Fitness for 5 genes in Pseudomonas putida KT2440

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500 ntPP_4626 and PP_4627 are separated by 97 nucleotidesPP_4627 and PP_4628 are separated by 21 nucleotidesPP_4628 and PP_4629 are separated by 115 nucleotidesPP_4629 and PP_5702 are separated by 59 nucleotides PP_4626: PP_4626 - holin regulator of murein hydrolases, at 5,250,674 to 5,251,060 _4626 PP_4627: PP_4627 - transcriptional regulator, LysR family, at 5,251,158 to 5,252,039 _4627 PP_4628: PP_4628 - conserved protein of unknown function, at 5,252,061 to 5,252,516 _4628 PP_4629: PP_4629 - Sensory box protein, at 5,252,632 to 5,253,060 _4629 PP_5702: PP_5702 - conserved protein of unknown function, at 5,253,120 to 5,253,737 _5702
Group Condition PP_4626 PP_4627 PP_4628 PP_4629 PP_5702
carbon source propionate (C) -0.0 -0.2 -4.7 +0.2 +0.1
carbon source Levulinic Acid (C) +0.2 -0.3 -3.8 +0.0 -0.1
carbon source Levulinic Acid (C) +0.1 -0.3 -3.9 +0.1 +0.4
pH Growth at pH6 and (C) D-Glucose -1.0 -0.8 -0.3 -0.2 -1.3
carbon source DL-3-Hydroxyisobutyric (C) -0.1 -0.4 -3.8 +0.6 +0.1
carbon source Levulinic Acid (C) +0.4 -0.0 -3.8 -0.0 -0.1
phage P. putida Missley MOI 0.1 -0.5 -0.4 +0.3 -0.1 -2.6
carbon source DL-3-Hydroxyisobutyric (C) +0.0 -0.2 -3.8 +0.4 +0.4
in planta Plant=Zea_mays-bx1; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days -0.5 -1.0 +0.2 -0.2 -1.2
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=144_hrs -0.3 -0.9 -1.1 +0.3 -0.7
pH pH 5 -1.2 -1.4 +0.4 +0.8 -1.1
carbon source Levulinic Acid (C) +0.4 +0.2 -3.6 +0.1 +0.5
pH Growth at pH6 and (C) D-Glucose -1.2 -0.7 +0.2 -0.8 +0.3
in planta Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=no_outgrowth_LB; Time=7_days +0.6 -0.2 -0.4 -1.8 -0.2
carbon source 2-Methylbutanoic (C) +0.0 -0.0 -2.5 +0.4 +0.2
carbon source 2-Methylbutanoic (C) +0.2 -0.3 -2.6 +0.6 +0.2
carbon source propionate (C) +0.2 -0.2 -1.9 +0.6 -0.2
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI +0.1 -1.2 +0.9 +0.3 -0.7
reactor 72hr timepoint from 1L M9/1% dextrose BATCH fermentation in 2L Sartorius Biostat reactor kept at 10% DO. -0.5 +0.2 -0.2 +1.4 -1.5
reactor 48hr timepoint of 1L M9/1% dextrose DISCONTINUOUS FED BATCH fermentation in 2L Sartorius Biostat set to 10% DO. -0.3 -0.3 -1.0 +1.7 +0.1
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=288_hrs +0.7 +0.4 -0.9 -0.6 +0.6
carbon source Lignin Monomers (C) -0.2 -0.6 +1.8 -0.4 +0.0
nitrogen source D-2-Aminobutyric (N) +0.5 +1.1 -0.5 +0.3 -0.7
carbon source 4-Hydroxyvalerate (C) (40mM) +0.4 +0.4 -0.8 +2.0 -0.3
carbon source 4-Hydroxyvalerate (C) (40mM) +0.5 +0.7 -1.3 +1.7 +0.0
carbon source 3-methyl-1-butanol 0.1 vol% (C) +0.0 -0.4 +3.3 +0.2 -0.8
nitrogen source 2,6-diaminopimelic (N) -0.0 -0.2 +0.5 +2.7 +0.0
carbon source Valerolactone (C) +0.6 +0.2 +0.5 +1.0 +0.7
reactor 72hr timepoint from 1L M9/1% dextrose BATCH fermentation in 2L Sartorius Biostat reactor kept at 30% DO with 20% v/v oleyl alcohol overlay -0.0 +0.0 -0.1 +2.8 +0.5
nitrogen source 2,6-diaminopimelic (N) -0.0 +0.1 +0.5 +2.7 +0.4
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