Polynucleobacter necessarius , a model for genome reduction in both free-living and symbiotic bacteria

Abstract

We present the complete genomic sequence of the essential symbiont Polynucleobacter necessarius (Betaproteobacteria), which is a valuable case study for several reasons. First, it is hosted by a ciliated protist, Euplotes; bacterial symbionts of ciliates are still poorly known because of a lack of extensive molecular data. Second, the single species P. necessarius contains both symbiotic and free-living strains, allowing for a comparison between closely related organisms with different ecologies. Third, free-living P. necessarius strains are exceptional by themselves because of their small genome size, reduced metabolic flexibility, and high worldwide abundance in freshwater systems. We provide a comparative analysis of P. necessarius metabolism and explore the peculiar features of a genome reduction that occurred on an already streamlined genome. We compare this unusual system with current hypotheses for genome erosion in symbionts and free-living bacteria, propose modifications to the presently accepted model, and discuss the potential consequences of translesion DNA polymerase loss.symbiosis | nonsynonymous mutation rates | Burkholderiales | protozoa | genome streamlining

Evolutionary costs and benefits of infection with diverse strains of Spiroplasma in pea aphids*

“…Endosymbiotic bacteria generally exhibit increased rates of sequence evolution than their free‐living relatives, which is attributed to the lower effective population size that comes with maternal transmission and the associated bottlenecks between host generations (Moran ; Woolfit and Bromham ; Boscaro et al. ). Long‐term vertical transmission is also expected to reduce the costs that symbionts impose on their hosts.…”

Biogeography and Character Evolution of the Ciliate Genus Euplotes (Spirotrichea, Euplotia), with Description of Euplotes curdsi sp. nov.

“…An important evolutionary event that is clearly tied to phylogeny and habitat is instead the origin of symbiosis between Euplotes species and the bacterium Polynucleobacter (or other betaproteobacteria) [18, 19, 66, 67]. This obligate relationship, explored in many details but of still mysterious function, was clearly made possible by the invasion of the bacteria’s habitat by Euplotes species.…”

Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes

“…Averaged over long spans of evolution, gene loss appears to be a more common process than gene gain as shown for different groups of bacteria and archaea [19,21,[23][24][25]. In obligate intracellular parasitic bacteria as well as in parasitic archaea, gene loss is the single dominant evolutionary process [7,[26][27][28]. However, genome reduction, often described as streamlining, also prevails in the evolution of bacterial saprophytes [24,29] and some free-living microbes, particularly in marine environments [23,25,30,31].…”