Transcriptional profiling of Pseudomonas aeruginosa biofilm life cycle stages reveals dispersal-specific biomarkers

Bacteria exhibit two lifestyles: planktonic, free-floating individual cells or sessile multicellular aggregates known as biofilms. The biofilm life cycle is characterized by three distinct stages: attachment, maturation and dispersal. Consequently, specific adaptations occur at each stage, governing cellular behaviors such as adhesion and the synthesis and degradation of extracellular matrix components. Characterizing stage-specific bacterial profiles therefore represents a valuable strategy for the development of novel antibiofilm therapies. Here, we used the model biofilm-forming bacterium Pseudomonas aeruginosa PAO1 to characterize the transcriptional profiles of each stage of the biofilm life cycle: attachment, biofilm maturation and spontaneous dispersal in closed cultures. We report that, relative to biofilm dispersal, surface attachment coincided with the upregulation of genes comprising the Pil-Chp mechanosensory system (2.00–7.37-fold), whereas biofilm maturation was characterized by the upregulation of genes involved in Pel polysaccharide synthesis (∼2.5-fold relative to either attachment or dispersal), siaD and PA4396 diguanylate cyclases as well as phosphodiesterases pipA, fimX and PA5442 (2.08–3.73-fold relative to biofilm dispersal). In contrast with cells undergoing biofilm maturation, dispersing cells upregulated genes responsible for the biosynthesis of alginate, rhamnolipid, and extracellular nucleases ( eddA , 3.28-fold; and eddB , 2.95-fold), as well as the transcriptional regulator of dispersal amrZ (6.27-fold). Additionally, genes involved in the biosynthesis and sensing of the dispersal signal cis-2-decenoic acid ( dspS , 2.04-fold; and dspI , 5.59-fold), canonical phosphodiesterases ( nbdA , 7.56-fold; and rbdA , 3.03-fold), four non-canonical HD-GYP phosphodiesterases and seven other c-di-GMP–related enzymes were also upregulated during dispersal. Altogether, this work provides benchmarking stage-specific transcriptional profiles characterizing the biofilm life cycle of P. aerugiosa in closed systems. Furthermore, it allowed the identification of a subset of fourteen genes as transcriptional biomarkers of dispersal, which were used to build reporter plasmids as tools to determine the onset of dispersal.