From a genomic species definition toward an Ecological Species Concept for bacteria – EcoGenome

The bacterial species is presently only defined by the measure of the genomic similarity of its members. Even if this definition has been recently confirmed by an international committee of taxonomists (Stackebrandt et al., 2002, Int. J. Syst. Evol. Microbiol. 52:1043-1047), the same committee also strongly encourages researches that would lead to a biologically sound concept for the bacterial genomic species. In the frame of these researches, the EcoGenome project proposes to investigate whether the present operational genomic definition for a bacterial species could be associated to a concept of Ecological Species. Current theory is that genomically coherent clusters of strains in clonally propagated organisms result from intense sweeping selections consecutive to adaptations of founder strains to new ecological niches. Thus, genomically coherent clusters of strains - and likely genomic species too - would be ecotypes adapted to specific ecological niches. The project aims at establishing such a relationship by looking for "species specific" genes and ecological niches in genomic species of the Agrobacterium tumefaciens complex, consisting of nine closely related, while readily different genomic species, which often live sympatrically in some ecosystems. Actually, according to the principle of competitive exclusion, the simultaneous presence of several species in a single ecosystem means that co-inhabiting species should exploit different ecological niches in this ecosystem. Comparing sympatric species will facilitate the discovery of species specific niches. In addition, investigating closely related species will facilitate the discovery of the finest genomic differences between species, which are thought to determine adaptations to species specific ecological niches. To improve our understanding of the reason why several closely related species of bacteria can coexist, the project actions aims at : Action 1, exploration of ecological specificities of A. tumefaciens species living sympatrically in soils, by determining experimentally their relative competitiveness in soil and rhizosphere biotopes; Action 2, determination of genomic specificity of sympatric A. tumefaciens species by comparative genomic hybridizations (CGH) using pangenomic microarrays; Action 3, establishment of a relationship between "species specific" niches and "species specific" genes, by combining metabolomic, transcriptomic and directed mutagenesis approaches along to identification of molecules from niches that specifically activate "species specific" genes. The methodological approach and procedures set up in the EcoGenome project is thought to be applicable to other bacterial group of interest, facilitating the discovery of novel environmental factors involved, for instances, in the persistence and dissemination of opportunistic or emerging pathogenic bacteria.