Fig. 3
Genome-wide gene expression differences in wild-type P. veronii after 1 h exposure to different soils in presence of toluene. a Multi-dimensional scaling (MDS) plot of quadruplicate RNA-sequencing data sets for each of the soils, in comparison to liquid and artificial porous matrix (APM), and Jonction. Distances correspond to leading log-fold-changes between each pair of RNA samples. Leading log-fold-change is the average (root-mean-square) of the largest absolute log-fold changes between each pair of samples. b Statistically significantly higher expressed genes (i.e., those with log2-fold-change > 2, false-discovery rate < 0.05, P < 0.01) in each soil vs. APM. c as b, for lower expressed genes in soil than APM. d–f Expression profiles of the comparisons between sand, silt and clay vs APM, respectively, plotted as function of genome location (chr1, chromosome 1, grey background bars; chr2, chromosome 2, yellow; plm, plasmid, blue). Bars organized according to the locus_tag number. Bars indicate the mean log2-fold change. Dark purple, statistically significantly higher; pink, lower expressed genes. Asterisks point to a number of gene clusters common to all three soil-APM comparisons. Kdp, cop and dmp gene clusters; see description in main text