Fitness for 5 genes in Pseudomonas putida KT2440

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500 ntPP_0001 and PP_0002 are separated by 9 nucleotidesPP_0002 and PP_0003 are separated by 18 nucleotidesPP_0003 and PP_0004 overlap by 4 nucleotidesPP_0004 and PP_0005 are separated by 630 nucleotides PP_0001: PP_0001 - probable chromosome-partitioning protein, at 147 to 1,019 _0001 PP_0002: PP_0002 - probable chromosome partition protein, at 1,029 to 1,820 _0002 PP_0003: PP_0003 - 16S RNA methyltransferase, at 1,839 to 2,489 _0003 PP_0004: PP_0004 - tRNA uridine 5-carboxymethylaminomethyl modification enzyme, at 2,486 to 4,381 _0004 PP_0005: PP_0005 - GTPase, at 5,012 to 6,382 _0005
Group Condition PP_0001 PP_0002 PP_0003 PP_0004 PP_0005
carbon source Tween 20 (C) -5.3 -1.3 -0.0 N.D. N.D.
nitrogen source NAG (N); with MOPS -4.0 -0.2 -2.0 N.D. N.D.
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=72_hrs -2.4 -1.2 -2.0 N.D. N.D.
nitrogen source nitrite (N) -3.2 -1.2 -1.2 N.D. N.D.
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=72_hrs -3.9 -1.0 -0.6 N.D. N.D.
no stress control Growth with no stress -4.3 +0.1 -1.2 N.D. N.D.
pH Growth at pH8 and (C) D-Glucose -4.2 -0.8 -0.2 N.D. N.D.
nitrogen source Ammonium chloride (N) -4.3 +0.0 -0.9 N.D. N.D.
carbon source acetate (C) -4.0 -1.2 +0.0 N.D. N.D.
stress Growth with Chloride 200 mM -4.4 -0.2 -0.5 N.D. N.D.
temperature shift Temperature shift 30_to_34; with MOPS -4.3 -0.4 -0.4 N.D. N.D.
pH Growth at pH6 and (C) D-Glucose -4.4 -0.5 -0.1 N.D. N.D.
temperature Growth at 25C -4.4 +0.5 -1.0 N.D. N.D.
carbon source Protocatechuic Acid (C) -4.3 -0.6 +0.2 N.D. N.D.
temperature shift Temperature shift 10_to_34; with MOPS -4.4 -0.2 -0.1 N.D. N.D.
carbon source Vanillic Acid (C) -4.5 -0.2 +0.0 N.D. N.D.
temperature shift Temperature shift 30_to_25 -4.1 -0.3 -0.3 N.D. N.D.
stress Growth with Chloride 500 mM; with MOPS -4.6 -0.1 -0.0 N.D. N.D.
in planta Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=no_outgrowth_LB; Time=7_days -4.1 -0.9 +0.3 N.D. N.D.
carbon source benzoic (C) -3.2 -0.4 -1.0 N.D. N.D.
temperature shift Temperature shift 30_to_25 -1.2 +0.1 -3.4 N.D. N.D.
carbon source butyrate (C) -3.1 -0.0 -1.3 N.D. N.D.
carbon source BC Lignin Sorghum 10 vol% (C) -2.9 -0.7 -0.8 N.D. N.D.
stress R2A with Polymyxin B sulfate 0.002 mg/ml -3.3 -0.1 -0.9 N.D. N.D.
in planta Plant=Zea_mays-bx1; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days -1.8 -1.1 -1.3 N.D. N.D.
pH Growth at pH7 and (C) Trisodium citrate -4.1 -0.3 +0.2 N.D. N.D.
temperature shift Temperature shift 30_to_21; with MOPS -4.1 -0.0 -0.0 N.D. N.D.
pH Growth at pH7 and (C) D-Glucose +1.2 -0.8 -4.0 N.D. N.D.
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=144_hrs +1.3 -1.3 -2.7 N.D. N.D.
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 +2.5 +1.7 +0.2 N.D. N.D.
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