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.2015 May 26:2:150023.
doi: 10.1038/sdata.2015.23. eCollection 2015.

Open science resources for the discovery and analysis of Tara Oceans data

Collaborators, Affiliations

Open science resources for the discovery and analysis of Tara Oceans data

Stéphane Pesant et al. Sci Data..

Abstract

The Tara Oceans expedition (2009-2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. The interpretation of such an extensive collection of samples in their ecological context requires means to explore, assess and access raw and validated data sets. To address this challenge, the Tara Oceans Consortium offers open science resources, including the use of open access archives for nucleotides (ENA) and for environmental, biogeochemical, taxonomic and morphological data (PANGAEA), and the development of on line discovery tools and collaborative annotation tools for sequences and images. Here, we present an overview of Tara Oceans Data, and we provide detailed registries (data sets) of all campaigns (from port-to-port), stations and sampling events.

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1. Sampling devices and working areas on-board SVTara.
Sampling devices and working areas on-board SVTara are shown from the vessel’s[a] side-view,[b] bird’s-eye-view of the deck, and[c] inside-view. They consist of the[1] Continuous Surface Sampling System [CSSS];[2] Rosette Vertical Sampling System [RVSS];[3] wet lab and storage in liquid nitrogen;[4] High Volume Peristaltic pump [HVP-PUMP];[5] dry lab;[6] oceanography engineers data acquisition and processing area;[7] winch;[8] video imaging area;[9] storage areas at room temperature;[10] storage areas at +4 °C and −20 °C;[11] MilliQ water system and AC-s system;[12] diving equipment, flowcytobot and ALPHA instruments; and[13] storage boxes. The flow of seawater from the continuous surface sampling system to the dry lab is shown in blue.
Figure 2
Figure 2. Sampling route and stations of theTara Oceans Expedition.
Sampling route of theTara Oceans Expedition (green track), showing station labels and areas (blue shade) where the annual mean oxygen concentration is <2 ml/l (WOA09), usually corresponding also to high CO2 concentration and low pH. Detailed information about each station is given in (Data Citation 7).
Figure 3
Figure 3. Sampling route, stations and topical experiments of theTara Oceans Expedition.
Sampling route of theTara Oceans Expedition (green track), showing stations where plankton were sampled in their environmental context (full red dots) and where only environmental conditions were measured (open red dots). Topical experiments are identified along the sampling route (light blue). Longhurst biogeographical provinces are shown in the background and those sampled duringTara Oceans Expedition are highlighted in blue.
Figure 4
Figure 4. Spatial representation and chronology of sampling events during a 24-48 h station.
Coloured markers along the route ofSV Tara (yellow surface track) correspond to sampling events targeting thesurface water layer (red, ),deep chlorophyll maximum layer (green, here at 50 m), and themesopelagic zone (blue, here at 400 m). At some stations, an Argo drifter (10-m floating anchor and satellite positioning) was used to follow the water mass during sampling (black surface track). White and grey markers correspond to day and night time deployments, respectively, of plankton nets [TYPE-MESH] and rosette [RVSS] casts that covered fixed depth layers of 0–100 m, 0–500 m or 0–1,000 m.
Figure 5
Figure 5. Empirical basis for the size-fractionation approach and the choice of sampling devices.
The horizontal plane shows the range of body/cell size and natural abundances reported in the literature (Table 2) for viruses (including giant viruses), prokaryotes, protists and metazoans (coloured boxes). The sampling devices used to collect plankton<5 μm in size (i.e., high volume peristaltic pump and rosette with Niskin bottles) and >5 μm in size (i.e., plankton nets) are illustrated as well on the horizontal plane. The vertical plane shows the volume of seawater required to capture 100, 75 and 50% of species richness reported in the literature (Table 2) for viruses (including giant viruses), prokaryotes, protists and metazoans (shaded boxes). The typical volume of seawater collected by sampling devices are shown in comparison (horizontal thick lines). Also illustrated on the vertical plane: Sieves were used to remove large organisms from protists net samples.
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References

Data Citations

    1. France Météo, Tara Oceans Consortium C., Tara Oceans Expedition P. 2014. PANGAEA.doi:10.1594/PANGAEA.836312 - DOI
    1. Boss E., Tara Oceans Consortium C., Tara Oceans Expedition P. 2014. PANGAEA.doi:10.1594/PANGAEA.836318 - DOI
    1. Reverdin G., Le Goff H., Tara Oceans Consortium C., Tara Oceans Expedition P. 2014. PANGAEA.doi:10.1594/PANGAEA.836320 - DOI
    1. Picheral M. 2014. PANGAEA.doi:10.1594/PANGAEA.836321 - DOI
    1. Picheral M. 2014. PANGAEA.doi:10.1594/PANGAEA.836319 - DOI

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