The objective of this PhD project is to investigate the evolution of vibrio virulence in relation to the oyster as host.

Oyster as a niche for vibrio evolution and pathogen emergence

Duration: Fall 2016-2019

Principal investigator : Frédérique Le Roux, PhD, HDR

Grant: Ifremer/Bretagne for the 3 years

Global change and anthropogenic activities have caused a worldwide increase in mass mortalities associated to infectious diseases, especially in marine organisms (Fey et al., PNAS, 2015). The great devastation of Crassostrea gigas juvenile observed in France over the last 6 years is a prime example for the far fetching effects of such mass mortalities threatening the sustainability of this important economic sector as well as biodiversity of wild populations (Le Roux et al., Front Mic 2015). Previous research efforts have mainly focused on the hypothesis that this disease results from the emergence of a new genotype of the herpes virus, OsHV-1 μvar (reviewed by Barbosa Solomieu et al., J Inv Path 2015). We demonstrated that the virus is neither essential nor sufficient to cause juvenile deaths, whereas bacteria are necessary for the disease process (Petton et al., Front Mic 2015). Using specificpathogen-free (SPF) oysters transferred in an oyster farm during a disease outbreak, we observed that rapid Vibrio colonization precedes viral replication and oyster death. Oyster-associated vibrios were analysed in the context of a metapopulation framework, i.e. considering potential overlap or differences of populations collected from spatially and temporally distinct habitats, which are connected by dispersal (Le Roux et al., Trends in Microbiology, 2016). Our analysis revealed that several populations of Vibrio show preferential association with oyster. Among them V. Crassostreae is particularly abundant in diseased animals and its pathogenicity relies in the presence of a large mobilizable plasmid (pVIR) (Bruto et al., in prep).

It should be noted that recurring mass mortalities are not observed in all regions where oysters have settled. Invasive populations of C. gigas in Northern Europe have only encountered isolated events (e.g. Southern Wadden sea, Waterman et al., 2008) or have been spared so far (i.e., Northern Wadden Sea, Wegner, personal observation). By exposing larvae from these two independent and genetically distinct invasion sources of C. gigas (Southern vs. Northern Wadden sea) to phylogenetically diverse pathogenic vibrios (including V. crassostreae), Wegner and coll demonstrated that hosts evolved resistance to newly encountered pathogen communities within a few generations. Resistance against sympatric and allopatric Vibrio strains was dominantly inherited in crosses between both invasion sources resulting in an overall higher resistance of admixed individuals when compared to pure lines (Wegner and Wendling, Proc Biol Sci 2014). The selective pressures leading to these geographic rather than phylogenetic matches are however unknown, but it seems likely that they result from adaptations enabling vibrios to live associated with oyster hosts. Preliminary results collected to test the feasibility of the present project, could demonstrate that V. crassostreae isolated in Northern Europe were not able to kill juvenile oysters produced in France and the pVir plasmid was not detected in these strains (Le Roux & Wegner unpublished data). The objective of this PhD project is to investigate the evolution of vibrio virulence in relation to the oyster as host.

· Hypothesis 1: Vibrio and oysters co-evolve

· Hypothesis 2: Pathogenic genotypes of Vibrio emerge in areas with mass mortalities

To this aim we will use independent and genetically distinct sources of C. gigas that represent a gradient of disease severity (i.e. Brest, experiencing recurring disease events, Texel occasionally suffering from disease and Sylt as a disease- free site). We will compare the population structure of vibrios in oysters and surrounding seawater to identify populations that colonize the oysters in the 3 locations. Experimental infections in the lab using sympatric/allopatric Vibrio isolates will evaluate i) whether strains isolated in Brest are more pathogenic than conspecifics from Texel and Sylt and ii) whether oysters (larvae and juveniles) from Brest, Sylt and Texel are less affected by sympatric strains. In addition, it will allow the exploration of life stage specific patterns of virulence. These data will be correlated with genome analyses of ~300 of strains (belonging to virulent population such as V. crassostreae) used in these experimental infections to build hypotheses of gene function in the context of interaction with oyster. These hypotheses will subsequently be tested by molecular genetics and mutant phenotype will be assessed by experimental challenge. The functions of gene will then be exploreD using cellular and structural biology.

Le Roux’s lab

The Station biologique de Roscoff (SBR, is a research unit jointly operatedby CNRS and UPMC (University Pierre & Marie Curie in Paris). Le Roux’s team (Genomic of Vibrio) belongs to the Research Unit - “Integrative Biology of Marine Models Laboratory” ( Le Roux’s team research investigates the molecular mechanisms involved in the emergence of vibrio pathogenic to marine invertebrates. These include molecular epidemiology with an emphasis on biodiversity, virulence and genome plasticity, environmental genomics and host/pathogen interaction. In support of Le Roux’s team, the SBR research infrastructure offers high-level computational skills (bioinformatics platform), structural biology (crystallography platform), and equipment to perform research in in vivo conditions with secured areas dedicated to these experimental challenges. In addition, this project will benefit from collaboration with Ifremer (Petton and coll) for SPF animals providing.


Principal investigator: Frédérique Le Roux, PhD, HDR

Tel : 02 98 2956 47

e-mail :

Five selected Peer Reviewed Publications

  • Le Roux F, Wegner MK, Polz MF. Oysters and Vibrios as a Model for Disease Dynamics in Wild Animals. Trends in Microbiology April 2016
  • Goudenège D, Travers MA, Lemire A, Petton B, Haffner P, Labreuche Y, Tourbiez D, Mangenot S, Calteau A, Mazel D, Nicolas JL, Jacq A, Le Roux F. A single regulatory gene is sufficient to alter Vibrio aestuarianus pathogenicity in oysters. Environ Microbiol. 2014
  • Lemire A, Goudenège D, Versigny T, Petton B, Calteau A, Labreuche Y, Le Roux F. Populations, not clones, are the unit of vibrio pathogenesis in naturally infected oysters. ISME J. 2014
  • Goudenège D, Labreuche Y, Krin E, Ansquer D, Mangenot S, Calteau A, Médigue C, Mazel D, Polz MF, Le Roux F. Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits. ISME J. 2013 Oct; 7(10):1985-96.
  • Cordero OX, Windschutte H, Kirkup B, Proehl S, Hussain F, Le Roux F, Mincer T, Polz MF (2012). Antibiotic production and resistance leads to social cohesion within bacterial populations in the wild. Science. 337:1228-31.

Other scientist implicated in the supervision:

Yannick Labreuche, PhD,

Collaborations (the PhD students may spend time in one of the following labs)

Pr Martin Polz, MIT, USA

Dr Mathias Wegner, AWI, Germany

Competence required:

Master 2 in Microbiology, molecular biology and/or genomic


Deadline for application: (CV, motivation and recommendation letters to be send to: 20 May 2016

Interviews: 20-30 May

Application to the doctoral school (Ecole doctorale complexité du vivant, UPMC): beginning of June

Oral selection by the doctoral school in July (NB: the candidate has to present his CV and PhD project to the doctoral school to be selected=>20 minutes)

Nicolas, Pade | MBA

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