GENOME FLEXIBILITY ACROSS DIFFERENT STRAINS OF THE HEXACHLOROCYCLANE-DEGRADING BACTERIUM SPHINGOBIUM FRANCENSE SP+ IDENTIFIED BY A GLOBAL APPROACH OF GENOME SEQUENCING AND MICROARRAY COMPARATIVE GENOMIC HYBRIDIZATION

Abstract

International audiencePhenotypic and genomic dynamics enable bacteria to adapt quickly to various ecological niches and environmental fluctuations such as the presence of xenobiotic compounds. We explored the different adaptive mechanisms in the bacterium Sphingobium francense, which is able to degrade lindane, a chlorinated xenobiotic compound historically used in agricultural and medicine. Previous studies demonstrated the association of mobile genetic elements with lin genes implicated in lindane catabolic pathways. We also observed that the wildtype, sp+, a lindane degrading strain, produces mutants (at a rate of 4 percent per replating) unable to degrade lindane. In order to study the role of mobile genetic elements in the adaptability of this bacterium, we developed an original strategy based on the pyrosequencing data obtained for the genome of Sphingobium francense sp+ and microarray comparative genomic hybridizations. This approach uses a two-color process to estimate the different types of genomic rearrangements that occurred in a mutant genome in comparison to the reference strain sp+ genome. For this study, five non-lindane degrading mutants and one revertant, which recovered the capacity to degrade lindane, were characterized. Analyzes of each microarray showed that the nonlindane degrading mutants underwent large genomic rearrangements and the selected mutants were genetically different. Moreover, we established the proximity between some environmental genes and mobile genetic elements. Some of these regions were deleted in the mutants reinforcing the observation that mobile genetic elements play an important role in bacterial adaptation to environmental perturbation. Thus, all the data obtained confirms the extraordinary plasticity of the Sphingobium genome linked to the presence of multiple mobile genetic elements, which are involved in the instability of lindane degradation capability and other environmental functional genes