Are bacterial species really ecotypes?

Defining bacterial species is still a debatable topic among bacteriologists. It has become clear that, periodic selection and recombination are two main drivers of bacterial species.
Here, we are curious to study the diversity and structure of a local population. For which, we studied a population that was comprised of two symbiovars of R. leguminosarum. The draft genomes of 72 isolates (36 viciae & 36 trifolii) from a square meter of soil were sequenced by Roche 454 sequencing and compared with the published genome of Rlv 3841. Chapter Two employs 305 core genes and genomic analysis to demonstrate the existence of five phenotypically indistinguishable (cryptic) genospecies in a local population. Most of the cryptic genospecies include both viciae and trifolii strains: the genospecies do not reflect the symbiovars. Chapter Three demonstrates that recombination plays a major role in shaping the chromosome of R. leguminosarum. Moreover, it demonstrates the preference of intra- genospecies recombination highlighting the occurrence of genetic isolation between genospecies that allows them to be represented as biological species. Chapter Four demonstrates the presence of core genes on different plasmids. The phylogenetic structure of Rlv 3841 replicons resembles the structure of core genes phylogeny indicating lack of genes transfer between genospecies in each replicon. However, the phylogenetic networks suggest horizontal transfer of nod genes that allow species members to have different host specificity. Chapter Five displays the genetic diversity present between two major genospecies (B and C) of R. leguminosarum.
Overall, our results provide direct evidence that core genes and genomic analysis such as ANI should be used to define bacterial species. Moreover, the host specific symbiotic genes are normal accessory genes that have no significant role in the demarcation of bacterial species.