Souchothèque de Bretagne

Roscoff Culture Collection Collection de Cultures de Roscoff

Station Biologique de Roscoff FR2424 et UMR7144

Director : Ian Probert - Scientific Director : D. Vaulot Curators Florence Le Gall, Priscillia Gourvil and Roseline Edern

The Roscoff Collection

• Set up in 1998 from research collection • 3.400 strains of marine microalgae, bacteria and viruses • Large phylogenetic coverage • Large coverage of oceanic regions (arctic to tropics)

Infrastructures

• Culture space – 2 culture rooms – 1 experiment room – 14 culture cabinets – 1 transfer laboratory

• 4 flow cytometers

– FACSAria – high speed sorter (2003) – FACSCanto – analysis (2008) – Beckmann Coulter Quanta – analysis (2009) – Accuri C6 – analysis (2011)

• 4 microscopes equiped for digital imaging

• Cryopreservation equipment

– Progressive freezer – -150°C freezer – Liquid nitrogen tanks

New Resource Center - 2015

Personnel

Daniel VAULOT DRCE CNRS Scientific director Ian PROBERT IR UPMC Director Florence LE GALL AI CNRS Curator Priscillia GOURVIL AI CDI Assistant curator Fabienne JALABERT IE CNRS Survey SOMLIT (20%) Dominique MARIE IR CNRS Flow cytometry specialist (20%) Roseline EDERN AI CDD Assistant curator Valerian LE ROY AI CDD Assistant curator

Isolation • Serial dilution • Plating • Single cell pipetting • Flow cytometry sorting

Caracterisation • Optical microscopy • Electronic microscopy • Flow cytometry • Pigment analysis by HPLC • Gene sequence

– 18S nuclear rRNA gene – 16S plastid rRNA gene – ITS, cox 1 (DNA barcoding) – petb for cyanobacteria

– Genomes, transcriptomes

RCC 465

• Started in 2011 • Now 1 095 algal strains are cryopreserved • Recent development

– Cryo-preserving natural samples for delayed culturing – Tests with macroalgae and metazoans – Tests with dinoflagellates

Cryopreservation

Database

• Locally under Microsoft Access • Isolation information (where, when, how)

• History at RCC (purification)

• Phenotypic and genetic data

• Distribution

• New web site (April 2014)

Strains

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Strains added each year

Recent additions Strains obtained by flow cytometry sorting

MICROVIR cruise – 2007 112 strains

Class Genus #Cyanophyceae Unknown 4Cyanophyceae Xenococcus ? 2Bacillariophyceae Centronella ? 1Bacillariophyceae Cymbella ? 1Bacillariophyceae Entomoneis ? 1Bacillariophyceae Extubocellulus 1Bacillariophyceae Haslea 1Bacillariophyceae Minutocellus 2Bacillariophyceae Nitszchia 1Bacillariophyceae Porosira 2Bacillariophyceae Skeletonema 2Bacillariophyceae Thalassiosira 3Bacillariophyceae Unknown 7Pelagophyceae Pelagococcus 1Pelagophyceae Unknown 1Prymnesiophyceae Emiliania 2Prymnesiophyceae Ochrosphaera 2Prymnesiophyceae unknown 1Cryptophyceae Proteomonas 1Mamiellophyceae Micromonas 3Nephroselmidophyceae Nephroselmis 3Prasinophyceae Prasinococcus 4Prasinophyceae Prasinoderma 2Prasinophyceae Pycnococcus 2Trebouxiophyceae Picochlorum 3Unknown Unknown 3

Major groups

Initially

• Cyanobacteria

• Picoeukaryotes (prasinophytes, pelagophytes etc…)

• Haptophytes (Coccolithophrids, Emiliania, Phaeocystis)

• Diatoms

Recently

• Phototrophic bacteria

• Bacteria associated to phytoplankton

• Eukaryotic parasites

• Symbionts

• Viruses of prasinophytes

159

583

569

427

1061

41

495

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99

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Virus

Bacteria

Alveolata

Stramenopiles

Haptophyta

Cryptophyta

Chlorophyta

Cercozoa

Other

Unknown

3,400 strains

Backup cultures not taken into account

Overview of RCC

Oct 2014

Division Class #Virus Phycodnaviridae 159Bacteria Cyanophyceae 413

Alphaproteobacteria 62Alveolata Dinophyceae 362

Perkinsea 207Stramenopiles Bacillariophyceae 217

Bolidophyceae 13Pelagophyceae 75Dictyochophyceae 34

Haptophyta Prymnesiophyceae 1008Pavlovophyceae 51

Cryptophyta Cryptophyceae 43Chlorophyta Mamiellophyceae 219

Prasinophyceae 145Trebouxiophyceae 54

Cercozoa Chlorarachniophyceae 16

3,400 strains Overview of RCC

Selection criteria: Genetic diversity Pigment type

Geographical origin Trophic regime

Strain name (clade number) pigment type 1 pigment type 2 pigment type 3a

pigment type 3b pigment type 3c pigment type 3d

Stars : public genomes Circles: unpublished genomes (Genoscope)

57 Genomes o 14 Prochlorococcus o 43 Synechococcus

3b

3b

3c’

Picocyanobacteria

Prochlorococcus Synechococcus

Type 1

Type 2

Type 3

Six et al., 2007

9 Kbp

28.5 Kbp

PBS

Regi

on le

ngth

3a

3c

3e-d (CA4)

PEII PC PE PE misc

Type 1 2 3

Phycobilisome rod genomic region

Emiliania huxleyi and Gephyrocapsa oceanica

170 strains

Bendif et al. 2014

Core Chlorophytes

Mamiellophyceae

*The figure represents the best ML tree. Bootstrap values are shown on the nodes and corresponded to maximum likelihood and Bayesian analysis respectively

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-/-

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A

B

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Clade VII

Clade IX

Prasinophytes

Lopes unpublished

Prasino clade VII

40 strains

Lopes unpublished Lopes unpublished

Deep group

Surface group

Heterogeneous group

Prasinoderma singularis New species from Pacific Ocean

Genomes

RCC Class Genus Species Ecotype Strain1983 Cyanophyceae Acaryochloris marina HICR111A156 Prochlorococcus marinus Low Light SS120-04/95158 sp. Low Light NATL1-M98162 sp. Low Light NATL2-M98407 sp. Low Light MIT93131086 Synechococcus sp. clade I CC9311753 sp. clade II CC9605539 sp. clade III WH8102790 sp. clade III M11.1515 sp. clade IV BL_107555 sp. clade IX RS9916752 sp. clade V WH78031084 sp. clade V.2 WH5701307 sp. clade V.3 MINSyn016-15m-01-AC6A11085 sp. clade VI WH7805556 sp. clade VIII RS99171105 Mamiellophyceae Bathycoccus prasinos BBan7827 Micromonas pusilla clade A NOUM17_clonal299 pusilla clade A NOUM17834 pusilla clade C CCMP15451115 Ostreococcus tauri clade C N68_3_21116 tauri clade C N68_3_41558 tauri clade C 68_11_41559 tauri clade C 68_10_5745 tauri clade C OTTH 0595-genome1114 tauri clade C N68_2_11731 Prymnesiophyceae Emiliania huxleyi CCMP1516

Transcriptomes 70 obtained or in progress

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Stramenopiles

Chlorophyta

Haptophyta

Others

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Bolidomonas

Pelagomonas

Clade VII

Emiliania

Phaeocystis

Papers

Papers mentionning RCC strains

Distribution 2 645 strains available

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 • Fermentalg

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 (NCMA), Bigelow Lab, Maine, USA • NIES, Tsukuba Japan

Two major projects linked to strain distribution • EU Infrastructure project ASSEMBLE (2008-2012) • EMBRC (European Marine Biological Research Center) – French contribution

financed in framework of « Investissement d’avenir »

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Strains distributed

OtherColloboration

Collaboration with NIES MCC in Japan

• Strain exchange

• Sampling opportunities

• Cryopreservation

• Flow cytometry (sorting)

http://roscoff-culture-collection.org

Financial support

Souchothèque de Bretagne (CPER 1998-2006 et 2007-2012)

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)

MACUMBA (Europe FP7)

EMBRC-France

Oceanomics

Selling strains since 2006