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Circular maps of the replicons encompassing the <i>P</i>. <i>veronii</i> 1YdBTEX2 genome.

<p>(A) Chromosome 1 (chr1) with indication of possible genomic islands (GEI) and prophages (pf). The outermost circles show the location and orientation of predicted coding regions (blue and cyan), followed by tRNA (olive green) and rRNA genes (black), predicted regions of genome plasticity (blue-green-brown) islands and prophages (grey). The inner circles represent BLASTN comparisons with the close relatives <i>P</i>. <i>fluorescens</i> SBW25 (red, Acc. No. AM181176.4), <i>P</i>. <i>trivialis</i> strain IHBB745 (deep pink, CP011507.1), <i>P</i>. <i>syringae</i> pv. syringae B728a (dark purple, CP000075.1), <i>P</i>. <i>putida</i> KT2440 (light purple, AE015451.1) and <i>P</i>. <i>knackmussii</i> B13 (persian green, HG322950). GC skew (dark magenta and yellow green) is shown in the most central circle. (B) As A, but for the chromosome 2 replicon (chr2). Inner circles, from outwards to inwards, predicted transposons (dark purple) and <i>tra</i> genes (green), regions of genome plasticity (blue-green-brown) and prophages (grey), followed by BLASTN comparisons to <i>P</i>. <i>fluorescens</i> SBW25 plasmid pQB103 (red, AM235768.1, NC_009444.1), <i>Pseudomonas stutzeri</i> strain 19SMN4 plasmid pLIB119 (deep pink, CP007510.1), <i>Pseudomonas mandelii</i> JR-1 plasmid (dark purple, CP005961.1) and <i>Pseudomonas resinovorans</i> NBRC 106553 plasmid pCAR1.3 (Persian green, AP013069.1). (C) As B, but for the plasmid replicon. The inner circles represent the BLASTN comparisons with <i>P</i>. <i>putida</i> S12 plasmid pTTS12 (red, CP009975.1), and <i>Pseudomonas</i> sp. VLB120 plasmid pSTY (purple, CP003962.1). Plots generated with DNAPlotter [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165850#pone.0165850.ref046" target="_blank">46</a>].</p

Overview of denitrification capacity of <i>P</i>. <i>veronii</i> 1YdBTEX2.

<p>(A) Overnight growth of <i>P</i>. <i>veronii</i> 1YdBTEX2 wild type (WT) and the Δ<i>nar</i> mutant in presence (+O₂, left) or absence of air but with 15 mM nitrate supplemented medium (+NO₃,–O₂, right panel) conditions. Note the gas formation in the right panel of the WT incubation. (B) Gene regions predicted for denitrification in the <i>P</i>. <i>veronii</i> 1YdBTEX2 chromosome 1 with trivial gene names indicated. Black bar represents the deleted region in <i>P</i>. <i>veronii</i> Δ<i>nar</i>.</p

Genome-wide gene expression differences in <i>P</i>. <i>veronii</i> 1YdBTEX2 after 1 h exposure to different carbon sources or growth environment.

<p>(A) Two-dimensional Principal Component Analysis of quadruplate global RNA-sequencing data sets of <i>P</i>. <i>veronii</i> 1YdBTEX2 incubated in liquid medium with succinate (Li-Su), or toluene (Li-To), or in sand with succinate (Sa-Su) or with toluene (Sa-To). (B) Venn diagram with the number of unique and common genes significantly differentially expressed (2-way ANOVA, ²log-fold-change [logFC] >1, false-discovery rate [FDR] <0.05, <i>P</i> <0.01) as result of change of carbon source (succinate to toluene) or environment (liquid to sand). (C) Smear-plot of global gene expression intensity (²log CPKM) versus expression changes (²log fold change) compared between cells incubated with toluene (Li-To) versus succinate (Li-Su); in grey, genes not statistically differentially expressed (logFC<1, FDR>0.05, <i>P</i> >0.01); magenta, genes with lower, and dark purple, genes with higher expression in presence of toluene (+). Blue, <i>ipb</i> genes; yellow, <i>dmp</i> genes; green, <i>ttg</i> genes (toluene efflux pump). (D) Gene expression changes as an effect of carbon source (succinate versus toluene, left) or of environment (liquid versus sand, right), and plotted as function of genomic location (chromosome 1, chr1; chromosome 2, chr2 and plasmid, plm; organized according to locus_tag number). Bars indicate ²log-fold change. Dark purple, statistically significantly higher expressed genes in presence of toluene (+, left) or sand (+, right); cyan, lower expressed genes in pink. Positions of the <i>ipb</i>, <i>dmp</i> and <i>ttg</i> genes are highlighted.</p

Comparison of catabolic gene transcription involved in toluene or <i>meta-</i>cleavage metabolism by <i>P</i>. <i>veronii</i> 1YdBTEX2 in liquid culture with succinate (Li-Su) or toluene (Li-To).

<p>(A) Normalized read counts across the <i>ipb</i> gene cluster (PVE_r2g0739-0753). Note the decrease as a result of the transposon insertion (white arrow). (B) Expression level (reads per kilobase per million, RPKM, ¹⁰log scale) of the <i>ipb</i> cluster genes (numbers refer to PVE_r2g loci). (C) as B, for the <i>dmp</i> cluster genes (PVE_r2g0708-0719), and the proposed gene encoding for the dihydrodiol dehydrogenase (PVE_r2g0805). (D) as B, for the <i>nah</i> cluster genes (PVE_r2g0834-0847).</p