Comparison of spontaneous and UV-induced Rif^r mutant frequencies.

<p>Presented are only the results with indigenous strains exhibiting statistically significantly increased mutation frequency (p<0.045) after the exposure to UV-C irradiation analysed with Mann-Whitney U test (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182484#pone.0182484.s014" target="_blank">S6 Table</a>).</p

Contribution of increased mutagenesis to the evolution of pollutants-degrading indigenous bacteria

<div><p>Bacteria can rapidly evolve mechanisms allowing them to use toxic environmental pollutants as a carbon source. In the current study we examined whether the survival and evolution of indigenous bacteria with the capacity to degrade organic pollutants could be connected with increased mutation frequency. The presence of constitutive and transient mutators was monitored among 53 pollutants-degrading indigenous bacterial strains. Only two strains expressed a moderate mutator phenotype and six were hypomutators, which implies that constitutively increased mutability has not been prevalent in the evolution of pollutants degrading bacteria. At the same time, a large proportion of the studied indigenous strains exhibited UV-irradiation-induced mutagenesis, indicating that these strains possess error-prone DNA polymerases which could elevate mutation frequency transiently under the conditions of DNA damage. A closer inspection of two <i>Pseudomonas fluorescens</i> strains PC20 and PC24 revealed that they harbour genes for ImuC (DnaE2) and more than one copy of genes for Pol V. Our results also revealed that availability of other nutrients in addition to aromatic pollutants in the growth environment of bacteria affects mutagenic effects of aromatic compounds. These results also implied that mutagenicity might be affected by a factor of how long bacteria have evolved to use a particular pollutant as a carbon source.</p></div

Median values of the spontaneous Rif^r mutant frequencies of the indigenous strains and the laboratory reference strain PaW85.

<p>Presented are only the results for strains exhibiting the mutant frequency statistically significantly different from that of the reference strain PaW85 (the Kruskal-Wallis test, p<0.006; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182484#pone.0182484.s009" target="_blank">S1 Table</a>). Isolate D2RT is missing from the figure because the median value of the frequency of Rif^r mutants of this strain was 0 (the mean value of Rif^r frequency of this strain was 1.07 x 10⁻⁹).</p

The phylogenetic tree of ImuC/DnaE2 protein sequences.

<p>The underlined proteins are from strains possessing <i>rulAB</i> genes and the ones marked with star are from strains where <i>rulAB</i> genes are located in the chromosome. Sequences derived from <i>P</i>. <i>fluorescens</i> strains PC20 and PC24 are shown in boldface. Sequences were aligned with ClustalX2 and further visualised with TreeViewX. Numbers at branch nodes indicate bootstrapping values for 1000 bootstrap replicates. Values under 500 were removed. The identifiers of the aligned sequences are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182484#pone.0182484.s015" target="_blank">S7 Table</a>.</p

The frequency of rifampicin resistant colonies in M9 minimal medium which contained either glucose, phenol (2.5 mM) or <i>p</i>-cresol (1.25 mM) as the only carbon source.

<p>Data were analysed using the Kruskal-Wallis test (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182484#pone.0182484.s019" target="_blank">S11 Table</a>). * designates P<0.025 and ** designates P<0.001.</p

The expression rate of the genes of error prone DNA polymerases after the exposure of cells to DNA damaging agent MMC (2 μg/ml).

<p>(A) The results are presented as relative fold difference between cells with and without MMC treatment. (B) The expression rate of the studied error-prone DNA polymerases normalized against <i>trpA</i>. Each data represents the mean from at least three replicate induction experiments.</p

The bacterial strains used in this study.

<p>The bacterial strains used in this study.</p

UV-C irradiation tolerance of indigenous strains.

<p>UV-C irradiation tolerance of indigenous strains.</p

Contribution of increased mutagenesis to the evolution of pollutants-degrading indigenous bacteria - Fig 3

<p><b>The phylogenetic trees of RulA (A) and RulB (B) protein sequences. Underlining indicates the genes of proteins which are located on plasmids.</b> Sequences derived from <i>P</i>. <i>fluorescens</i> strains PC20 and PC24 are shown in boldface. Sequences were aligned with ClustalX2 and further visualised with TreeViewX. Numbers at branch nodes indicate bootstrapping values for 1000 bootstrap replicates. Values under 500 were removed. The identifiers of the aligned sequences are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182484#pone.0182484.s015" target="_blank">S7 Table</a>.</p

The comparison of spontaneous and UV-C irradiation (5 J/m²) induced Rif^r mutant frequencies.

<p>Each data represents the median value from three replicate UV-mutagenesis assays. Data were analysed using the Mann-Whiteny U test (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182484#pone.0182484.s017" target="_blank">S9 Table</a>).</p