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Table 3 Common differentially expressed genes of Pseudomonas veronii wild-type during transition in soils

From: Genome-wide gene expression changes of Pseudomonas veronii 1YdBTEX2 during bioaugmentation in polluted soils

Gene ID Gene Gene function Log2 fold-change in comparisona
Sand vs APM Silt vs APM Clay vs APM Jonction vs APM One-way ANOVAb
Natural soils vs Controls Jonction vs Controls
PVE_r1g2130 lpdV dihydrolipoyl dehydrogenase 2.07 2.42 0.31 2.14 2.00 2.00
PVE_r1g2131 bkdB dihydrolipoamide branched chain transacylase 3.07 2.39 1.75 3.11 2.57 2.00
PVE_r1g2132 bkdA2 2-oxoisovalerate dehydrogenase subunit beta 3.65 3.16 2.50 3.78 3.25 3.58
PVE_r1g2133 bkdA1 2-oxoisovalerate dehydrogenase subunit alpha 3.44 3.13 1.60 3.84 3.01 3.58
PVE_r1g5053 hibA probable 3-hydroxyisobutyrate dehydrogenase 2.83 3.40 1.86 3.10 2.91 2.92
PVE_r1g5054 ALDH6B2 methylmalonate-semialdehyde dehydrogenase 3.63 3.54 2.91 3.98 3.45 3.81
PVE_r1g2545 narK nitrate/nitrite transporter NarK 3.80 1.97 0.00 4.20 2.76 3.87
PVE_r1g2546 narG respiratory nitrate reductase 1 alpha chain 3.72 2.33 −0.60 3.68 2.77 3.37
PVE_r1g2547 narY respiratory nitrate reductase 2 beta chain 3.51 2.41 0.03 3.35 2.68 3.04
PVE_r1g2548 narJ nitrate reductase molybdenum cofactor assembly chaperone 2.84 2.58 0.19 2.85 2.36 2.56
PVE_r1g2549 narI respiratory nitrate reductase 1 gamma chain 2.60 2.14 0.11 2.56 2.04 2.29
PVE_r1g0681 copA copper-exporting P-type ATPase A 2.39 3.30 0.38 3.51 2.56 3.22
PVE_r1g6093 copC copper resistance protein C 4.53 6.00 1.61 3.22 5.04 3.05
PVE_r2g0903 copC copper resistance protein C 1.27 6.39 1.21 3.35 5.00 3.12
PVE_p0049 copB copper resistance protein B 3.00 2.86 1.63 2.58 2.68 2.45
PVE_p0050   hypothetical secreted protein 3.19 3.64 2.11 3.19 3.18 3.03
PVE_p0051 copA copper resistance protein A 3.02 3.50 1.38 2.25 2.97 2.13
PVE_p0052   hypothetical secreted protein 4.04 6.54 0.70 3.53 5.35 3.26
PVE_r1g0242   membrane protein 2.78 2.25 2.60 2.51 2.57 2.51
PVE_r1g0243 pgaB poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase 2.57 1.88 2.34 2.57 2.09 2.52
PVE_r1g0244 pgaC poly-beta-1,6-N-acetyl-D-glucosamine synthase 2.29 1.40 2.03 2.52 2.09 2.46
PVE_r1g0245 pgaD biofilm PGA synthesis protein PgaD 2.72 1.66 2.11 2.56 2.07 2.46
  1. a Log2 fold-change in condition compared with control in soil (FDR < 0.05, p < 0.01)
  2. b.One-way ANOVA (analysis of variance) in the condition “soil”; natural or polluted vs controls (LQ and APM)