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Background  In many prokaryotic genera a clustered phylogeny is observed, akin to the occurrence of species in sexually reproducing organisms. For some taxa, homologous recombination has been invoked as the underlying mechanism providing genomic cohesion among conspecific individuals. Whether this mechanism is applicable to prokaryotes in freshwaters with low habitat connectivity – i.e. elevated geographic barriers to gene flow – is unclear. To investigate further we studied genomic trends within the globally abundant PnecC cluster (genus  Polynucleobacter ,  Betaproteobacteria ) and analyzed homologous recombination within the affiliated species  P. asymbioticus .    Results  Comparisons among 20 PnecC genomes revealed a clearly discontinuous distribution of nucleotide sequence similarities. Among the nine conspecific individuals ( P. asymbioticus ) all average nucleotide identity (ANI) values were greater than 97%, whereas all other comparisons exhibited ANI values lower than 85%. The reconstruction of recombination and mutation events for the  P. asymbioticus  core genomes yielded an r/m ratio of 7.4, which is clearly above estimated thresholds for recombination to act as a cohesive force. Hotspots of recombination were found to be located in the flanking regions of genomic islands. Even between geographically separated habitats a high flux of recombination was evident. While a biogeographic population structure was suggested from MLST data targeting rather conserved loci, such a structure was barely visible when whole genome data was considered. However, both MLST and whole genome data showed evidence of differentiation between two lineages of  P. asymbioticus . The ratios of non-synonymous to synonymous substitution rates as well as growth rates in transplantation experiments suggested that this divergence was not selectively neutral.    Conclusions  The high extent of homologous recombination among  P. asymbioticus  bacteria can act as a cohesive force that effectively counteracts genetic divergence. At least on a regional scale, homologous recombination can act across geographically separated ecosystems and therefore plays an important role in the evolution and consistency of bacterial freshwater species. A species model akin to the biological species concept may be applicable for  P. asymbioticus . Nonetheless, two genetically distinct lineages have emerged and further research may clarify if their divergence has been initiated by reinforced geographical barriers or has been evolving in sympatry.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4199-z) contains supplementary material, which is available to authorized users.

Genomic divergence and cohesion in a species of pelagic freshwater bacteria