European Directory of Marine Environmental Data (EDMED)

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General
Data set name

Marine Flow Cytometry Data from the Mediterranean Institute Of Oceanography (MIO), France (from 1993)

Data holding centreMediterranean Institute of Oceanography, UMR 7294 UMR IRD 235, MARSEILLE
CountryFrance  France
ProjectMediterranean Ocean Observing System on Environment (MOOSE)(MOOSE); Marine Ecosystems Response in the Mediterranean Experiment(MERMEX); Mediterranean Integrated STudies at Regional And Local Scales(MISTRALS); JERICO : Towards a joint European research infrastructure network for coastal observatories(JERICO); JERICO-NEXT : Towards a joint European research infrastructure network for coastal observatories(JERICO-NEXT); Continuous High Resolution Observation of the MEditerranean sea(CHROME); Observing Submesoscale Coupling At High Resolution (OSCAHR)(OSCAHR)
Time periodSince 1993 (ongoing)
OngoingYes
Geographical area

Mediterranean Sea; English Channel; Atlantic Ocean; Pacific Ocean; Antarctic Ocean; China Sea; Saint Lawrence River; Kerguelen Islands

Observations 
Parameters

Bacteria generic abundance in water bodies; Phytoplankton generic abundance in water bodies

Instruments

Flow cytometers

Description 
Summary

Flow Cytometry can be defined as a measure (-metry) of the optical properties of cells (cyto-) as they are transported by a liquid sheath (flow) through a light source excitation (most often one or several laser beams). Similar cells, i.e. with similar optical properties, define a population. Thanks to flow cytometry, pico- and nano-phytoplankton, heterotrophic prokaryotes, virus and heterotrophic nanoflagellates can be analysed. Flow cytometry analysis is performed at a high throughput, typically hundreds up to several thousand cells analysed per second depending on the flow cytometer model. The analysis is multiparametric, generating multiple and complex information: for each particle (cell) analysed, light scattering (forward and sideward scatter), and various fluorescences intensities (typically green, orange, red and yellow wavelength ranges). Either average or median, area under the curve, maximal value of the optical recorded pulse shape discriminate clusters are expressed in arbitrary unit. The cell abundances can also be readily determined for each group. In the case of some automated instruments equipped with an image in flow device, pictures of the cells can be taken in order to identify them. This is particularly efficient for cells larger than 20 micrometres. The datasets come from various locations around the world, including the Mediterranean Sea, English Channel, Atlantic Ocean, Pacific Ocean, etc. Data currently available in our database have been collected since 1993 using several benchtop and/or automated flow cytometers belonging, after 2012, to the Mediterranean Institute of Oceanography (MIO), and formerly to the Oceanographic Center of Marseille (COM). Benchtop sensors are centralised in a Regional Flow Cytometry Platform (PRECYM, https://precym.mio.univ-amu.fr/spip.php?rubrique50) hosted by the MIO: Cytoron Absolute (ORTHO Diagnostic Systems), Accuri C6, FACS Calibur and Influx (BD Biosciences), MoFlo (DAKO, Dk). The automated flow cytometers used by MIO are: the submersible Cytosub, the CytoSense and recently the CytoPro (Cytobuoy b.v., The Netherlands). Automated sensors are deployed in situ, onboard research or opportunity (Ferry) vessels, or on a buoy moored in situ. Benchtop flow cytometers are calibrated on a daily basis thanks to calibrated microspheres. Microscphers are also added to each sample as an internal standard. For automated flow cytometers, calibration is also performed using calibrated microscopheres. On a daily basis when benchtop analyses are run or if an automated beads analysing system is included. If not, the analyses of beads are performed as often as possible. Data have been collected under the framework of numerous national and international research projects: A*MIDEX CHROME ((Continuous High-Resolution Observation of the Mediterranean, https://en-chrome.mio.univ-amu.fr/?page_id=42)), JERICO and JERICO NEXT (http://www.jerico-ri.eu/), OSCAHR (Observing Submesoscale Coupling At High Resolution, http://www.mio.univ-amu.fr/OSCAHR/), MOOSE, SOMLIT, DEWEX-Mermex, PEACETIME-Mermex, Celt2sat LEFE, etc. The data have been collected by researchers of the Cybele team (Biogeochemical cycle and functional role of planktonic microorganisms assemblage team) of the Mediterranean Institute of Oceanography (M.I.O) located in Marseille, France. MIO is the holder of the flow cytometry data – Melilotus THYSSEN and Gérald GREGORI are the main people responsible for the dataset. Various access restrictions may apply to the different subsets of these datasets.

OriginatorsMediterranean Institute of Oceanography, UMR 7294 UMR IRD 235, MARSEILLE
References

Gregori G., Denis M., Robinson Jp (2004) On the use of standardized bead suspensions to derive absolute counts in flow cytometry: Evidence for a concentration threshold, CYTOMETRY PART A, vol. 59A p.145-145; Denis M., Thyssen M., Martin V., Manca B. and Vidussi F. (2010) Ultraphytoplankton basin-scale distribution in the Eastern Mediterranean Sea in winter: link to hydrodynamism and nutrients, Biogeosciences. 7 : 2227-2244, doi:10.5194/bg-7-2227-2010; Gregori G., Denis M., Seorbati Sergio, Citterio Sandra (2003) Resolution of viable and membrane-compromised free bacteria in aquatic environments by flow cytometry., Current Protocols In Cytometry,vol. Chapter 11; Denis M., Thyssen M., Dugenne M., Grégori G. (2014) Recent advances in assessing the Dynamics of phytoplankton assemblages by high frequency analysis at the single cell level., Biophysics and Bioengineering Letters. 7 : 77-85; Gregori G., Denis M., Lefevre D., Romano Jc (2003) Viability of heterotrophic bacteria in the Bay of Marseilles, Comptes Rendus Biologies, vol. 326 p.739-750; Gregori G., Denis M., Lefevre D., Beker B. (2002) A flow cytometric approach to assess phytoplankton respiration., Methods In Cell Science : An Official Journal Of The Society For In Vitro Biology, vol. 24 p.99-106; Gregori G., Colosimo A, Denis M. (2001) Phytoplankton group dynamics in the Bay of Marseilles during a 2-year survey based on analytical flow cytometry, Cytometry, vol. 44 p.247-256; Gregori G., Citterio S., Ghiani A., Labra M., Sgorbati S., Brown S., Denis M. (2001) Resolution of viable and membrane-compromised bacteria in freshwater and marine waters based on analytical flow cytometry and nucleic acid double staining, Applied And Environmental Microbiology, vol. 67 p.4662-70; Denis M., Neau E. and Leveau M. (1988) Potentiometric and optical resolution of cytochromes c and c1 in purified mitochondria from higher plant tissue, Eur. Biophys. J. 16: 259-265; Denis M., Arnaud S. and Malatesta F. (1989) Hydrogen peroxide is the end product of oxygen reduction by the terminal oxidase in the marine bacterium Pseudomonas nautica 617, FEBS Lett. 247: 475-479; Denis M., Martin V. and Andersen V. (2000) Short-term variations of the vertical distribution of cyanobacteria in the open Mediterranean Sea, Scientia Marina 64(2): 157-163. (0.6); Dugenne M., Thyssen M., Nerini D., Mante C., Poggiale J.-C., Garcia N., Garcia F., Gregori G. (2014) Consequence of a sudden wind event on the dynamics of a coastal phytoplankton community: an insight into specific population growth rates using a single cell high frequency approach, Frontiers In Microbiology, vol. 5 p.485; Thyssen M., Gregori G., Grisoni Jean-Michel, Pedrotti Maria-Luiza, Mousseau L., Artigas Luis Felipe, Marro Sophie, Garcia N., Passafiume O., Denis M. (2014) Onset of the spring bloom in the northwestern Mediterranean Sea: influence of environmental pulse events on the in situ hourly-scale dynamics of the phytoplankton community structure, Frontiers In Microbiology, vol. 5 p.387; Thyssen M., Denis M. (2010) Temporal and Spatial High-Frequency Monitoring of Phytoplankton by Automated Flow Cytometry and Pulse-Shape Analysis, Global Change: Mankind-Marine Environment Interactions pp 293-298; Thyssen M., Ferreyra Gustavo, Moreau Sébastien, Schloss Irene, Denis M., Demers Serge (2011) The combined effect of ultraviolet B radiation and temperature increase on phytoplankton dynamics and cell cycle using pulse shape recording flow cytometry, Journal Of Experimental Marine Biology And Ecology, vol. p.95;107; Thyssen M., Mathieu Delphine, Garcia N., Denis M. (2008) Short-term vaiation of phytoplankton assemblages in Mediterranean coastal waters recorded with an automated submerged flow cytometer, Journal Of Plankton Research, vol. 30 p.1027-1040; Thyssen M., Garcia N., Denis M. (2008) Sub meso scale phytoplankton distribution in the north east Atlantic surface waters determined with an automated flow cytometer, Biogeosciences Discussions, vol. 5 p.2471-2503; Thyssen M., Tarran Glen A., Zubkov Mikhail V., Holland Ross J., Gregori G., Burkill Peter H., Denis M. (2008) The emergence of automated high-frequency flow cytometry: revealing temporal and spatial phytoplankton variability, Journal Of Plankton Research, vol. 30 p.333-343; Thyssen M., Lefevre D., Caniaux Guy, Ras Josephine, Fernandez Camila I., Denis M. (2006) Spatial distribution of heterotrophic bacteria in the northeast Atlantic (POMME study area) during spring 2001, Journal Of Geophysical Research, vol. 110 p.C07S16-16; Gregori G., Rajwa Bartek, Patsekin Valery, Jones James, Furuki Motohiro, Yamamoto Masanobu, Paul robinson J (2013) Hyperspectral Cytometry, Current Topics in Microbio. and Imm., vol. p.1-20; Gregori G., Patsekin Valery, Rajwa Bartek, Jones James, Ragheb Kathy, Holdman Cheryl, Robinson J Paul (2011) Hyperspectral cytometry at the single-cell level using a 32-channel photodetector, Cytometry. Part A The Journal Of The International Society For Analytical Cytology, vol. 81 p.35-44; Denis M., V. Martin, A. Momzikoff, G. Gondry, L. Stemmann, S. Demers, G. Gorsky, V. Andersen (2003) Pulsed remineralisation in the northwestern Mediterranean Sea: an hypothesis, J. Mar. Syst. 39: 19-41. (1.1); Gregori G. (2012) Analyse de l’ADN et du cycle cellulaire des bactéries marines par cytométrie en flux, Cycle Cellulaire Et Cytométrie En Flux, vol. p.282; Denis M., Thyssen M., Martin V., Manca B. and Vidussi F. (2010) Ultraphytoplankton distribution and upper ocean dynamics in the eastern Mediterranean during winter, Biogeosciences Discuss. 6 : 6839-6887

Data web sitehttp://seadatanet.maris2.nl/v_cdi_v3/search.asp
Availability 
OrganisationMediterranean Institute of Oceanography, UMR 7294 UMR IRD 235, MARSEILLE
AvailabilityUnrestricted; by negotiation
ContactTHYSSEN and GREGORI (Research scientists)
Address

Mediterranean Institute of Oceanography, UMR 7294 UMR IRD 235, MARSEILLE
163 Avenue de Luminy Bâtiment Méditerranée
Marseille Cedex 9

13288
France

Telephone+33(0)4 91 82 92 12
Emailscientific_fcm_mio@osupytheas.fr
Administration 
Collating centreMediterranean Institute of Oceanography, UMR 7294 UMR IRD 235, MARSEILLE
Local identifierFCM_marine_data_MIO
Global identifier6744
Last revised2017-11-28