Qualitative and Quantitative Analysis of the Pseudomonas aeruginosa Transcriptome in Planktonic Cultures and Static Biofilms

Important insights into how bacteria sense and respond to varied habitats can be achieved by the elucidation of global gene expression responses. In this study, we evaluated how gene expression differs in mature Pseudomonas aeruginosa biofilms as opposed to planktonic cells by the use of RNA sequencing technology that gives raise to both qualitative and quantitative information on the transcriptome. We identified more than 2400 putative transcriptional start sites (TSS) within the PA14 genome. Those included many TSS located within the same promoter region, antisense to coding sequences or in previously unannotated regions indicating novel genes. Quantitative analysis revealed the down-regulation of metabolic genes together with a reduced motility and virulence in the static biofilm as compared to planktonic cultures. Most importantly, as opposed to hybridization-based methods, RNA sequencing is not restricted to a preselected gene set, and we identified 19 previously described small regulatory RNAs to be differentially expressed in the biofilms and many genes of the accessory genome. Taken together, in this study we provide an example of the advantages of RNA sequencing over established methods that can add a new layer of complexity to the study of bacterial transcriptomes as it allows the simultaneous analysis of gene expression, the determination of TSS and operon structures and the use of the RNA sequencing data to (re-) annotate the genome.