Genomic divergence and cohesion in a species of pelagic freshwater bacteria

Abstract

BackgroundIn 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.ResultsComparisons 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.ConclusionsThe 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 materialThe online version of this article (10.1186/s12864-017-4199-z) contains supplementary material, which is available to authorized users.

Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

“…The oxygenated hypolimnion is generally found in deep oligo-mesotrophic holomictic lakes and is inhabited by specific bacterioplankton lineages [ 38 ]. While inhabitants of the epilimnion may migrate over long distances using neighboring shallow lakes and ponds as “stepping stones” [ 45 , 48 ], hypolimnion inhabitants are more likely to be isolated due to the limited occurrence of their habitat. Therefore, we hypothesized that hypolimnion-specific lineages would be more deeply diversified among lakes than epilimnion-specific lineages.…”

Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence

“…Evolution of prokaryotic populations is strongly affected by homologous recombination, which is regarded as a major contributor to maintaining genetic cohesion by preventing sequence divergence via gene conversion 6–9 . Efficient homologous recombination between two genomes requires the presence of (nearly) identical nucleotide sequences flanking the exchanged genomic regions.…”

Opening a next‐generation black box: Ecological trends for hundreds of species‐like taxa uncovered within a single bacterial >99% 16S rRNA operational taxonomic unit

“…Comparative genomic analyses suggested that species of the genus Polynucleobacter are biologically maintained by intensive intraspecific recombination, which is opposed by interspecific recombination barriers that separate core gene pools of related species (Hoetzinger & Hahn, 2017). The coherence of the intraspecific gene pool of at least one species is even maintained across populations separated by geographic distances of up to 3,000 km, indicative of a high dispersal potential of the species (Hoetzinger et al, 2021).…”