Fig. 2: The abundance of specific mRNA transcripts increases in the extracellular matrix of P. aeruginosa biofilms relative to planktonic cells.

Extracellular mRNA transcripts identified through RNA analysis of five-day P. aeruginosa biofilms. a Volcano plot of total RNA sequenced from the biofilm matrix of five-day P. aeruginosa biofilms and planktonic P. aeruginosa cells (16 h). mRNA transcripts that are highly abundant in planktonic cells compared to the biofilm matrix are highlighted in grey in the left part of the image with a negative log 2-fold change. mRNA transcripts with a positive log 2-fold change and higher negative log10 p-value such as PA3724 (lasB), PA2250 (IpdV), PA2248 (bkDA-2) and PA2513 (antB), are more abundant in the extracellular biofilm matrix and are highlighted in bold in the right-hand part of the image. A higher negative log 10 p-value indicates a higher probability of the presence of that particular mRNA transcript in either planktonic cells or in the biofilm matrix of P. aeruginosa. b–g Standardised gene counts (%) of highly abundant mRNA transcripts (b) lasB, (c) bkDA-2, (d) IpDV, (e) antB, (f) ssrA and (g) crcZ in extracellular biofilm matrix and intracellular biofilm cells across different days of biofilm growth (days 1-5). All extractions and sequencing were performed in biological triplicates. The standard deviation bars indicated in Fig. 2b–g are generated based on the mean values calculated from biological triplicates. The negative binomial model was fitted to estimate size factors and dispersion. Significance was determined using DeSeq2 to identify differentially expressed genes which incorporates two two-tailed Wald test with a P < 0.01. Relevant source data for Fig. 2a–g have been deposited to public repository and can be found in the data availability section.