Abstract
Polynucleobacter asymbioticus strain QLW-P1DMWA-1T represents a group of highly successful heterotrophic ultramicrobacteria that is frequently very abundant (up to 70% of total bacterioplankton) in freshwater habitats across all seven continents. This strain was originally isolated from a shallow Alpine pond characterized by rapid changes in water temperature and elevated UV radiation due to its location at an altitude of 1300 m. To elucidate the strain’s adjustment to fluctuating environmental conditions, we recorded changes occurring in its transcriptomic and proteomic profiles under contrasting experimental conditions by simulating thermal conditions in winter and summer as well as high UV irradiation. To analyze the potential connection between gene expression and regulation via methyl group modification of the genome, we also analyzed its methylome. The methylation pattern differed between the three treatments, pointing to its potential role in differential gene expression. An adaptive process due to evolutionary pressure in the genus was deduced by calculating the ratios of non-synonymous to synonymous substitution rates for 20 Polynucleobacter spp. genomes obtained from geographically diverse isolates. The results indicate purifying selection.
Highlights
The model bacterium Polynucleobacter asymbioticus strain QLW-P1DMWA-1T (Meincke et al, 2012) belongs to the class Gammaproteobacteria (Parks et al, 2018)
Small cells with a streamlined genome appear to follow a trend of small-scale changes in gene expression and methylation, significantly contributing to bacterial acclimatization
We document that methylation patterns in the bacterial genome are constantly revised in response to rapid environmental changes, possibly via de novo methylation
Summary
The model bacterium Polynucleobacter asymbioticus strain QLW-P1DMWA-1T (Meincke et al, 2012) belongs to the class Gammaproteobacteria (Parks et al, 2018). Ultramicrobacteria (cell volume < 0.1 μm3) in general are numerically dominant organisms in many freshwater ecosystems (Proctor et al, 2018) They display extreme (e.g., LD12 Alphaproteobacteria and acI Actinobacteria) or moderate genome streamlining (e.g., genus Polynucleobacter) (Hahn et al, 2005; Newton et al, 2007; Salcher et al, 2011; Neuenschwander et al, 2017). We chose distinct experimental parameters for this strain, i.e., incubation scenarios at 4◦C, at 26◦C, and at 26◦C with UV irradiation (hereafter denoted as 26◦C∗) These experimental conditions reflect the abiotic factors common in the strain’s Alpine habitat (Hahn et al, 2012)
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