Tara Pacific - A pan-ecosystemic approach to the -omics complexity of coral reef holobionts across the Pacific Ocean
Published April 11, 2022 | Version Preliminary v20220321
Dataset Open

Chlorophyll a concentration, particulate organique carbon, and particle mean size index [gamma; 0.2 - 20 µm] measured using an hyperspectral spectrophotometer [ACS, Wetlabs] during the Tara Pacific Expedition 2016-2018

Creators

  • 1. School of Marine Sciences, University of Maine, USA
  • 2. Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, F-06230 Villefranche-sur-Mer, France
  • 3. Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, France
  • 4. Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012 Paris, France
  • 5. PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan Cedex, France
  • 6. PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, France
  • 7. Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
  • 8. Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
  • 9. Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
  • 10. Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
  • 11. Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP 29680 Roscoff, France & Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016 Paris, France
  • 12. Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
  • 13. Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100 Rehovot, Israel
  • 14. Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France and Department of Medical Genetics, CHU of Nice, France
  • 15. Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650 Banyuls sur mer, France
  • 16. Université Côte d'Azur, CNRS, Inserm, IRCAN, France
  • 17. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
  • 18. Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Principality of Monaco
  • 19. The Ohio State University, Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Columbus, Ohio, 43210 USA
  • 20. Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093 Zürich, Switzerland
  • 21. Marine Biodiscovery Laboratory, School of Chemistry and Ryan Institute, National University of Ireland, Galway, Ireland
  • 22. Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012 Paris, France
  • 23. Oregon State University, Department of Microbiology, 220 Nash Hall, 97331Corvallis OR USA
  • 24. Department of Biology, University of Konstanz, 78457 Konstanz, Germany
  • 25. Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
  • 26. Tara Pacific Consortium

Description

The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean, and sampled the surface of oceanic waters at 249 locations, resulting in the collection of nearly 58,000 samples (Gorsky et al. 2019, Planes et al. 2019, Flores et al. 2020). The expedition was designed to systematically study corals, fish, plankton, and seawater, and included the collection of samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide the continuous dataset originating from the hyperspectral and multispectral spectrophotometers [ACS] instruments acquiring continuously during the full course of the campaign. Surface seawater was pumped continuously through a hull inlet located 1.5 m under the waterline using a membrane pump (10 LPM; Shurflo), circulated through a vortex debubbler, a flow meter, and distributed to a number of flow-through instruments. An [ACS] spectrophotometer (WETLabs) measured hyper-spectral (4 nm resolution) attenuation and absorption in the visible and near infrared except between Panama and Tahiti where an AC-9 multispectral spectrophotometer (WETLabs) was used instead. The flow was automatically directed through a 0.2 µm filter for 10 minutes every hour before being circulated through the spectrophotometer to eliminate the impact of biofouling and instrument drift and estimate particulate absorption [ap] and attenuation [cp] (Slade et al. 2010). Chlorophyll a content was estimated from particulate absorption line height at 676 nm (Boss et al. 2001). The particulate organic carbon concentration [poc] was estimated using an empirical relation (Gardner et al. 2006) between measured [poc] and measured [cp]. An indicator for size distribution of particles between 0.2 and ~20 µm [gamma] was calculated from [cp] (Boss et al 2001). The data was processed with custom software for underway optical data (InLineAnalysis software available on GitHub). The detailed information regarding the data processing is given in the processing report attached with the data and in Lombard et al. (In prep.). These results are preliminary: no matchup with in-situ chlorophyll from HPLC or [poc] measurements were performed.

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Additional details

Cites
Journal article: 10.1371/journal.pbio.3000483 (DOI)
Journal article: 10.3389/fmars.2019.00750 (DOI)
Journal article: 10.1175/BAMS-D-18-0224.1 (DOI)
Journal article: 10.1175/2010JTECHO755.1 (DOI)
Journal article: 10.1016/j.mio.2013.11.002 (DOI)
Journal article: 10.1016/j.dsr2.2006.01.029 (DOI)
Journal article: 10.1364/ao.40.004885 (DOI)
Software: https://github.com/OceanOptics/InLineAnalysis/commit/451e8636c047a4d09f878d3d0dcfc341ac5c2e99 (URL)

References

  • Planes S, Allemand D, Agostini S, Banaigs B, Boissin E, Boss E, Bourdin G, Bowler C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Ghiglione J-F, Gilson E, Lombard F, Moulin C, Pesant S, Poulain J, Reynaud S, Romac S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, de Vargas C, Vega Thurber R, Voolstra CR, Wincker P, Zoccola D, the Tara Pacific Consortium (2019) The Tara Pacific expedition—A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean. PLOS Biology 17:e3000483. doi: 10.1371/journal.pbio.3000483
  • Gorsky G, Bourdin G, Lombard F, Pedrotti ML, Audrain S, Bin N, Boss E, Bowler C, Cassar N, Caudan L, Chabot G, Cohen NR, Cron D, De Vargas C, Dolan JR, Douville E, Elineau A, Flores JM, Ghiglione JF, Haëntjens N, Hertau M, John SG, Kelly RL, Koren I, Lin Y, Marie D, Moulin C, Moucherie Y, Pesant S, Picheral M, Poulain J, Pujo-Pay M, Reverdin G, Romac S, Sullivan MB, Trainic M, Tressol M, Troublé R, Vardi A, Voolstra CR, Wincker P, Agostini S, Banaigs B, Boissin E, Forcioli D, Furla P, Galand PE, Gilson E, Reynaud S, Sunagawa S, Thomas OP, Thurber RLV, Zoccola D, Planes S, Allemand D, Karsenti E (2019) Expanding Tara Oceans Protocols for Underway, Ecosystemic Sampling of the Ocean-Atmosphere Interface During Tara Pacific Expedition (2016–2018). Frontiers in Marine Science 6:750. doi: 10.3389/fmars.2019.00750
  • Flores JM, Bourdin G, Altaratz O, Trainic M, Lang-Yona N, Dzimban E, Steinau S, Tettich F, Planes S, Allemand D, Agostini S, Banaigs B, Boissin E, Boss E, Douville E, Forcioli D, Furla P, Galand PE, Sullivan MB, Gilson É, Lombard F, Moulin C, Pesant S, Poulain J, Reynaud S, Romac S, Sunagawa S, Thomas OP, Troublé R, de Vargas C, Thurber RV, Voolstra CR, Wincker P, Zoccola D, Bowler C, Gorsky G, Rudich Y, Vardi A, Koren I (2020) Tara Pacific Expedition's Atmospheric Measurements of Marine Aerosols across the Atlantic and Pacific Oceans: Overview and Preliminary Results. Bulletin of the American Meteorological Society 101:E536–E554. doi: 10.1175/BAMS-D-18-0224.1
  • Fabien Lombard, Guillaume Bourdin, Stephane Pesant, Emilie Boissin, Julie Poulain, Sarah Romac, Maria Luiza Pedrotti, Nicolas Cassar, Pascal Conan, Eric Douville, J. Michel Flores, Seth G. John, Rachel L. Kelly, Yajuan Lin, Dominique Marie, Mireille Pujo-Pay, Jean François Ghiglione, Gilles Reverdin, Alberto Baudena, Ophélie Da Silva, Christian R. Voolstra, David A. Paz-Garcíax, Zoé Meriguet, Amanda Elineau, Laetitia Jalabert, Ilan Koren, Assaf Vardi, Benjamin C.C. Hume , Megan Clampitt, Sylvain Agostini, Ryan McMinds, Eric Röttinger, Celine Dimier, Josephine Ras, Clémentine Moulin, Guillaume Iwankow, Bernard Banaigs, Chris Bowler, Didier Forcioli, Paola Furla, Pierre E. Galand, Eric Gilson, Stéphanie Reynaud, Matthew B. Sullivan, Shinichi Sunagawa, Olivier Thomas, Romain Troublé, Rebecca Vega Thurber, Patrick Wincker, Didier Zoccola, Denis Allemand, Serge Planes, Colomban de Vargas, Emmanuel Boss, Gaby Gorsky (in preparation for Scientific Data) Open science resources from the Tara Pacific expedition across the surface ocean and coral reef ecosystems
  • Slade, W.H., Boss, E., Dall'Olmo, G., Langner, M.R., Loftin, J., Behrenfeld, M.J., Roesler, C., Westberry, T.K., 2010. Underway and Moored Methods for Improving Accuracy in Measurement of Spectral Particulate Absorption and Attenuation. Journal of Atmospheric and Oceanic Technology 27, 1733–1746. https://doi.org/10.1175/2010JTECHO755.1
  • Boss, E., Picheral, M., Leeuw, T., Chase, A., Karsenti, E., Gorsky, G., Taylor, L., Slade, W., Ras, J., Claustre, H., 2013. The characteristics of particulate absorption, scattering and attenuation coefficients in the surface ocean; Contribution of the Tara Oceans expedition. Methods in Oceanography 7, 52–62. https://doi.org/10.1016/j.mio.2013.11.002
  • Gardner, W.D., Mishonov, A.V., Richardson, M.J., 2006. Global POC concentrations from in-situ and satellite data. Deep Sea Research Part II: Topical Studies in Oceanography 53, 718–740. https://doi.org/10.1016/j.dsr2.2006.01.029
  • Boss, E., Twardowski, M.S., Herring, S., 2001. Shape of the particulate beam attenuation spectrum and its inversion to obtain the shape of the particulate size distribution. Appl. Opt. 40, 4885. https://doi.org/10.1364/AO.40.004885
  • InLineAnalysis software: https://github.com/OceanOptics/InLineAnalysis/commit/451e8636c047a4d09f878d3d0dcfc341ac5c2e99