Abstract
The oyster Crassostrea gigas is the most cultured species of bivalve in the world and is confronted with infectious diseases involving bacteria of the genus Vibrio. Among these Vibrio, the species V. aestuarianus, initially described in 1983 as a bacterium of estuarine environments, has been associated with mortality of adult oysters in Europe since 2001. In 2012, mortality of adult cockles Cerastoderma edule associated with this species have also been reported. However, the processes leading to the emergence of pathogenic bivalve lineages have remained unknown. During this thesis, we sought to clarify (1) the population structure of V. aestuarianus and their genomic determinants, (2) the evolutionary events that participated in the emergence and evolution of the subspecies, and (3) the habitats, cycles and species sensitive toV. aestuarianus. We have shown that pathogenic V. aestuarianus strains fall into two subspecies withdifferent evolutionary histories. V. aestuarianus francensis, described in 2008, includes pathogenic oyster strains while V. aestuarianus cardii includes pathogenic cockle strains. Both subspecies cause disease in their host populations in summer, and temperature has been identified as a favorable factor for disease development. V. aestuarianus francensis impacts oyster farming and we show that two distinct lineages have spread across Europe for at least 20 years. This subspecies is characterized by low genetic diversity and essentially clonal evolution. Strains of V. aestuarianus francensis have a specialist lifestyle, with a habitat restricted to oysters. One of the events that favored its emergence could be the acquisition and genomic integration of a mobile genetic element containing genes coding for proteins involved in copper export. Currently, the subspecies V. aestuarianus cardii impacts cockles only in France. The phenotypic and genetic diversity in this subspecies is greater than in the subspecies V. aestuarianus francensis. Several genetic groups with different levels of virulence towards cockles could be identified and the comparison of genomes between these groups made it possible to identify potential virulence factors.