Souchothèque de Bretagne Roscoff Culture Collection Collection de Cultures de Roscoff Station Biologique de Roscoff FR2424 et UMR7144 Director D. Vaulot.

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Presentation transcript:

Souchothèque de Bretagne Roscoff Culture Collection Collection de Cultures de Roscoff Station Biologique de Roscoff FR2424 et UMR7144 Director D. Vaulot Curators Florence Le Gall & Ian Probert

The Roscoff Collection Set up in 1998 from research collection 1,900 strains (January 2010) Large coverage of oceanic regions (arctic to tropics) Many novel species

Why focusing on picoplankton ?  Ecology –Dominates vast oceanic regions, especially oligotrophic ones –Important in coastal areas (Micromonas)  Biodiversity –New algal classes (Bolidophyceae) –Many « uncultivated » groups  Biological models –Adaptation to extreme conditions (oligotrophy, low light) –Compacts genomes (Prochlorococus, Ostreococcus)  Applications –Aquaculture –Novel molecules

Infrastructures Culture space –2 culture rooms –1 experiment room –10 culture cabinets –1 transfer laboratory Cryopreservation equipment –Progressive freezer –-150°C freezer –Liquid nitrogen tanks 3 flow cytometers –FACSAria – high speed sorter (2003) –FACSCanto – analysis (2008) –Beckmann Coulter Quanta – analysis (2009) 4 microscopes, three of which equiped for digital imaging New location with expanded culture and lab space in 2012

New Resource Center

Personnel Daniel VAULOT DR1 CNRSDirector Florence LE GALL AI CNRSCurator Ian PROBERT Ingénieur CDDCurator Fabienne JALABERT IE CNRSSurvey SOMLIT (20%) Dominique MARIE IR CNRSFlow cytometry specialist (20%) Priscillia GOURVIL CDDTechnician Roseline EDERN CDDTechnician Experts Frédéric PARTENSKY DR2 CNRS RoscoffCyanobacteria Christophe SIX, Maître de conférences RoscoffCyanobacteria Nathalie SIMON Maître de conférences RoscoffPrasinophyceae Laure GUILLOU CR1 CNRS RoscoffHeterotrophic eukaryotes Wenche EIKREM, Université d’OsloPrasinophyceae

Financial support  Souchothèque de Bretagne (CPER et )  GénoMer (CPER) et Ouest-Génopole  PicoManche: PRIR Région Bretagne  Programme CNRS Aventis  CRB (Ministère de la Recherche)  PROMOLEC (Europe FP5)  PICODIV (Europe FP5)  Marine Genomics (Europe FP6)  Plankton*Net (Europe FP6)  ASSEMBLE (Europe FP7)  Selling strains since 2006

Isolating picoplankton - Cruises BIOSOPE 2004 OLIPAC 1994 MINOS, PROSOPE, BOUM 1999 Indian Ocean 2003 EUMELI 1991 CHLOMAX 1987 ROSCOFF 2000 MICROVIR 2007 MALINA 2009

An example BIOSOPE cruise 2004 Cultures

On board the ship Precultures (50 mL or plates) -> 170 –Prefiltered 3 or 0.6 µm –Enriched in K/100, Pro/100 or Rice –Put in light:dark incubator at 20°C Sorting by flow cytometry (plates or tube) -> 104 –1, 10, 1000 cells –K/10 or Pro/10 Reanalysis after days –dilution –sorting "Quick" transfer to Roscoff mostly in tubes

In Roscoff Initially : 445 pre-cultures –256 High light, 189 Low light Screening –microscopy –flow cytometry Purification –Serial dilution –Single cell pipetting (diatoms, coccolithophorids...) –Plating –Sorting by flow cytometry Finally –212 cultures added to RCC (some lost since)

Cyanobacteria Prasinococcus Prasinoderma Pycnococcus Micromonas Picochlorum Phaeocystis Pelagomonas

Recent additions BOUM cruise – strains MALINA cruise – strains MICROVIR cruise – strains

Caracterisation Optical microscopy Flow cytometry Electronic microscopy Pigment analysis by HPLC Gene analysis –18S rRNA gene –ITS, cox 1 (DNA barcoding) Genome sequencing RCC 465 RCC 944

Database Locally under Microsoft Access Original data History at RCC Where it was sent to Transferred to Web mySQL server On-line catalog updated weekly

Data base linked to Google map

Major groups Cyanobacteria Picoeukaryotes (prasinophytes, pelagophytes etc…) Haptophytes (Coccolithophrids, Emiliania, Phaeocystis) Diatoms New Phototrophic bacteria Dinoflagellate parasites Viruses of prasinophytes

1,900 strains Backup cultures not taken into account Overview of RCC January 2011

HLI Prochlorococcus (MED4, MIT9515) HLII Prochlorococcus (MIT9312, MIT9301, AS9601) Synechococcus sp. CC9605 Synechococcus sp. RS9903 Synechococcus sp. RS9907 Synechococcus sp. RS9902 Synechococcus sp. WH 8109 Synechococcus sp. WH 8002 Synechococcus sp. RS9904 Synechococcus sp. RS9908 Synechococcus sp. RS9910 Synechococcus sp. RS9911 Prochlorococcus sp. NATL2A Prochlorococcus sp. NATL1A Prochlorococcus marinus SS120 Prochlorococcus sp. MIT9211 Prochlorococcus sp. MIT9303 Prochlorococcus sp. MIT9313 NAC1-5 MB11A04 5X15 BL107 EBAC392 Synechococcus sp. RS9912 Synechococcus sp. RS9919 Synechococcus sp. Almo3 Synechococcus sp. UW01 Synechococcus sp. WH 8016 Synechococcus sp. WH 8020 Synechococcus sp. CC9311 SAR7 Synechococcus sp. WH 7803 Synechococcus sp. WH 7805 Synechococcus sp. WH 8018 Synechococcus sp. Eum14 Synechococcus sp. Oli31 Synechococcus sp. RS9920 Synechococcus sp. WH 8102 Synechococcus sp. C129 Synechococcus sp. Max42 Synechococcus sp. WH 8103 SAR139 SAR100 Synechococcus sp. RS9905 Synechococcus sp. RS9915 Synechococcus sp. Minos02 Synechococcus sp. Minos12 Synechococcus sp. RS9914 Synechococcus sp. RS9918 Synechococcus sp. WH 8101 Synechococcus sp. RS9906 Synechococcus sp. RS9913 Synechococcus sp. RS9917 Synechococcus sp. RS9901 Synechococcus sp. Minos11 Synechococcus sp. RS9916 Synechococcus sp. RS9921 Synechococcus sp.RCC307 Synechococcus sp. PCC6301 Cyanobium sp. NS Synechococcus sp. RS9909 IV II V VI VII III (mobiles) VIII IX X I Arbre ARNr 16S rRNA Fuller et al. (2003) AEM Marine cyanobacteria Synechococcus sp. RS9916 Synechococcus sp. WH 5701 BL107 Synechococcus sp. WH 7805 Recent genomes Published genomes Genoscope genomes Prochlorococcus Synechococcus diapo F. Partensky Strains isolated by RCC

Ostreococcus Smallest eukaryote: 0.8 µm 55 strains : Thau lagoon Méditerranean Sea English Channel Tropical Atlantic Red Sea Thau Deep strains Genomes : 2 published Several in progress

Bolidomonas Guillou et al Novel species Novel species Florenciella Eikrem et al Partenskyiella Ota et al. 2008

Genomes

More genomes PROMETHEUS project Genoscope

Distribution 1200 strains available for distribution Research teams  Equipes de la Station Biologique de Roscoff  IFREMER, Brest  Institut PASTEUR, Paris  Observatoire Océanologiques Banyuls sur Mer, Villefranche sur Mer  Norvège  Royaume-Uni  Allemagne  Espagne  USA  Inde  Chine  Turquie Private laboratories  SOMAIG  SANOFI  Océanopolis Education  Lycée Janson de Sailly (Paris)  Lycée Hoche (Versailles) Other collections  ALGOBANK, Université de Caen  Pasteur Culture Collection, Institut Pasteur, Paris  Culture Collection of Marine Phytoplankton (CCMP), Bigelow Lab, Maine, USA  NIES, Tsukuba Japan

Outlook  Moving to new building  Add strains  Japan 2010  Collaboration with NIES  Cryopreservation  Development of robust protocols  Start with species with large number of strains (Ostreococcus, Synechococcus, Emiliania)  Identification & description of strains  DNA barcoding  Description of new species :  Prasinophyceae (W. Eikrem, Oslo)  Pelagophyceae (W. Eikrem, Oslo)  Chlorarachniophyceae (S. Ota)  Genomes of 30 strains (TARA-PROMETHEUS)