The Pseudomonas aeruginosa Transcriptome in Planktonic Cultures and Static Biofilms Using RNA Sequencing

Abstract

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 rise to both quantitative and qualitative information on the transcriptome. Although a large proportion of genes were consistently regulated in both the stationary phase and biofilm cultures as opposed to the late exponential growth phase cultures, the global biofilm gene expression pattern was clearly distinct indicating that biofilms are not just surface attached cells in stationary phase. A large amount of the genes found to be biofilm specific were involved in adaptation to microaerophilic growth conditions, repression of type three secretion and production of extracellular matrix components. Additionally, we found many small RNAs to be differentially regulated most of them similarly in stationary phase cultures and biofilms. A qualitative analysis of the RNA-seq data revealed more than 3000 putative transcriptional start sites (TSS). By the use of rapid amplification of cDNA ends (5′-RACE) we confirmed the presence of three different TSS associated with the pqsABCDE operon, two in the promoter of pqsA and one upstream of the second gene, pqsB. Taken together, this study reports the first transcriptome study on P. aeruginosa that employs RNA sequencing technology and provides insights into the quantitative and qualitative transcriptome including the expression of small RNAs in P. aeruginosa biofilms.

Dispersed cells represent a distinct stage in the transition from bacterial biofilm to planktonic lifestyles

“…25). The dispersed cell physiology is, to a certain extent, similar to that of early exponential phase cells, which also have lower expression levels of rsmY and rsmZ and higher expression levels of type II and type III secretion systems compared with late exponential phase cells 39,40 . However, the early exponential phase of growth can only be reached by cultivating planktonic bacterial cells under optimal growth conditions for several generations, while the dispersed cell phenotype appeared immediately after dispersal from biofilms and can be retained without growth (Fig.…”

A dynamic periplasmic electron transfer network enables respiratory flexibility beyond a thermodynamic regulatory regime

“…Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci as previously described (Doetsch et al, 2012). The normalization of gene expression and statistical testing using a negative binomial distribution were performed using the R package 'DESeq' (Anders and Huber, 2010).…”

Biofilm streamers cause catastrophic disruption of flow with consequences for environmental and medical systems

“…Although biofilms are desirable in waste-water treatment (6), biofilms primarily cause undesirable effects such as chronic infections or clogging of industrial flow systems (1)(2)(3). Cells in biofilms display many behavioral differences from planktonic cells, such as a 1,000-fold increase in tolerance to antibiotics (7,8), an altered transcriptome (9)(10)(11), and spatially heterogeneous metabolic activity (12,13). Some of these physiological peculiarities of biofilm-dwelling cells may be due to strong gradients of nutrients and metabolites, which also affect biofilm morphology and composition (14,15).…”