Le Quorum Sensing Bactérien Dans L'environnement Marin

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Le quorum sensing bactériendans l’environnement marin : diversitémoléculaireet génétiquedes auto-inducteurs Margot Doberva

To cite this version: Margot Doberva. Le quorum sensing bactérien dans l’environnement marin : diversité moléculaireet génétiquedes auto-inducteurs. Ecosystèmes.UniversitéPierre´ et Marie Curie - Paris VI, 2016. Fran¸cais. .

HAL Id: tel-01377951 https://tel.archives-ouvertes.fr/tel-01377951 Submitted on 8 Oct 2016

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SOMMAIRE 9

LISTE DES ABBRÉVIATIONS 15

TABLE DES ILLUSTRATIONS 17

TABLE DES TABLEAUX 19

CHAPITRE I : INTRODUCTION : LA COMMUNICATION INTERCELLULAIRE CHEZ LES MICRO ORGANISMES 23

I1 LES BACTERIES MARINES ET LEURS ENVIRONNEMENTS 23 I 1 1 LES BACTERIES MARINES: QUELLE PLACE DANS L'ENVIRONNEMENT MARIN ? 23 I 1 1 1 Les bactéries libres : la colonne d'eau 24 I‐1‐1 2 Les bactéries attachées : la neige marine 24 I‐1‐1‐3 Les bactéries associées au phyto et zoo plancton 25 I‐1‐1‐4 La communauté bactérienne du sédiment 25 I‐1‐1‐5 Les bactéries associées aux macro‐ algues ‐ 25 I‐1‐1‐6 Les bactéries associées aux plantes 26 I‐1‐1‐7 Les bactéries associées aux invertébrés‐ marins 26 I‐1‐1‐8 Les bactéries associées aux vertébrés marins 27 I‐1‐2‐L' IMPLICATION DES BACTERIES MARINES DANS LE RESEAU TROPHIQUE ET LES CYCLES BIOGEOCHIMIQUES ‐ ‐ ‐ 27

I‐1‐3 DE L'ECOLOGIE MICROBIENNE A L'ECOLOGIE CHIMIQUE 29 I2 LE QUORUM SENSING : LA COMMUNICATION BACTERIENNE INTERCELLULAIRE 31

I‐2‐1 HISTORIQUE : DE L'ETUDE DE LA BIOLUMINESCENCE A LA DECOUVERTE ET LA COMPREHENSION DU MECANISME DE QUORUM SENSING 31

I‐2‐2 LE MECANISME GENERAL DU QUORUM SENSING BACTERIEN 32

I 2 3 LES PHENOTYPES REGULES PAR QUORUM SENSING CHEZ LES BACTERIES 34 I‐2‐3 1 La nodulation 34 I‐2‐3 2 Les facteurs de virulence 35 I‐2‐3‐3 La mobilité bactérienne 35 I‐2‐3‐4 La fructification 36 I‐2‐3‐5 Le transfert d'ADN 36 I‐2‐3‐6 Les biofilms 36 I‐2‐3‐7 Les produits extracellulaires 37 I‐2‐3‐8 L'incorporation du phosphore 37 I‐2‐3‐9 La morphologie cellulaire 38 I‐2‐3‐10 La bioluminescence 38 I‐2‐4‐LES MOLECULES SIGNAL CHEZ LES BACTERIES 39 I‐2‐4‐1 Les Auto Inducteurs de types 1 et 2 : molécules et gènes codant les voies de biosynthèse ‐ ‐ 40 I‐2‐4‐1 1 Les Auto‐ Inducteurs de type 1 (AI 1) 40 I 2 4 1 2 L'Auto Inducteur de type 2 (AI 2) 43 I‐2‐4‐1‐3 Phylogénie ‐ des gènes impliqués dans‐ la production des AI 1 & 2 44 I‐2‐4‐2‐Les autres‐ molécules signal ‐ 48 I‐2‐4‐2‐1 L'Auto Inducteur de type 3 (AI 3) ‐ ‐ 48 I‐2‐4‐2 2 Le Cholerae Auto Inducteur (CAI) 48 ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ � �

Ie 2 4 2 3 L 3 hydroxy Palmitic Acid Methyl Ester (PAME) 48 I 2 4 2 4 Le Pseudomonas Quinolone Signal (PQS) 49 I‐2‐4‐2‐5 Les DiKetoPiperazines‐ (DKP) 49 I‐2‐4‐2‐6 Les Diffusible Signal Factor (DSF) 50 I‐2‐4‐2‐7 Le butyrolactone (GBL) 51 I‐2‐4‐2‐8 Les facteurs A/B/C/D/E 51 I‐2‐4‐2‐9 Les Auto Inducing Peptides (AIP) 51 I‐2‐4‐2‐10 La bradyoxetine (CDF) 52 I‐2‐4‐2‐11 L'indole ‐ : l'acide indole 3 acétique (IAA) 53 I‐2‐4‐2‐12 L'acide tropodithietique (TDA) 53 I‐2‐4‐4‐Les AI 1 : centre des interconnexions‐ ‐ de plusieurs voies de QS bactérien 55 I‐2‐4‐5‐Les autres activités biologiques des molécules signal 56 I‐2‐5‐L' INHIBITION ‐ DU QUORUM SENSING BACTERIEN 57 I‐2‐5‐1 Les facteurs abiotiques 57 I‐2‐5 2 Les inhibiteurs moléculaires (mimétisme et réaction chimique) 58 I‐2‐5‐3 Les enzymes (acylases et lactonases) 60 I‐2‐5‐4 Les applications de l’inhibition du quorum sensing 61 I‐2‐6‐LE QUORUM SENSING INTRA ET INTER DOMAINES 62 I‐2‐6‐1 La communication intra domaine 62 I‐2‐6 1 1 Le quorum sensing entre‐ les Archées‐ 62 I‐2‐6‐1 2 Le quorum sensing entre‐ les Eucaryotes 63 I‐2‐6‐3‐La communication inter domaines 64 I‐2‐6‐3‐1 La communication entre les plantes et les bactéries 64 I‐2‐6‐3 2 La communication entre‐ les animaux et les bactéries 65 I‐2‐7‐INFLUENCE‐ DE L'ENVIRONNEMENT ET CONCEPT DE QUORUM SENSING 65 I‐2‐8‐QUELS‐ MECANISMES DE QUORUM SENSING BACTERIEN SONT RETROUVES DANS LES DIFFERENTS

ECOSYSTEMES‐ ‐ MARINS ? 67 I‐2‐8 1 Le QS chez bactéries libres de la colonne d'eau 67 I 2 8 2 Le QS chez les bactéries attachées 68 I‐2‐8‐3 Le QS dans la communauté bactérienne du sédiment 68 I‐2‐8‐4 Le QS chez bactéries associées au plancton 69 I‐2‐8‐5 Le QS chez les bactéries associées aux macro algues 70 I‐2‐8‐6 Le QS chez les bactéries associées aux plantes 70 I‐2‐8‐7 Le QS chez les bactéries associées aux invertébrés‐ marins 70 I‐2‐8‐8 Le QS chez les bactéries associées aux vertébrés marins 71 I‐3‐ LES‐ OBJECTIFS ET LES METHODES DE CE TRAVAIL DE RECHERCHE 72 I‐3‐1‐LES OBJECTIFS DE CETTE THESE DE DOCTORAT 72 I 3 1 1 Quelle est la diversité taxonomique et moléculaire des bactéries marines cultivables utilisant‐ ‐ le QS basé sur les AI 1 ? 73 I‐3‐1‐2 Quelle est la prévalence du quorum sensing basé sur les AI et 2 chez les bactéries marines ? ‐ 74 I‐3‐1‐3 Quel est le rôle fonctionnel du QS chez les Rhodobacteraceae ‐ dans ‐ l'environnement marin naturel ? 75 I‐3‐2‐QUELLES TECHNIQUES UTILISER POUR ABORDER LES QUESTIONS LIEES AU QUORUM SENSING EN MILIEU MARIN ? 76 I‐3‐2 1 Les méthodes dépendantes des techniques de culture : de la microbiologie pasteurienne aux approches de chimie des substances naturelles 76 I‐3‐2‐2 Les méthodes indépendantes des techniques de culture : les approches de génomique environnementale 77 ‐ ‐ ‐

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CHAPITRE II : PUBLICATION : LARGE DIVERSITY AND ORIGINAL STRUCTURES OF AHLS IN MARIBIUS SP MOLA 401, AN OLIGOTROPHIC MARINE ROSEOBACTER BACTERIA 83 ABSTRACT 84

INTRODUCTION 85

MATERIALS & METHODS 88 CULTURE OF MARIBIUS MOLA 401 STRAIN 88 PHYLOGENETIC ANALYSES OF MARIBIUS MOLA 401 16S RRNA AND QUORUM SENSING GENES 88

AHLS STANDARDS USED IN THIS STUDY 89

EXTRACTION OF AHLS FROM MARIBIUS SP. MOLA 401 SUPERNATANTS 89

HPLC MICROFRACTIONNEMENT 90

CULTURE OF BIOSENSOR STRAINS 90 LC MS ANALYSES 91

MS/MS SPECTRA DESCRIPTION 93 MOLECULAR‐ FORMULA DETERMINATION 94

RESULTS & DISCUSSION 95 PRESENCE AND CHEMICAL FEATURES OF AHLS IN MARIBIUS SP. 95 LINKING GENETIC AND CHEMICAL FEATURES 99

ECOLOGY OF MARIBIUS SP. MOLA401 103

CONCLUSIONS 104

AKNOWLEDGEMENTS 105 BIBLIOGRAPHY 106 SUPPLEMENTARY FIGURE : CHROMATOGRAMS OF FRACTIONS M1M22 AND AHLS MS/MS SPECTRA (FROM A TO U) 111

CHAPITRE III : PUBLICATION : DIVERSITY OF QUORUM SENSING AUTOINDUCER SYNTHASES IN THE GLOBAL OCEAN SAMPLING METAGENOMIC DATABASE 125 ABSTRACT 126

INTRODUCTION: 127

MATERIALS & METHODS 130 CONSTRUCTION OF REFERENCE DATABASES FOR AI SYNTHASE PROTEINS 130 SCREENING FOR AI SYNTHASES IN THE GOS METAGENOME 130

NORMALIZATION OF AI COUNTS IN GOS METAGENOMES TO SINGLE COPY GENES 131

PHYLOGENETIC ANALYSIS 132

RESULTS 133 FEATURES OF AI SYNTHASE PROTEIN REFERENCE DATABASES 133 ABUNDANCE AND DIVERSITY OF LUXI SYNTHASES IN THE GOS DATASET 135

ABUNDANCE AND DIVERSITY OF HDTS SYNTHASES IN THE GOS DATASET 137

ABUNDANCE AND DIVERSITY OF LUXS SYNTHASES IN THE GOS DATASET 141

DIVERSITY OF AINS SYNTHASES IN THE GOS DATASET 143

CORRELATION WITH ENVIRONMENTAL VARIABLES 143

DISCUSSION 145 AKNOWLEDGEMENTS 149 BIBLIOGRAPHY 150

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CHAPITRE IV : DISCUSSION GENERALE & PERSPECTIVES : DIVERSITE, PREVALENCE ET EXPRESSION DU QUORUM SENSING BASE SUR LES AHLS DANS L’ENVIRONNEMENT MARIN 159 V1 QUELLE EST LA PREVALENCE DU QS BASE SUR LES AHLS DANS L'ENVIRONNEMENT MARIN ? 159 V 1 1 LA PRESENCE D'AHLS CHEZ LES BACTERIES ISSUES DES DIVERS ECOSYSTEMES MARINS 159 V 1 2 LA PRESENCE DE GENES CODANT LES AHL SYNTHASES DANS L'ENVIRONNEMENT MARIN 167

V‐1‐3 L'EXPRESSION DES GENES CODANT LES AHL SYNTHASES DANS L'ENVIRONNEMENT MARIN 169 ‐ ‐

V‐2‐ Q UELS LIENS ENTRE LA DIVERSITE MOLECULAIRE DE LA FAMILLE DES AHLS ET CELLE DES GENES CODANT LES AHL SYNTHASES ? 172 V 2 1 LA FAMILLE DE GENES CODANT LES AHL SYNTHASE LUXI 172 V 2 2 LA FAMILLE DE GENES CODANT LES AHL SYNTHASES HDTS 172

V‐2‐3 LIEN GENE CODANT L'AHL SYNTHASE ET AHLS SYNTHETISEES 173 ‐ ‐

V‐3‐ Q UELS SONT LES ROLES FONCTIONNELS DES AHLS DANS L'ENVIRONNEMENT MARIN ? 174 V 3 1 DIVERSITE POTENTIELLE DES FONCTIONS DES AHLS 174 V 3 2 SUIVI ENVIRONNEMENTAL DE L'EXPRESSION DU GENE LUXI DE ROSEOBACTER 175

V‐3‐3 EXTINCTION DU GENE LUXI DE MARIBIUS SP : TROUVER LE(S) PHENOTYPE(S) REGULE(S) 176 ‐ ‐ ‐ ‐

BIBLIOGRAPHIE GENERALE 179

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ANNEXES 209

COMMUNICATIONS SCIENTIFIQUES LIEES A CE TRAVAIL DE THESE 209 PRESENTATIONS ORALES 209 POSTER 209

ARTICLES SCIENTIFIQUES ORIGINAUX ET DE REVUE 211

Genome sequence of the sponge associated Ruegeria halocynthiae Strain MOLA R1/13b, a marine Roseobacter with two quorum sensing based communication systems 212 ABSTRACT 213 GENOME ANNOUNCEMENT 213 REFERENCES 215

Genome sequence of Maribius sp. Strain MOLA 401, a marine Roseobacter with a quorum sensing cell dependent physiology 217 ABSTRACT 218 GENOME ANNOUNCEMENT 218 REFERENCES 220

Revue : Fundamental aspects of bioluminescence in marine microorganisms 225 ABSTRACT 226 INTRODUCTION 227 BIOLUMINESCENCE IN DINOFLAGELLATES 229 “Shining” sea and spatial distribution of bioluminescent dinoflagellates 229 Ecological function of bioluminescence 237 Three mostly studied bioluminescent species 238 Regulation of bioluminescence in dinoflagellates 240 General aspects 240 The dinoflagellate flash model 243 Clock control in Lingulodinium polyedrum 244 Scintillon translocation in Pyrocystis 245 BIOLUMINESCENCE IN MARINE BACTERIA 246 Milky sea phenomenon and ecological function of bioluminescence 246 The taxonomy of bioluminescent bacteria 247 Quorum sensing and lux related light production 250 General aspects 250 Regulation of Vibrio fischeri ‐ bioluminescence by quorum sensing 251 Vibrio fischeri versus V. harveyi bioluminescence regulation 253 Bioluminescent bacteria living in symbiosis 255 Vibrios metazoan associations 255 Ecological consequences of host symbiont interaction 256 CONCLUSION ‐ 259 ACKNOWLEDGEMENTS ‐ 261

TABLEAUX ANNEXES 279

Schéma bilan de cette thèse de doctorat 311

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Vol. 74: 107–119, 2015 AQUATIC MICROBIAL ECOLOGY Published online February 12 doi: 10.3354/ame01734 Aquat Microb Ecol

Diversity of quorum sensing autoinducer synthases in the Global Ocean Sampling metagenomic database

Margot Doberva1, Sophie Sanchez-Ferandin2, Eve Toulza3,4, Philippe Lebaron1, Raphaël Lami1,*

1Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologie Marines (LBBM), Observatoire Océanologique, 66650 Banyuls/Mer, France 2Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650, Banyuls/Mer, France 3UPVD Université de Perpignan, UMR 5244, IHPE, 66860 Perpignan cedex 9, France 4CNRS, UMR 5244, 2EI, 66860 Perpignan cedex 9, France

ABSTRACT: Quorum sensing (QS) is a cell-to-cell signalling pathway that allows bacteria to synchronize their genetic expression. It is mediated by autoinducers (AI), including (1) acyl-homoserine lactones (AHLs or AI-1), produced by Proteobacteria using AinS, LuxI and HdtS synthase fam- ilies and (2) furanosyl-diester-borate (FDB or AI-2), produced by a large range of phylogenetically diverse bacteria and synthetized by the LuxS family. Few data have been collected about the presence and importance of QS in marine waters using culture independent methods. In this study, we examined the presence and the diversity of AI-1 and AI-2 synthases in the Global Ocean Sampling (GOS), a large metagenomic database, covering 68 stations across 3 oceans. We built 4 reference protein databases with maximal phylogenetic coverage containing all known AI synthase sequences to retrieve AI synthases sequences from the GOS metagenomes. We retrieved 29 environmental sequences affiliated to LuxI (synthesizing AI-1), 653 related to HdtS (AI-1), 31 related to LuxS (AI-2) and only one for AinS (AI-1). AI synthases sequences were found in the 3 oceans covered by the GOS cruise and spanned a large phylogenetic diversity. These data revealed a large number of new marine AI sequences, suggesting that QS based on AI-1 diffusion is a wide- spread mechanism in the marine environment.

KEY WORDS: Quorum sensing · Acyl-homoserine lactone synthases · Global Ocean Sampling · Environmental metagenomes

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INTRODUCTION concentration is reached, targeted bacterial partners can respond to these compounds and modify their Quorum sensing (QS) is a cell-to-cell bacterial gene expression, and thus their behaviour and phe- communication mechanism, allowing bacteria to notype (Withers et al. 2001, Bassler 2002). It has been sense their population density (Nealson 1977) and shown that QS systems regulate and synchronize coordinate their gene expression levels (Bassler activities like biofilm production (Parsek & Green- 1999, Fuqua & Greenberg 2002) and physiological berg 2005, Dickschat 2010), nodulation (Cha et al. activities (Miller & Bassler 2001). To perform QS- 1998, Loh et al. 2002), bioluminescence (Waters & based communication, bacteria produce, secrete and Bassler 2005), virulence factor production (Smith & accumulate small hormone-like molecules called Iglewski 2003) and many others (Diggle et al. 2007). autoinducers (AI) in the nearby environment (Fuqua The coordination of bacterial community activities et al. 1994). As cell density increases, the concentra- conveys an ecological advantage to the population tion of these AI increases. When a given threshold (Case et al. 2008).

*Corresponding author: [email protected] © Inter-Research 2015 · www.int-res.com

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 LL LL              l   

  L       I I   fi   �          L     � M     L  fi I  fi     L     I  fi                                     fi 

 ��            M       M    ��  ��  ��     L  S ��     S      ��    �� L  ﬁ  ��    L ��     ��  ��     M  ��  ��    L   ��     ��         I �� M ��  ��  L    ��   ﬁ

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Genome Sequence of the Sponge-Associated Ruegeria halocynthiae Strain MOLA R1/13b, a Marine Roseobacter with Two Quorum- Sensing-Based Communication Systems

Margot Doberva,a,b Sophie Sanchez-Ferandin,c,d Yoan Ferandin,a,b Laurent Intertaglia,e,f Julie Croué,a,b Marcelino Suzuki,a,b Philippe Lebaron,a,b Raphaël Lamia,b Sorbonne Universités, UPMC Université Paris 06, USR 3579, LBBM, Observatoire Océanologique, Banyuls-sur-Mer, Francea; CNRS, USR 3579, LBBM, Observatoire Océanologique, Banyuls-sur-Mer, Franceb; Sorbonne Universités, UPMC Université Paris 06, UMR 7232, BIOM, Observatoire Océanologique, Banyuls-sur-Mer, Francec; CNRS, UMR 7232, BIOM, Observatoire Océanologique, Banyuls-sur-Mer, Franced; Sorbonne Universités, UPMC Université Paris 06, UMS 2348, Observatoire Océanologique, Banyuls-sur-Mer, Francee; CNRS, UMS 2348, Observatoire Océanologique, Banyuls-sur-Mer, Francef

Ruegeria halocynthiae MOLA R1/13b is an alphaproteobacterium isolated from the Mediterranean sea sponge Crambe crambe. We report here the genome sequence and its annotation, revealing the presence of quorum-sensing genes. This is the ﬁrst report of the full genome of a Ruegeria halocynthiae strain.

Received 26 August 2014 Accepted 8 September 2014 Published 9 October 2014 Citation Doberva M, Sanchez-Ferandin S, Ferandin Y, Intertaglia L, Croué J, Suzuki M, Lebaron P, Lami R. 2014. Genome sequence of the sponge-associated Ruegeria halocynthiae strain MOLA R1/13b, a marine Roseobacter with two quorum-sensing-based communication systems. Genome Announc. 2(5):e00998-14. doi:10.1128/genomeA.00998-14. Copyright © 2014 Doberva et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Raphaël Lami, [email protected].

uegeria halocynthiae MOLA R1/13b (MOLA culture collection genome. The genome annotation also revealed 3 genes encoding Rno. WDCM911; see http://collection.obs-banyuls.fr/index RhtB/lysE-like proteins, known to be involved in long chain ho- .php) was isolated in 1:5 marine R2A agar (in 75% seawater) at moserinelactones transmembrane transport (3). This is the first 20°C, from the sponge Crambe crambe collected on 20 January report of quorum-sensing genes within the marine species Ruege- 2010 from a 12-m depth at the Bay of Banyuls (48°28’823!N, ria halocynthiae. Thus, this draft genome reinforces previous ob- 3°08’038!E, France). A major step in our isolation protocol is that servations suggesting that marine bacteria are able to communi- sponge homogenates were acclimated for 24 h at 16°C with marine cate using quorum sensing in sponge microenvironments where R2A added at a 1:200 final dilution, before strain isolation. Based on these cells can be found at high concentrations (4, 5) its 16S rRNA gene sequences, the strain is phylogenetically related to Nucleotide sequence accession number. The whole-genome Ruegeria halocynthiae MA1-6 (99% sequence identity to 16SrRNA shotgun project has been deposited at DDJB/EMBL/GenBank un- genes) and belongs to the Rhodobacteraceae (Roseobacter clade). der the accession no. JQEZ00000000. Thestrainwascultivatedin100mLofmarinebroth2216medium (BD, Difco, Sparks, MD) at 25°C over 48 h. DNA was extracted using ACKNOWLEDGMENTS a cetyltrimethylammonium bromide (CTAB)-based method (1). This work was support by a UPMC-Emergence grant. Genome sequencing steps conducted by MrDNA platform (Texas) We thank the Bio2Mar (http://bio2mar.obs-banyuls.fr) platform for included fragmentation, ligation to sequencing adapters, and purifi- access to instrumentation and to MrDNA (http://www.mrdnalab.com) cation. Following the amplification and denaturation steps, libraries for sequencing the genome. weresequencedinapool.Atotalof50ngofDNAwasusedtoprepare We declare no conflicts of interest. the library using the Nextera DNA sample preparation kit (Illumina). REFERENCES Library insert size was determined by an Experion automated electrophoresis station (Bio-Rad). The insert size of the libraries ranged 1. Dempster EL, Pryor KV, Francis D, Young JE, Rogers HJ. 1999. Rapid DNA extraction from ferns for PCR-based analyses. BioTechniques 27:66–68. from 300 to 850 bp (average, 500 bp). The library (12 pM) was loaded 2. Fuqua WC, Winans SC, Greenberg EP. 1994. Quorum sensing in bacteria: (in a pool) to a 600 Cycles v3 Reagent cartridge (Illumina), and the the LuxR-LuxI family of cell density-responsive transcriptional regulators. sequencing was performed on a Miseq sequencer (Illumina) and de J. Bacteriol. 176:269–275. novo assembled with NGEN v11 (DNASTAR, Inc). The genome 3. Zakataeva NP, Aleshin VV, Tokmakova IL, Troshin PV, Livshits VA. was annotated using Prokka 1.7 (www.vicbioinformatics.com/ 1999. The novel transmembrane Escherichia coli proteins involved in the amino acid efflux. FEBS Lett. 452:228–232. http://dx.doi.org/10.1016/ software.prokka.shtml. S0014-5793(99)00625-0. The sequence draft genome sequence of Ruegeria halocynthiae 4. Vacelet J, Donadey C. 1977. Electron microscope study of the association MOLA R1/13b is 4,320,292 bp, with a G"C content of 58.3%, between some sponges and bacteria. J. Exp. Mar. Biol. Ecol. 30:301–314. including 4,205 coding sequences, 2 rRNAs, and 53 tRNAs. The http://dx.doi.org/10.1016/0022-0981(77)90038-7. 5. Taylor MW, Schupp PJ, Baillie HJ, Charlton TS, de Nys R, Kjelleberg S, genome annotation revealed the presence of genes involved in Steinberg PD. 2004. Evidence for acyl homoserine lactone signal produc- quorum sensing. Two autoinducer type 1 synthases homologous tion in bacteria associated with marine sponges. Appl. Environ. Microbiol. to luxI and 6 corresponding luxR receptors (2) are detected in the 70:4387–4389. http://dx.doi.org/10.1128/AEM.70.7.4387-4389.2004.

September/October 2014 Volume 2 Issue 5 e00998-14 Genome Announcements genomea.asm.org 1 �

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Genome Sequence of Maribius sp. Strain MOLA 401, a Marine Roseobacter with a Quorum-Sensing Cell-Dependent Physiology

Margot Doberva,a,b Sophie Sanchez-Ferandin,c,d Yoan Ferandin,a,b Laurent Intertaglia,e,f Fabien Joux,g,h Philippe Lebaron,a,b Raphaël Lamia,b Sorbonne Universités, UPMC Université Paris, USR 3579, LBBM, Observatoire Océanologique, Banyuls-sur-Mer, Francea; CNRS, USR3579, LBBM, Observatoire Océanologique, Banyuls-sur-Mer, France; Sorbonne Universités, UPMC Université Parisb; UMR7232, BIOM, Observatoire Océanologique, Banyuls-sur-Mer, Francec; CNRS, UMR7232, BIOM, Observatoire Océanologique, Banyuls-sur-Mer, Franced; Sorbonne Universités, UPMC Université Paris, UMS 2348, Observatoire Océanologique, Banyuls- sur-Mer, Francee; CNRS, UMS2348, Observatoire Océanologique, Banyuls-sur-Mer, Francef; Sorbonne Universités, UPMC Université Paris, UMR 7621, LOMIC, Observatoire Océanologique, Banyuls-sur-Mer, Franceg; CNRS, UMR 7621, LOMIC, Observatoire Océanologique, Banyuls-sur-Mer, Franceh

Maribius sp. strain MOLA401 is an alphaproteobacterium isolated from a coral reef lagoon located in New Caledonia, France. We report the genome sequence and its annotation which, interestingly, reveals the presence of genes involved in quorum sensing. This is the ﬁrst report of a full genome within the genus Maribius.

Received 26 August 2014 Accepted 28 August 2014 Published 2 October 2014 Citation Doberva M, Sanchez-Ferandin S, Ferandin Y, Intertaglia L, Joux F, Lebaron P, Lami R. 2014. Genome sequence of Maribius sp. strain MOLA 401, a marine Roseobacter with a quorum-sensing cell-dependent physiology. Genome Announc. 2(5):e00997-14. doi:10.1128/genomeA.00997-14. Copyright © 2014 Doberva et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Raphaël Lami, [email protected].

aribius sp. strain MOLA401 (MOLA culture collection protein, known to be involved in long-chain homoserinelactone MWDCM911 [http://collection.obs-banyuls.fr/index.php]) was transmembrane transport (5). This is the first report of quorum- isolated on 3 December 2004, at a 4-m depth, from marine waters sensing genes within the marine genus Maribius. Thus, this draft in the southwest lagoon of New Caledonia (France) (22°21.23= genome reinforces previous observations suggesting that marine S/166°23.43= E). The sampling station was located between oligo- bacteria are able to communicate using quorum sensing in mi- trophic water near the coral barrier and mesotrophic waters in the croenvironments (6) where these cells can be found at high con- near-shore environment subjected to terrestrial inputs and efflu- centrations. ents from the city of Nouméa (146,000 inhabitants) (1). Based on Nucleotide sequence accession number. The whole-genome its 16S rRNA gene sequences, the strain is phylogenetically related shotgun project has been deposited at DDJB/EMBL/GenBank un- to Maribius pelagius B5-6T (96% sequence identity of 16S rRNA der the accession number JQEY00000000. genes) and belongs to the Rhodobacteraceae (Roseobacter clade). ACKNOWLEDGMENTS Thestrainwascultivatedin100mLofmarinebroth2216medium This work was supported by a UPMC Emergence grant. (BD Difco, Sparks, MD) at 25°C for 48 h. DNA was extracted using a We thank the Bio2Mar (http://bio2mar.obs-banyuls.fr) platform for cetyltrimethylammonium bromide (CTAB)-based method (2). Ge- access to instrumentation and to MrDNA for sequencing the genome. nome sequencing steps conducted by MrDNA (Texas) included fragmentation, ligation to sequencing adapters, and purification. Follow- REFERENCES ing the amplification and denaturation steps, libraries were 1. Conan P, Joux F, Torréton JP, Pujo-Pay M, Douki T, Rochelle-Newall E, sequenced in a pool. A total of 50 ng of DNA was used to prepare the Mari X. 2008. Effect of solar ultraviolet radiation on bacterio- and phytoplankton activity in a large coral reef lagoon (southwest New Caledonia). library, using the Nextera DNA sample preparation kit (Illumina). Aquat. Microb. Ecol. 52:83–98. http://dx.doi.org/10.3354/ame01204. The library insert size was determined by an Experion automated 2. Dempster EL, Pryor KV, Francis D, Young JE, Rogers HJ. 1999. Rapid electrophoresis station (Bio-Rad). The insert sizes of the libraries DNA extraction from ferns for PCR-based analyses. BioTechniques 27: ranged from 300 to 850 bp (average, 500 bp). The library (12 pM) was 66–68. 3. Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioin- loaded (in a pool) to a 600-cycle v3 reagent cartridge (Illumina) and formatics 30:2068 –2069. http://dx.doi.org/10.1093/bioinformatics/ the sequencing was performed on a MiSeq sequencer (Illumina) and btu153. de novo assembled with NGEN v. 11 (DNASTAR, Inc.). The genome 4. Fuqua WC, Winans SC, Greenberg EP. 1994. Quorum sensing in bacteria: was annotated using Prokka 1.7 (3). the luxR-luxI family of cell density-responsive transcriptional regulators. J. Bacteriol. 176:269–275. The draft genome sequence of Maribius sp. strain MOLA401 is 5. Zakataeva NP, Aleshin VV, Tokmakova IL, Troshin PV, Livshits VA. 3,856,666 bp, with a GC content of 67.6%, including 3,764 coding 1999. The novel transmembrane Escherichia coli proteins involved in the sequences, 1 rRNA, and 50 tRNAs. The genome annotation re- amino acid efflux. FEBS Lett. 452:228–232. http://dx.doi.org/10.1016/ vealed the presence of genes involved in quorum sensing. The S0014-5793(99)00625-0. 6. Hmelo LR, Mincer TJ, VanMooy BA. 2011. Possible influence of bacterial autoinducer type 1 synthase homologuous to luxI, and its corre- quorum sensing on the hydrolysis of sinking particulate organic carbon in sponding receptor luxR (4) are located in the same operon. The marine environments. Environ. Microbiol. Rep. 3:682– 688. http:// genome annotation also revealed a gene encoding an RhtB-like dx.doi.org/10.1111/j.1758-2229.2011.00281.x.

September/October 2014 Volume 2 Issue 5 e00997-14 Genome Announcements genomea.asm.org 1

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