Comparative genomics reveals response of Rhodococcus pyridinivorans B403 to phenol after evolution

Rhodococcus pyridinivorans B403 is a promising bacterium for degrading phenolic pollutants. In the application, the high-concentration substrate has a significant inhibitory effect on cell growth and phenol degradation, which makes adaptive evolution study of bacteria an important guarantee for further application. The present work found evolved R. pyridinivorans (X1 and X2) had enhanced tolerance to phenolic pollutants as compared to the ancestor strain: the minimum inhibitory concentrations (MIC) of phenol, m-cresol, and catechol increased from 1.2, 0.7, 0.8 g/L to 1.8, 1.0, 1.2 g/L of strain X1, and to 2.4, 1.2, 1.4 g/L of strain X2, respectively. Furthermore, compared to B403, X1, and X2 accumulated more biomass in 500-mg/L cresol medium and degraded phenols more efficiently. Correspondingly, genome sequencing revealed that the mutation sites in genes were annotated as encoding phosphotransferase, MFS transporter, AcrR regulator, and GlpD regulator in the adapted strains, which were closely associated with improved phenol tolerance and degradation. The conclusions provided theoretical basis for the phenol tolerance and degradation, which could promote construction of engineering bacteria for practical application. KEY POINTS: • Evolved strains were more resistant to phenols • Evolved strains degraded phenols more quickly • Genome sequencing elucidated mechanisms of enhanced phenol tolerance and degradation.