Fitness for 5 genes in Pseudomonas putida KT2440

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500 ntPP_3547 and PP_3548 are separated by 667 nucleotidesPP_3548 and PP_3549 overlap by 4 nucleotidesPP_3549 and PP_3550 are separated by 30 nucleotidesPP_3550 and PP_3551 are separated by 178 nucleotides PP_3547: PP_3547 - putative NAD(P)-binding oxidoreductase with NAD(P)-binding Rossmann-fold domain, at 4,021,364 to 4,022,305 _3547 PP_3548: PP_3548 - multidrug efflux transport system - permease subunit, at 4,022,973 to 4,024,508 _3548 PP_3549: PP_3549 - multidrug efflux transport system - membrane fusion protein, at 4,024,505 to 4,025,698 _3549 PP_3550: PP_3550 - putative Transcriptional regulator EmrR, at 4,025,729 to 4,026,202 _3550 PP_3551: PP_3551 - DNA-binding response regulator, LuxR family, at 4,026,381 to 4,027,013 _3551
Group Condition PP_3547 PP_3548 PP_3549 PP_3550 PP_3551
carbon source butyrate (C) -0.1 -0.0 -0.4 N.D. -3.6
carbon source Butanol (C) +0.0 -0.1 -0.3 N.D. -2.4
carbon source Butanol (C) -0.1 +0.1 -0.2 N.D. -2.4
stress R2A with Polymyxin B sulfate 0.002 mg/ml -0.5 -0.0 +0.1 N.D. -2.1
pH D-Glucose (C) pH 6 +0.0 +0.0 +0.1 N.D. -2.6
stress MOPS minimal media_Glucose20mM with Carbenicillin 100 .g/mL -0.0 -0.0 +0.0 N.D. -2.4
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=288_hrs -0.2 +0.1 -0.1 N.D. -2.1
supernatant Supernatant; Trichoderma atroviride IMI dcr22mutant grown in Vogels_fungal_media, filtered; 0.8X -0.4 -0.1 -0.3 N.D. -1.5
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=0_hrs +0.1 -0.1 +0.0 N.D. -2.2
r2a control with 0.2% methanol R2A control with 0.2% methanol -0.0 +0.1 -0.3 N.D. -2.0
carbon source 2-Methylbutanoic (C) -0.1 -0.0 +0.3 N.D. -2.3
in planta Plant=Zea_mays; PlantTreatment=NaCl_and_Fusarium; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16_outgrowth_LB; Time=7_days -0.3 +0.2 +0.1 N.D. -2.3
carbon source Butanol (C) -0.0 -0.1 -0.3 N.D. -1.8
carbon source butyrate (C) +0.1 +0.1 -0.1 N.D. -2.2
in planta Plant=Zea_mays; PlantTreatment=NaCl_and_Fusarium; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16_outgrowth_LB; Time=7_days +0.1 -0.1 +0.3 N.D. -1.9
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI ago3mutant -0.2 -0.0 +0.4 N.D. -1.6
in planta Plant=Zea_mays; PlantTreatment=34_degrees_celsius; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16_outgrowth_LB; Time=7_days -0.5 -0.2 +0.4 N.D. +1.3
phage P. putida Missley MOI 0.1 +0.4 +0.1 -0.8 N.D. +1.3
stress Growth with Chloride 200 mM -0.1 +0.1 -0.6 N.D. +1.7
carbon source ferulate (C); with MOPS -0.3 +0.2 -0.2 N.D. +1.5
carbon source D-Glucose (C) -0.1 -0.0 -0.4 N.D. +2.0
temperature shift Temperature shift 30_to_25; with MOPS +0.2 +0.2 -0.6 N.D. +1.7
carbon source carbon source 3-O-methyl-glucose 50 mM -0.5 -0.1 +0.4 N.D. +1.8
carbon source Valeric (C) -0.1 -0.1 -0.5 N.D. +2.5
carbon source Delta-Nonalactone (C) -0.0 +0.1 -0.2 N.D. +2.0
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=288_hrs +0.3 -0.2 -0.2 N.D. +2.1
carbon source 1-Pentanol (C) +0.2 -0.0 -0.1 N.D. +1.9
carbon source Valeric (C) +0.0 +0.1 -0.1 N.D. +2.1
carbon source Valeric (C) +0.0 +0.0 -0.3 N.D. +2.9
in planta Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=20h_outgrowth_LB; Time=7_days -0.1 +0.1 +0.4 N.D. +3.3
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