Genomic evolution of bacterial populations under co-selection by antibiotics and phage

Bacteria live in dynamic systems where selection pressures can alter rapidly, forcing adaptation to the prevailing conditions. In particular, bacteriophages and antibiotics of anthropogenic origin are major bacterial stressors in many environments. We previously observed that populations of the bacterium Pseudomonas fluorescens SBW25 exposed to the lytic bacteriophage SBW25Φ2 and a non-inhibitive concentration of the antibiotic streptomycin (co-selection) achieved higher levels of phage resistance compared to populations exposed to the phage alone. In addition, the phage became extinct under co-selection while remaining present in the phage alone environment. Further, phenotypic tests indicated that these observations might be associated with increased mutation rate under co-selection. In this study, we examined the genetic causes behind these phenotypes by whole-genome sequencing clones isolated from the end of the experiments. We were able to identify genetic factors likely responsibl...