Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis

In this review, we synthesise current models and recent comparative genomic studies describing how bacterial species may emerge through adaptation to a new ecological niche and maintain themselves in the same niche over long time periods. We notably consider the impact of genetic exchange with phylogenetically close relatives living in sympatry and how this leads to the heterogeneous evolution of different genes within the bacterial genome. This heterogeneity provides landmarks to recognise genes that determine adaptation to the ecological niche, and we present reverse ecology strategies to unravel ecological properties of bacterial populations.