BioProject

We studied adaptation of the metabolically versatile bacterium Pseudomonas aeruginosa to standard laboratory conditions by propagating mismatch repair-deficient P. More...

We studied adaptation of the metabolically versatile bacterium Pseudomonas aeruginosa to standard laboratory conditions by propagating mismatch repair-deficient P. aeruginosa in exponential phase for 24 days in rich medium. In the selective environment of this large-bottleneck mutation accumulation experiment, the bacteria developed shorter lag phases, higher growth rates and higher maximum cell densities. Transcriptional profiling and phenotyping for growth in different media revealed that higher fitness under laboratory conditions evolved via different pathways. Although common adaptive mutations or mutations that define trade-offs were not identified, there was a convergent evolution of transcriptional profiles associated with a shift from biofilm-associated to planktonic lifestyles. Our results indicate that under constant planktonic conditions P. aeruginosa uses several genetic pathways in order to fine-tune adaptation towards faster growth. The selected mutations in the different genetic pathways show a great variety of biofilm, virulence and motility phenotypic trade-offs, thus implying that on the population level, the adaptation of P. aeruginosa to constant conditions does not compromise its versatility. Methods: mRNA profiles were generated for Pseudomonas aeruginosa samples derived from LB-cultures grown to an OD600 =0.4-0.6. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina). The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using Stampy pipeline with default settings. Overall design: Pseudomonas aeruginosa PA14 mutS::Tn mismatch repair-deficient strain was subjected to in vitro evolution in this study. This strain was obtained from a PA14 transposon insertion library. Cultures WBN1, 2, 4, 5, 6 were obtained from single colonies of PA14 mutS::Tn and passaged in exponential phase in LB for 24 days using 100-cell bottlenecks. The last passage of each WBN culture was streaked on LB agar to obtain 6 single-colony-derived clones, which were saved in liquid nitrogen. RNA sequencing was performed for three randomly selected clonal isolates from each WBN line. The first number in the name of each clone (e.g. "4" in WBN4-1) refers to the culture the clone is derived from. The second number in the name of each clone (e.g. "1" in WBN4-1) refers to the clone itself. The RNA of non-evolved PA14 mutS::Tn was sequenced as control. Less...