Fitness for 5 genes in Pseudomonas putida KT2440

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500 ntPP_1214 and PP_1215 are separated by 185 nucleotidesPP_1215 and PP_1216 are separated by 109 nucleotidesPP_1216 and PP_1217 overlap by 4 nucleotidesPP_1217 and PP_1218 are separated by 125 nucleotides PP_1214: PP_1214 - putative transcriptional regulatory protein, at 1,392,084 to 1,392,830 _1214 PP_1215: PP_1215 - Crossover junction endodeoxyribonuclease RuvC, at 1,393,016 to 1,393,540 _1215 PP_1216: PP_1216 - Holliday junction ATP-dependent DNA helicase RuvA, at 1,393,650 to 1,394,267 _1216 PP_1217: PP_1217 - Holliday junction ATP-dependent DNA helicase RuvB, at 1,394,264 to 1,395,310 _1217 PP_1218: PP_1218 - putative acyl-CoA thioesterase, at 1,395,436 to 1,395,888 _1218
Group Condition PP_1214 PP_1215 PP_1216 PP_1217 PP_1218
carbon source 3-methyl-1-butanol 0.1 vol% (C) -2.4 -4.5 -4.8 -2.6 +0.4
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs +0.3 -4.8 -5.1 -3.0 -0.6
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=288_hrs -1.2 -5.6 -2.0 -4.0 +0.3
carbon source 3-methyl-1-butanol (C) -0.4 -4.7 -3.5 -2.9 +0.2
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=144_hrs -3.4 -2.6 -2.6 -2.2 -0.4
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI -1.1 -5.8 -1.7 -2.0 +0.2
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 -6.5 -2.5 -2.5 +0.8
carbon source 3-methyl-1-butanol (C) -0.7 -3.6 -4.1 -2.3 +0.3
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=72_hrs -0.7 -4.1 -2.8 -2.4 -0.2
in planta Plant=Zea_mays; PlantTreatment=34_degrees_celsius; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16_outgrowth_LB; Time=7_days -2.8 -3.4 -2.1 -1.4 -0.4
supernatant Supernatant; Trichoderma atroviride IMI dcr22mutant grown in Vogels_fungal_media, filtered; 0.8X -0.4 -4.1 -2.8 -2.2 -0.2
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=144_hrs -1.6 -1.2 -4.2 -2.3 -0.3
in planta Plant=Zea_mays-bx1; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days -1.5 -1.7 -4.2 -1.6 -0.5
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI ago3mutant -0.4 -2.8 -4.9 -1.1 -0.2
in planta Plant=Zea_mays-B73; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days -1.3 -2.8 -3.9 -1.4 -0.0
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=144_hrs -0.4 -2.4 -4.4 -1.7 -0.5
carbon source 1,5-Pentanediol (C) -0.7 -3.4 -2.2 -2.6 -0.3
carbon source 3-methyl-1-butanol 0.25 vol% (C) +0.0 -4.5 -1.9 -2.9 +0.1
in planta Plant=Zea_mays-bx1; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days -1.0 -4.0 -2.4 -1.9 +0.2
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI tmk3mutant -0.1 -5.8 -2.2 -1.0 +0.1
supernatant Supernatant; Trichoderma atroviride IMI dcr22mutant grown in Vogels_fungal_media, filtered; 0.8X -0.2 -3.4 -3.1 -2.5 +0.1
phage P. put South MOI 10 -0.3 -1.1 -5.3 -1.6 -0.7
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=144_hrs +0.1 -4.2 -1.6 -2.4 -0.4
supernatant Supernatant; Trichoderma atroviride IMI dcr22mutant grown in Vogels_fungal_media, filtered; 0.8X +0.4 -2.5 -2.6 -2.9 -0.8
phage P. putida South MOI 10 -1.8 -4.4 +0.3 -0.7 -1.8
carbon source Delta-Undecalactone (C) +0.2 -3.5 -3.2 -1.5 -0.4
carbon source Protocatechuic Acid (C) -0.9 -3.4 -3.0 -1.4 +0.4
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs +1.6 -3.9 -1.6 -2.7 -1.0
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=72_hrs -4.4 +0.9 -1.3 -2.4 +0.2
reactor 24hr timepoint of 1L M9/1% dextrose CONTINUOUS FED BATCH fermentation in 2L Sartorius Biostat, feed rate 1g/hr dextrose, set to 30% DO. +1.1 +3.4 +2.6 +1.9 -0.1
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