Fitness for 5 genes in Pseudomonas putida KT2440

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500 ntPP_4588 and PP_4589 are separated by 113 nucleotidesPP_4589 and PP_4590 are separated by 2 nucleotidesPP_4590 and PP_4591 overlap by 4 nucleotidesPP_4591 and PP_4592 are separated by 177 nucleotides PP_4588: PP_4588 - putative oxidoreductase (nitroreductase family), at 5,207,069 to 5,207,662 _4588 PP_4589: PP_4589 - D-isomer specific 2-hydroxyacid dehydrogenase family protein, at 5,207,776 to 5,208,708 _4589 PP_4590: PP_4590 - conserved protein of unknown function, at 5,208,711 to 5,209,004 _4590 PP_4591: PP_4591 - Ribonuclease D, at 5,209,001 to 5,210,134 _4591 PP_4592: PP_4592 - putative metal dependent hydrolase, at 5,210,312 to 5,211,949 _4592
Group Condition PP_4588 PP_4589 PP_4590 PP_4591 PP_4592
supernatant Supernatant; Trichoderma atroviride IMI dcr22mutant grown in Vogels_fungal_media, filtered; 0.8X -0.9 -0.4 -0.1 -1.5 -2.0
supernatant Supernatant; Trichoderma atroviride IMI dcr22mutant grown in Vogels_fungal_media, filtered; 0.8X -0.7 -0.5 -0.1 -1.0 -1.7
supernatant Supernatant; Trichoderma atroviride IMI dcr22mutant grown in Vogels_fungal_media, filtered; 0.8X -0.4 -0.6 -0.0 -0.6 -1.7
in planta Plant=Zea_mays; PlantTreatment=34_degrees_celsius_and_Fusarium; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16_outgrowth_LB; Time=7_days -0.4 -0.1 -0.2 -2.6 +0.3
in planta Plant=Zea_mays; PlantTreatment=25mM_NaCl; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16_outgrowth_LB; Time=7_days -0.2 -0.1 -0.8 -1.8 +0.1
pH Growth at pH8 and (C) D-Glucose -0.3 -0.2 -0.2 -1.9 -0.1
carbon source ferulate (C); with MOPS -0.7 +0.1 -0.4 -1.6 -0.0
in planta Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=20h_outgrowth_LB; Time=7_days -0.4 -0.2 -0.6 -1.4 +0.0
phage P. putida Sci Big MOI 0.1 -0.8 -0.5 +0.3 -1.5 +0.0
in planta Plant=Zea_mays; PlantTreatment=34_degrees_celsius; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16_outgrowth_LB; Time=7_days +0.0 +0.2 -0.2 -2.3 -0.1
in planta Plant=Zea_mays; PlantTreatment=34_degrees_celsius; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16_outgrowth_LB; Time=7_days -0.2 -0.3 -0.0 -2.0 +0.0
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=288_hrs -0.1 -0.3 -0.4 -1.5 -0.1
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=144_hrs -0.3 -0.2 +0.2 -1.7 -0.2
in planta Plant=Zea_mays; PlantTreatment=34_degrees_celsius_and_Fusarium; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16_outgrowth_LB; Time=7_days +0.0 -0.0 -0.1 -2.5 +0.3
in planta Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=20h_outgrowth_LB; Time=7_days -0.3 -0.0 -0.5 -1.5 +0.0
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=288_hrs -0.2 -0.1 -0.2 -2.0 +0.3
in planta Plant=Zea_mays; PlantTreatment=NaCl_and_Fusarium; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16_outgrowth_LB; Time=7_days -0.2 +0.0 -0.3 -1.8 +0.2
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=144_hrs -0.1 +0.2 -0.5 -1.9 +0.2
in planta Plant=Zea_mays-B73; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days +0.3 -0.2 -0.3 -2.0 +0.2
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs -0.5 +0.2 -0.3 -1.5 +0.1
nitrogen source Propandiamine (N) +0.2 -0.3 -0.3 -1.6 -0.1
in planta Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=no_outgrowth_LB; Time=7_days -0.1 +0.0 +0.4 -1.3 -1.0
in planta Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16h_outgrowth_LB; Time=7_days -0.2 -0.2 +0.3 -1.8 +0.0
in planta Plant=Zea_mays-B73; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days +0.2 +0.1 -0.6 -1.6 +0.0
reactor 48hr timepoint from 1L M9/1% dextrose BATCH fermentation in 2L Sartorius Biostat reactor kept at 10% DO. -0.4 -0.0 -0.5 -1.2 +0.3
carbon source ferulate (C); with MOPS -0.6 +0.2 +0.1 -0.9 -0.5
in planta Plant=Zea_mays; PlantTreatment=Fusarium; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16h_outgrowth_LB; Time=7_days +0.4 -0.1 -0.5 -1.5 +0.1
stress R2A with Polymyxin B sulfate 0.001 mg/ml -0.2 -0.2 -0.5 +0.4 -1.0
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs -0.3 -0.1 +0.6 -1.0 -0.4
nitrogen source D-2-Aminobutyric (N) +0.2 +0.0 +0.4 -1.8 -0.0
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