WOrld oCEAN biOressources, biotechnologies, and Earth-systeM servICeS BIOTECHNOLOGIES ET BIORESSOURCES « Biotechnologie et Bioressources pour la Valorisation

WOrld oCEAN biOressources, biotechnologies, and Earth-systeM servICeS

BIOTECHNOLOGIES ET BIORESSOURCES

« Biotechnologie et Bioressources pour la Valorisation des Ecosystèmes Marins Planctoniques »

Mots-clés:Océans, Plancton, Biotechnologies bleues, Phénotypage haut débit, Séquencage haut-débit, Biomolécules marines, Biomonitoring, Eco-systémique, Micro-algues.

2013-2020

Réunion WP2, Villefranche sur Mer, 11/02/2014

Objectif : Rédaction du rapport ANR 2013

Work package n°2: Production and primary analysis of environmental data

Objectives:

WP2 will process, analyze, and archive in format compatible to the OCEANOMICS data warehouse (WP1) the physico-chemical and bio-optical data from in situ sensors deployed on-board TARA at each station and along the cruise track, and from samples collected for a posteriori lab- based analyses (see Table A2 in Annex I).

These data represent >50 different parameters that will also be compared to remote sensing satellite data.

All together, these so-called ‘environmental data’ will be used for a detailed characterization of the water-masses from which high-throughput biological data (WP3-4) are extracted. WP2 contains 5 tasks.

WP2: annual report, Feb. 11 2014

Task 2.1 In situ physical data.Task 2.2 Remote sensing physical data. Task 2.3. Bio-optical data. Task 2.4 Bio-chemical dataTask 2.5 Environmental data archiving.



People involved:P4 – LOV UMR7093 : Gabriel Gorsky, Marc Picheral, Lars Stemmann, Lionel Guidi, Annick Bricaud,

Fabrizio Dortenzio, David Antoine, Edouard Leymarie, Vincent Taillandier, Joséphine RasP1 – SBR UMR7144: Pascal MorinP10 – LPO UMR 6523: Sabrina Speich (Univ. Brest), Nicolas Grima (CNRS), Bruno Blanke (CNRS),

Annaig Prigent (Ifremer), Thierry Reynaud (Ifremer), Cécile Cabanes (CNRS)CP1 - PANGAEA : Stéphane Pesant

Collaborations: Daniele Iudicone (SZN)Emmanuel Boss, Alison Chase (U. Maine)Zbigniew Kolber (U. California)

Personal OCEANOMICS WP2 (Postdoc 2 years, Engineer 5 years, technician 2 years)LOV (P4): Lionel Guidi (postdoc 1 year Nov 2012-October 2013), Tatiana Donnay (CDD IE, 1 year since Nov. 2012) , Corinne Desnos (CDD 1 year since Nov. 2012), Jean Baptiste Romagnan (CDD IR, 2 years)

Pangea: XXXXXX (CDD 2 years)

Reste donc 1 year Postdoc and 1 year Technician (Zooscan)

Other non permanent peopleat LPO: 2 years postdoc (OCEANOMICS)at LOV: François Roullier (PhD, CDD 3 months) , Léo Berline (Postdoc)



Task 2.1: In situ physical and biogeochemical data

Investigators Sub-Task Deadline

Marc Picheral, Stemmann, Berline, Guidi

(1) Production/analysis of CTD data (T, S, O2) from rosette June 2014

Legoff (2) Production/analysis of TSG data June 2014

Subtask list:

Text Document describing the Deliverable, the data QC, the link to PANGEAtables and pdf document with all stations showing CTD rosette profilestables and pdf document with all profiles showing parameters at sampled depth by rosettetables and pdf document with TSG plots for all stations and between stationsFiles:Matlab filesODV files…. Something specific for Pangea ??



Task 2.2: Remote sensing physical data

Responsible Sub-Task Deadline

S. Speich, F. Kokoszka 1 Post-processing (calibration/validation) and analysis of SST, SSS, Sea Surface Height (SSH), chlorophyll (ocean colour) and wind data from satellites Jan 2015

S. Speich, Postdoc OCEANOMICS, A. Prigent, C. Cabanes

2 Intercalibration of in situ and remote sensed SST, SSS and chlorophyll data; Water mass context for every station Jan 2016

S. Speich, Postdoc OCEANOMICS, B. Blanke, N. Grima

3 Characterization of the large and fine scale physical contexts for every in situ station using observations and numerical models Jan 2017

S. Speich, PhD/Postdoc,, D. Iudicone, F. d’Ovidio, L. Stemmann, C. de Vargas

4 Analyses of ocean interconnections related with fluid dynamical niches and biogeography for every station Jan 2018

Subtask list:



Task 2.2: Remote sensing physical data


D2.2.1 (Delivery time March 2015) Post-processing (calibration/validation) and analysis of SST, SSS, Sea Surface Height (SSH), chlorophyll (ocean colour) and wind data from satellites. Work achieved : We have post-processed SST, SSH, and Chlorophyll-a satellite data. We are gathering SSS data from Aquarius (L2 level) and SMOS (L3 level) satellites. We will produce the processed data for each station in the coming year. For the Meteorological data : we are evaluating different satellite data products as well as Meteorological Reanalyses (ERA-INTERIM, NCEP).

D2.2.2 (Delivery time March 2016) Intercalibration of in situ and remote sensed SST, SSS and chlorophyll. We have started to compare remote-sensed data with CTD data for each station. Later next year we will compare the TSG underway data collection from Tara to the remote-sensed variables by collocating in space and time the data.

D2.2.3 (Delivery time March 2017) Intercalibration of Mercator Model Forecasts. We will start this task together with D2.2.4 in the coming months. In particular, we will test Mercator Forecasts as well as Mercator Reanalyses. We will compare the collected CTD and STG data sets with simulated water masses dynamics and properties. In relation with D2.2.4 and by using results obtained in D.2.2.1 and D2.2.2, as well as the subsurface ocean properties derived from the Argo profiling floats array, we will establish if Mercator was able to reproduce the observed fine-scale structure (eddies, jets, western-boundary currents, upwellings, …).

D2.2.4 (Delivery time March 2018) Characterization of the large and fine scale physical contexts for every in situ station. We have started to conceive appropriate data analyses and indicators to apply to the entire data collection (remote-sensed data, Tara CTDs and STGs, Tara bottle data, the CLS SURCOUF product, Meteorological variables from Reanalyses, Mercator simulations if the validation/calibration process will be successful) to characterize the dynamical and mass-water context of each station.


Task 2.3: Bio-optical dataInvestigators Sub-Task Deadline

Marc Picheral, Annick Bricaud, Emmanuel Boss

(1) Production/analysis of bio-optical data from profilers June 2014

Emmanuel Boss, Annick Bricaud (2) Production/analysis of hyperspectral optical data from the in-

line ac-s system

June 2014

Zbigniew Kolber?? (3) Production/analysis of data from underway Fast Repetition Rate Fluorometer

??

Emmanuel Boss, Alison Chase, Edouard Leymarie,David Antoine

(4) Production/analysis of hyperspectral radiometric data June 2014

Lars Stemmann , Lionel Guidi, Marc Picheral

(5) Analysis of data from the UVP June 2014



Task 2.4: Bio-chemical data


Pascal Morin ? D.2.4.1 - Analysis of nutrient data Jan. 2014

Joséphine Ras,Annick Bricaud

D.2.4.2 – HPLC analyses of pigment dataJan. 2014

Lars Stemmann ? D.2.4.3 – Characterisation of carbonate chemistry Jan. 2014



Task 2.5: Environmental data archiving and publishing


Stéphane PESANT Archive and publish validated datasets at PANGAEA As data becomes available, starting April 2013




• Data publications at PANGAEA are fully citable with persistent and resolvable DOIs

• Data DOIs at PANGAEA are linked to Paper DOIs from Journal Publishers



Task 2.5: Environmental data archiving and publishing• Some journal publishers now have dynamic links from their online papers to

related datasets archived at PANGAEA• Thomson Reuters now starts to build Impact Factors based on Dataset DOIs




• Metadata can be extensive; WORK is needed to hamonise vocabularies (T1.2)

• Access to data is available online; WORK is needed to setup a data access services (T1.2)



Particulate flux (>200μm mg C m-2 j-1)

progress in Environmental data/genomic integration

Article pour lot à soumettre à Nature (printemps 2014)

Article on Oceanography and biogeochemestry as a reference for other paper:Classification by water mass, classification by trophic status


Particulate flux (>200μm mg C m-2 j-1)

Impact of OMZ on carbone exportto the deep sea

progress in UVP valorisation: biological pump

Particles size distribution and carbon flux across the Arabian Sea Oxygen Minimum ZoneF. Roullier, L. Berline, L. Guidi, A. Sciandra, X. Durrieu De Madron, M. Picheral, S. Pesant, and L. Stemmann, Biogeosciences Discuss., 10, 19271-19309, 2013

More work in collaboration with GEOMAR


to Calculate Global Sequestration:

To Calculate regional map of b

897 estimates of bdistributed over

34 provinces

To combined with Sed. trap and Th. fluxes

progress in UVP valorisation, biological pump


Zooplankton and particles abundances (0-200 m, ind m-3)

progress in UVP valorisation: Particle and zooplankton


Variations of size parameter (red line) and total chl a concentration (blue line, log scale) at stations along the TARA transect

- As expected, at the global scale the size parameter Sf varies inversely to [Chl a] (picoplankton dominates in clear waters, microplankton in chl-rich waters). - However, at the regional scale, decouplings and time shifts are observed between Sf and [Chl a] -> to be studied

In progress at LOV: analysis of changes in the size structure of algal populations

An indicator of dominant algal size (Sf), between 0 (100% microphytoplankton) and 1 (100% picophytoplankton), is derived from the shape of each (normalized) phytoplankton absorption spectrum (Ciotti et al. 2002)

-The size parameter values derived from ac-s data are currently compared to taxonomic pigment concentrations (at stations) for validation- The objective of this optical approach is to give access to changes in algal size structure at high spatial resolution


In progress at University of Main : spectral decomposition of particulate light absorption

An indicator of dominant algal category Example of decomposition results for a measured particulate absorption spectrum from the Equatorial Pacific, near the Marquesas keys during the Tara Oceans expedition.

Example of correlation between particulate light absorption at different wavelength and pigment


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WOrld oCEAN biOressources, biotechnologies, and Earth-systeM servICeS BIOTECHNOLOGIES ET BIORESSOURCES « Biotechnologie et Bioressources pour la Valorisation