'Eau (SANDRE) http://www.sandre.eaufrance.fr.
Plankton community sampled during the Tara Europa expedition with a WP2 net (200µm) and analysed with a ZooScan
The Tara EUROPA expedition (April 2023 – July 2024) sampled plankton – from microplankton (20 µm) to macroplankton (a few centimeters) along European coasts. Meso- and macroplankton were sampled using a 200 µm WP2 net yielding F200 samples for ZooScan analysis. Images were acquired, processed and identified at the Quantitative Imaging Platform of Villefranche (PIQv)
Darwin Core Archive of Plankton community sampled during the Tara Europa expedition with a WP2 net (200µm) and analysed with a ZooScan
Meiofauna, nematodes and associated sediment characteristics of the mangrove-colonized banks of Cayenne estuary (French Guiana) during the wet season of 2022
Since 2015, an interdisciplinary team of researchers collect and analyze data on French Overseas mangroves with conservation aims, following French legislation called “Directive Cadre sur l’Eau” (DCE) and the demands of the Institutions. In March 2022, the working group has been sampling in French Guiana, namely in the Cayenne estuary during an unforeseen rainy season which marked the rainfall record of the past decades. The locations chosen along the estuary mirrored the opposite marine and terrestrial inputs as well as the influence of the city of Cayenne at the mouth of the estuary. The transects at every sampling location aimed at representing the local heterogeneity of the mangroves, from uncolonized bare mud to dense roots and tall adult trees. Biotic (meiofauna and nematodes) as well as abiotic parameters (pH, redox potential, salinity, CHN, stable isotopes, grain size and pigments) have been sampled for.
Darwin Core Archive of Meiofauna, nematodes and associated sediment characteristics of the mangrove-colonized banks of Cayenne estuary (French Guiana) during the wet season of 2022
Global scale surface micro-plankton dataset collected with Bongo nets and imaged with FlowCam during the Tara Pacific Expedition
The Tara Pacific expedition sampled differents ecosystems of the oceans during a two-year expedition (2016-2018), collecting environmental data and surface plankton of Atlantic and Pacific Ocean, from viruses to metazoans, on board the 36-metre Tara Schooner. Mesoplankton and plastics were collected with the Bongo nets by scuba divers using an underwater scooter. Samples were taken from the surface, near reefs and lagoons in the Pacific. See https://doi.org/10.17882/102694 and https://doi.org/10.5194/essd-17-2761-2025 for more details.
Darwin Core Archive of Global scale surface micro-plankton dataset collected with Bongo nets and imaged with FlowCam during the Tara Pacific Expedition
Channel Ground Fish Survey 2024 - Leg 2 - Phytoplankton diversity at high spatial and temporal resolution (IFCB)
The Channel Ground Fish Survey (CGFS) 2024 autumn fisheries campaign - Leg 2 (1 - 17 October, 2024) ) was coordinated by IFREMER on the "Thalassa" R.V. (French Oceanographic Fleet). Phytoplankton was sampled in the eastern English Channel from Cherbourg to Boulogne sur Mer, in both French and English waters. The Imaging FlowCytoBot (IFCB) enabled imaging of nano- and microphytoplankton (10 µm to 150 µm) every 30 minutes from underwater continuous pumping in surface waters (3m), as well as in surface samples collected by Niskin bottles. Images and metadata were acquired, retrieved from IFCB using the ROI viewer software and the SYKEPIC tool, processed and identified at the Laboratoire d'Océanologie et Géosciences (CNRS UMR 8187 LOG). The dataset corresponds to the 78 stations sampled during the campaign, along with the continuous data. There are two samples per station to process a total of 10 mL of sampled seawater.
Darwin Core Archive of Channel Ground Fish Survey 2024 - Leg 2 - Phytoplankton diversity at high spatial and temporal resolution (IFCB)
Plankton community sampled during the Tara Europa expedition with a Régent net (680µm) and analysed with a ZooScan
The Tara EUROPA expedition (April 2023 – July 2024) sampled plankton – from microplankton (20 µm) to macroplankton (a few centimeters) along European coasts. Meso- and macroplankton were sampled using a 680 µm Régent net yielding F680 samples for ZooScan analysis. Images were acquired, processed and identified at the Quantitative Imaging Platform of Villefranche (PIQv).
Darwin Core Archive of Plankton community sampled during the Tara Europa expedition with a Régent net (680µm) and analysed with a ZooScan
Specific diversity data of macrobenthic communities in the "Rivière de Morlaix" study site in the English Channel from 1977 to 1996
The experiment was designed to study long-term changes in communities strucutre in response to global change (climatic change) and local anthropogenis pressures (e.g. eutrophication). Muddy sand macrobenthic communities are monitored five times a year at the "Rivière de Morlaix" site. The different parameters wich are measured are: (1) total and specific abundances, (2) specific richness
Darwin Core Archive of Specific diversity data of macrobenthic communities in the "Rivière de Morlaix" study site in the English Channel from 1977 to 1996
CARPARC - Phytoplankton diversity at high spatial and temporal resolution (IFCB)
The CARPARC oceanographic campaign (3 - 8 may 2024) was coordinated by IFREMER on the "Côtes de la Manche" R.V. (French Oceanographic Fleet) in the frame of the CARPARC project funded by the OFB. Phytoplankton was sampled in French waters of the Eastern English Channel in the Parc Naturel Marin des Caps et Marais d'Opale (EPMO). The Imaging FlowCytoBot enabled imaging of nano- and microphytoplankton (10 µm to 150 µm), every 30 minutes from underwater continuous pumping in surface waters (3m), as well as in surface samples collected by Niskin bottles. Images and metadata were acquired, retrieved from IFCB using the ROI viewer software and the SYKEPIC tool, processed and identified at the Laboratoire d'Océanologie et Géosciences (CNRS UMR 8187 LOG). The discrete dataset corresponds to the 37 stations sampled during the campaign, along with the continuous data. There are two samples per station to process a total of 10 mL of sampled seawater.
Darwin Core Archive of CARPARC - Phytoplankton diversity at high spatial and temporal resolution (IFCB)
IFREMER - French Research Institute for Exploitation of the Sea
Institut Universitaire Européen de la Mer