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  • Fondation Tara Expeditions; FondTara; Tara_Oceans_2009-2013; Tara Oceans Expedition  (4)
  • Acoustics  (1)
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  • 1
    Publication Date: 2023-03-08
    Description: The present data set provides a tab separated text file compressed in a zip archive. The file includes metadata for each TaraOceans V9 rDNA metabarcode including the following fields:md5sum = unique identifier; lineage = taxonomic path associated to the metabarcode; pid = % identity to the closest reference barcode from V9_PR2; sequence = nucleotide sequence of the metabarcode; refs = identity of the best hit reference sequence(s); TARA_xxx = number of occurrences of this barcode in each of the 334 samples; totab = total abundance of the barcode ; cid = identifier of the OTU to which the barcode belongs; and taxogroup = high-taxonomic level assignation of this barcode. The file also includes three categories of functional annotations: (1) Chloroplast: yes, presence of permanent chloroplast; no, absence of permanent chloroplast ; NA, undetermined. (2) Symbiont (small partner): parasite, the species is a parasite; commensal, the species is a commensal; mutualist, the species is a mutualist symbiont, most often a microalgal taxon involved in photosymbiosis; no the species is not involved in a symbiosis as small partner; NA, undetermined. (3) Symbiont (host): photo, the host species relies on a mutualistic microalgal photosymbiont to survive (obligatory photosymbiosis); photo_falc, same as photo, but facultative relationship; photo_klep, the host species maintains chloroplasts from microalgal prey(s) to survive; photo_klep_falc, same as photo_klep, but facultative; Nfix, the host species must interact with a mutualistic symbiont providing N2 fixation to survive; Nfix_falc, same as Nfix, but facultative; no, the species is not involved in any mutualistic symbioses; NA, undetermined. For example, the collodarian/Brandtodinium symbiosis is annotated: Chloroplast, "no"; Symbiont (small), "no"; Symbiont (host), "photo", for the collodarian host; and: Chloroplast, "yes"; Symbiont (small), "mutualist"; Symbiont (host), "no", for the dinoflagellate microalgal endosymbiont.chloroplast = "yes", "no" or "NA"; symbiont.small = "parasite", "commensal", "mutualist", "no" or "NA"; symbiont.host = "photo", "photo_falc", "photo_klep", "Nfix", no or NA; benef = "Nfix", "no" or "NA"; trophism = Metazoa , heterotroph , NA , photosymbiosis , phototroph according to the previous fields.
    Keywords: Fondation Tara Expeditions; FondTara; Tara_Oceans_2009-2013; Tara Oceans Expedition
    Type: Dataset
    Format: application/zip, 710.6 MBytes
    Location Call Number Limitation Availability
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  • 2
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    Unknown
    PANGAEA
    In:  Supplement to: De Vargas, Colomban; Audic, Stephane; Henry, Nicolas; Decelle, Johan; Mahe, Jean-Claude; Logares, Ramiro; Lara, Enrique; Berney, Cédric; Le Bescot, Noan; Probert, Ian; Carmichael, Margaux; Poulain, Julie; Romac, Sarah; Colin, Sébastien; Aury, Jean-Marc; Bittner, Lucie; Chaffron, Samuel; Dunthorn, Micah; Engelen, Stefan; Flegontova, Olga; Horák, Aleš; Jaillon, Olivier; Lima-Mendez, Gipsi; Lukes, Julius; Malviya, Shruti; Morard, Raphael; Mulot, Matthieu; Scalco, Eleonora; Siano, Raffaele; Zingone, Adriana; Picheral, Marc; Searson, Sarah; Kandels-Lewis, Stefanie; Acinas, Silvia G; Gorsky, G; Grimsley, Nigel; Hingamp, Pascal; Iudicone, Daniele; Not, Fabrice; Ogata, Hiroyuki; Sieracki, Michael E; Speich, Sabrina; Stemmann, Lars; Sunagawa, Shinichi; Wincker, Patrick; Karsenti, Eric (2015): First Tara Oceans V9 rDNA metabarcoding dataset. zenodo, https://doi.org/10.5281/zenodo.15600
    Publication Date: 2024-01-06
    Description: The present data set provides an Excel file in a zip archive. The file lists 334 samples of size fractionated eukaryotic plankton community with a suite of associated metadata (Database W1). Note that if most samples represented the piconano- (0.8-5 µm, 73 samples), nano- (5-20 µm, 74 samples), micro- (20-180 µm, 70 samples), and meso- (180-2000 µm, 76 samples) planktonic size fractions, some represented different organismal size-fractions: 0.2-3 µm (1 sample), 0.8-20 µm (6 samples), 0.8 µm - infinity (33 samples), and 3-20 µm (1 sample). The table contains the following fields: a unique sample sequence identifier; the sampling station identifier; the Tara Oceans sample identifier (TARA_xxxxxxxxxx); an INDSC accession number allowing to retrieve raw sequence data for the major nucleotide databases (short read archives at EBI, NCBI or DDBJ); the depth of sampling (Subsurface - SUR or Deep Chlorophyll Maximum - DCM); the targeted size range; the sequences template (either DNA or WGA/DNA if DNA extracted from the filters was Whole Genome Amplified); the latitude of the sampling event (decimal degrees); the longitude of the sampling event (decimal degrees); the time and date of the sampling event; the device used to collect the sample; the logsheet event corresponding to the sampling event ; the volume of water sampled (liters). Then follows information on the cleaning bioinformatics pipeline shown on Figure W2 of the supplementary litterature publication: the number of merged pairs present in the raw sequence file; the number of those sequences matching both primers; the number of sequences after quality-check filtering; the number of sequences after chimera removal; and finally the number of sequences after selecting only barcodes present in at least three copies in total and in at least two samples. Finally, are given for each sequence sample: the number of distinct sequences (metabarcodes); the number of OTUs; the average number of barcode per OTU; the Shannon diversity index based on barcodes for each sample (URL of W4 dataset in PANGAEA); and the Shannon diversity index based on each OTU (URL of W5 dataset in PANGAEA).
    Keywords: Fondation Tara Expeditions; FondTara; Tara_Oceans_2009-2013; Tara Oceans Expedition
    Type: Dataset
    Format: application/zip, 51.7 kBytes
    Location Call Number Limitation Availability
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  • 3
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    Unknown
    PANGAEA
    In:  Supplement to: De Vargas, Colomban; Audic, Stephane; Henry, Nicolas; Decelle, Johan; Mahe, Jean-Claude; Logares, Ramiro; Lara, Enrique; Berney, Cédric; Le Bescot, Noan; Probert, Ian; Carmichael, Margaux; Poulain, Julie; Romac, Sarah; Colin, Sébastien; Aury, Jean-Marc; Bittner, Lucie; Chaffron, Samuel; Dunthorn, Micah; Engelen, Stefan; Flegontova, Olga; Horák, Aleš; Jaillon, Olivier; Lima-Mendez, Gipsi; Lukes, Julius; Malviya, Shruti; Morard, Raphael; Mulot, Matthieu; Scalco, Eleonora; Siano, Raffaele; Zingone, Adriana; Picheral, Marc; Searson, Sarah; Kandels-Lewis, Stefanie; Acinas, Silvia G; Gorsky, G; Grimsley, Nigel; Hingamp, Pascal; Iudicone, Daniele; Not, Fabrice; Ogata, Hiroyuki; Sieracki, Michael E; Speich, Sabrina; Stemmann, Lars; Sunagawa, Shinichi; Wincker, Patrick; Karsenti, Eric (2015): First Tara Oceans V9 rDNA metabarcoding dataset. zenodo, https://doi.org/10.5281/zenodo.15600
    Publication Date: 2024-01-06
    Description: The present data set provides a tab separated text file compressed in a zip archive. The file includes metadata for each TaraOceans V9 rDNA metabarcode including the following fields: md5sum = unique identifier; lineage = taxonomic path associated to the metabarcode; pid = % identity to the closest reference barcode from V9_PR2; sequence = nucleotide sequence of the metabarcode; refs = identity of the best hit reference sequence(s); TARA_xxx = number of occurrences of this barcode in each of the 334 samples; totab = total abundance of the barcode ; cid = identifier of the OTU to which the barcode belongs; and taxogroup = high-taxonomic level assignation of this barcode. The file also includes three categories of functional annotations: (1) Chloroplast: yes, presence of permanent chloroplast; no, absence of permanent chloroplast ; NA, undetermined. (2) Symbiont (small partner): parasite, the species is a parasite; commensal, the species is a commensal; mutualist, the species is a mutualist symbiont, most often a microalgal taxon involved in photosymbiosis; no the species is not involved in a symbiosis as small partner; NA, undetermined. (3) Symbiont (host): photo, the host species relies on a mutualistic microalgal photosymbiont to survive (obligatory photosymbiosis); photo_falc, same as photo, but facultative relationship; photo_klep, the host species maintains chloroplasts from microalgal prey(s) to survive; photo_klep_falc, same as photo_klep, but facultative; Nfix, the host species must interact with a mutualistic symbiont providing N2 fixation to survive; Nfix_falc, same as Nfix, but facultative; no, the species is not involved in any mutualistic symbioses; NA, undetermined. For example, the collodarian/Brandtodinium symbiosis is annotated: Chloroplast, "no"; Symbiont (small), "no"; Symbiont (host), "photo", for the collodarian host; and: Chloroplast, "yes"; Symbiont (small), "mutualist"; Symbiont (host), "no", for the dinoflagellate microalgal endosymbiont.chloroplast = "yes", "no" or "NA"; symbiont.small = "parasite", "commensal", "mutualist", "no" or "NA"; symbiont.host = "photo", "photo_falc", "photo_klep", "Nfix", no or NA; benef = "Nfix", "no" or "NA"; trophism = Metazoa , heterotroph , NA , photosymbiosis , phototroph according to the previous fields.
    Keywords: Fondation Tara Expeditions; FondTara; Tara_Oceans_2009-2013; Tara Oceans Expedition
    Type: Dataset
    Format: application/zip, 252.1 MBytes
    Location Call Number Limitation Availability
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  • 4
    facet.materialart.
    Unknown
    PANGAEA
    In:  Supplement to: De Vargas, Colomban; Audic, Stephane; Henry, Nicolas; Decelle, Johan; Mahe, Jean-Claude; Logares, Ramiro; Lara, Enrique; Berney, Cédric; Le Bescot, Noan; Probert, Ian; Carmichael, Margaux; Poulain, Julie; Romac, Sarah; Colin, Sébastien; Aury, Jean-Marc; Bittner, Lucie; Chaffron, Samuel; Dunthorn, Micah; Engelen, Stefan; Flegontova, Olga; Horák, Aleš; Jaillon, Olivier; Lima-Mendez, Gipsi; Lukes, Julius; Malviya, Shruti; Morard, Raphael; Mulot, Matthieu; Scalco, Eleonora; Siano, Raffaele; Zingone, Adriana; Picheral, Marc; Searson, Sarah; Kandels-Lewis, Stefanie; Acinas, Silvia G; Gorsky, G; Grimsley, Nigel; Hingamp, Pascal; Iudicone, Daniele; Not, Fabrice; Ogata, Hiroyuki; Sieracki, Michael E; Speich, Sabrina; Stemmann, Lars; Sunagawa, Shinichi; Wincker, Patrick; Karsenti, Eric (2015): First Tara Oceans V9 rDNA metabarcoding dataset. zenodo, https://doi.org/10.5281/zenodo.15600
    Publication Date: 2024-01-06
    Description: The present data set provides a tab separated text file compressed in a zip archive. The file includes metadata for each TaraOceans V9 rDNA OTU including the following fields: md5sum = identifier of the representative (most abundant) sequence of the swarm; cid = identifier of the OTU; totab = total abundance of barcodes in this OTU; TARA_xxx = number of occurrences of barcodes in this OTU in each of the 334 samples;rtotab = total abundance of the representative barcode; pid = percentage identity of the representative barcode to the closest reference sequence from V9_PR2; lineage = taxonomic path assigned to the representative barcode ; refs = best hit reference sequence(s) with respect to the representative barcode ; taxogroup = high-taxonomic level assignation of the representative barcode. The file also includes three categories of functional annotations: (1) Chloroplast: yes, presence of permanent chloroplast; no, absence of permanent chloroplast ; NA, undetermined. (2) Symbiont (small partner): parasite, the species is a parasite; commensal, the species is a commensal; mutualist, the species is a mutualist symbiont, most often a microalgal taxon involved in photosymbiosis; no the species is not involved in a symbiosis as small partner; NA, undetermined. (3) Symbiont (host): photo, the host species relies on a mutualistic microalgal photosymbiont to survive (obligatory photosymbiosis); photo_falc, same as photo, but facultative relationship; photo_klep, the host species maintains chloroplasts from microalgal prey(s) to survive; photo_klep_falc, same as photo_klep, but facultative; Nfix, the host species must interact with a mutualistic symbiont providing N2 fixation to survive; Nfix_falc, same as Nfix, but facultative; no, the species is not involved in any mutualistic symbioses; NA, undetermined.
    Keywords: Fondation Tara Expeditions; FondTara; Tara_Oceans_2009-2013; Tara Oceans Expedition
    Type: Dataset
    Format: application/zip, 16.5 MBytes
    Location Call Number Limitation Availability
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  • 5
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Capotondi, A., Jacox, M., Bowler, C., Kavanaugh, M., Lehodey, P., Barrie, D., Brodie, S., Chaffron, S., Cheng, W., Dias, D. F., Eveillard, D., Guidi, L., Iudicone, D., Lovenduski, N. S., Nye, J. A., Ortiz, I., Pirhalla, D., Buil, M. P., Saba, V., Sheridan, S., Siedlecki, S., Subramanian, A., de Vargas, C., Di Lorenzo, E., Doney, S. C., Hermann, A. J., Joyce, T., Merrifield, M., Miller, A. J., Not, F., & Pesant, S. Observational needs supporting marine ecosystems modeling and forecasting: from the global ocean to regional and coastal systems. Frontiers in Marine Science, 6, (2019): 623, doi:10.3389/fmars.2019.00623.
    Description: Many coastal areas host rich marine ecosystems and are also centers of economic activities, including fishing, shipping and recreation. Due to the socioeconomic and ecological importance of these areas, predicting relevant indicators of the ecosystem state on sub-seasonal to interannual timescales is gaining increasing attention. Depending on the application, forecasts may be sought for variables and indicators spanning physics (e.g., sea level, temperature, currents), chemistry (e.g., nutrients, oxygen, pH), and biology (from viruses to top predators). Many components of the marine ecosystem are known to be influenced by leading modes of climate variability, which provide a physical basis for predictability. However, prediction capabilities remain limited by the lack of a clear understanding of the physical and biological processes involved, as well as by insufficient observations for forecast initialization and verification. The situation is further complicated by the influence of climate change on ocean conditions along coastal areas, including sea level rise, increased stratification, and shoaling of oxygen minimum zones. Observations are thus vital to all aspects of marine forecasting: statistical and/or dynamical model development, forecast initialization, and forecast validation, each of which has different observational requirements, which may be also specific to the study region. Here, we use examples from United States (U.S.) coastal applications to identify and describe the key requirements for an observational network that is needed to facilitate improved process understanding, as well as for sustaining operational ecosystem forecasting. We also describe new holistic observational approaches, e.g., approaches based on acoustics, inspired by Tara Oceans or by landscape ecology, which have the potential to support and expand ecosystem modeling and forecasting activities by bridging global and local observations.
    Description: This study was supported by the NOAA’s Climate Program Office’s Modeling, Analysis, Predictions, and Projections (MAPP) Program through grants NA17OAR4310106, NA17OAR4310104, NA17OAR4310108, NA17OAR4310109, NA17OAR4310110, NA17OAR4310111, NA17OAR4310112, and NA17OAR4310113. This manuscript is a product of the NOAA/MAPP Marine Prediction Task Force. The Tara Oceans consortium acknowledges support from the CNRS Research Federation FR2022 Global Ocean Systems Ecology and Evolution, and OCEANOMICS (grant agreement ‘Investissement d’Avenir’ ANR-11-BTBR-0008). This is article number 95 of the Tara Oceans consortium. MK and SD acknowledge support from NASA grant NNX14AP62A “National Marine Sanctuaries as Sentinel Sites for a Demonstration Marine Biodiversity Observation Network (MBON)” funded under the National Ocean Partnership Program (NOPP RFP NOAA-NOS-IOOS-2014-2003803 in partnership between NOAA, BOEM, and NASA), and the NOAA Integrated Ocean Observing System (IOOS) Program Office. WC, IO, and AH acknowledge partial support from the Joint Institute for the Study of the Atmosphere and Ocean (JISAO) under NOAA Cooperative Agreement NA15OAR4320063, Contribution No. 2019-1029. This study received support from the European H2020 International Cooperation project MESOPP (Mesopelagic Southern Ocean Prey and Predators), grant agreement no. 692173.
    Keywords: Marine ecosystems ; Modeling and forecasting ; Seascapes ; Genetics ; Acoustics
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Limitation Availability
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