Global change linked to temperature increase and ocean acidification but also more direct anthropogenic influences, such as aquaculture, have caused a worldwide increase in the reports of Vibrio-associated illness, affecting humans but also animals such as corals and mollusks. In particular, over the last 4 years, Vibrio splendidus and V. aestuarianus have been associated with recurrent mortality outbreaks of oyster beds (Crassostrea gigas) in France. Investigating the “emergence of Vibrio pathogenesis events” requires the analysis of microbial evolution at the gene, genome and population level, in order to identify genomic modifications linked to increased virulence, resistance and/or prevalence, or to recent host shift.
The study of Vibrio distribution on fine phylogenetic and spatial scales has demonstrated that vibrios coexisting in the water column can be divided into closely related populations, which pursue different lifestyles (free living, particle and animal-associated), defined as ecological population. Thus it is possible to analyze animal-associated vibrios 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 (here oyster and water column).
In contrast to species that are pathogenic to humans, little data are available regarding oyster pathogens. Recent advances in genomics along with the availability of specific pathogen free (SPF) oysters will be helpful to resolve our lack of knowledge concerning the emergence of opportunistic oyster pathogens in natural Vibrio populations.
The overall aim of this project is to investigate the partitioning of vibrios into ecologically distinct populations at fine environmental and genotypic scales of resolution. This will allow to determine (i) from what types of microhabitats oyster pathogens emerge and, consequently, what types of populations serve as reservoirs of pathogens, (ii) how populations shift during disease events, and (iii) what genomic features correlate to differential microhabitat association (including pathogenesis). To this end, we will use a combination of population modeling, comparative and functional genomic analysis in addition to experimental pathology.
- In task 1, we will compare the population structure of vibrios in oysters and surrounding water. We will determine to what extent Vibrio populations are assembled neutrally in oysters or whether specific colonization processes occur and result in association with specific populations. Further, we will determine how Vibrio population structure changes during pathogenicity events. Even if population assembly is overall neutral, one can expect that during pathogenicity events specific genotypes or groups of genotypes outgrow others, resulting in a characteristic shift in population structure.
- In task 2, we will determine the pathogenicity potential among large numbers of Vibrio strains representative of ecological populations. Using SPF oysters, we will test how strains and genotypes affect host survival. These data will be correlated with genome analyses of 100s of strains used in these experimental infections to build hypotheses of gene function in the context of oyster pathogenesis. These hypotheses will be tested by molecular genetics approaches.
- In task 3, we will investigate the function of observed V. splendidus diversity in diseased oysters. Oysters will be challenged by pools of strains, individually assayed for pathogenesis in task 2, and both colonization and virulence will be assessed. These analyses will enable to determine whether or not colonization efficiency is linked to virulence. If we detect pools showing a higher virulence than that of their individual constituents, comparative genomic analyses will be performed to enable prediction of sets of genes that promote virulence in combination but not singly.