Fitness for 5 genes in Pseudomonas putida KT2440

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500 ntPP_4262 and PP_4263 overlap by 8 nucleotidesPP_4263 and PP_4264 are separated by 105 nucleotidesPP_4264 and PP_4265 are separated by 186 nucleotidesPP_4265 and PP_4266 are separated by 55 nucleotides PP_4262: PP_4262 - Cytochrome oxidase maturation protein, cbb3-type, at 4,847,704 to 4,847,919 _4262 PP_4263: PP_4263 - putative membrane-bounded cytochrome biogenesis cycZ-like domain, copper tolerance protein, at 4,847,912 to 4,848,595 _4263 PP_4264: PP_4264 - oxygen-independent coproporphyrinogen III dehydrogenase, at 4,848,701 to 4,850,083 _4264 PP_4265: PP_4265 - DNA-binding transcriptional dual regulator, at 4,850,270 to 4,851,004 _4265 PP_4266: PP_4266 - Adenine phosphoribosyltransferase, at 4,851,060 to 4,851,608 _4266
Group Condition PP_4262 PP_4263 PP_4264 PP_4265 PP_4266
micoeukaryotes Tetrahymena sp., Mixed culture-1 -3.4 -2.3 -1.2 -2.9 +0.4
stress R2A with Fusaric 480 ug/mL -2.6 +0.8 -2.0 -4.4 -0.1
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=0_hrs -2.9 -5.6 -0.5 +0.7 +0.0
stress R2A with Fusaric 240 ug/mL +0.1 -3.5 -0.9 -4.1 +0.2
stress Geraniol 1 vol% -2.8 -2.2 -1.2 -1.6 -0.4
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=72_hrs -4.3 -2.4 -0.8 +0.3 -0.8
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI tmk3mutant -1.6 -0.5 -0.9 -1.5 -3.3
stress R2A with Polymyxin B sulfate 0.001 mg/ml -0.8 -1.0 -0.7 -5.6 +0.2
stress R2A with Fusaric 240 ug/mL -3.3 -0.1 -0.5 -3.8 -0.1
stress R2A with Polymyxin B sulfate 0.001 mg/ml -1.7 -0.8 +0.2 -5.0 -0.4
supernatant Supernatant; Trichoderma atroviride IMI dcr22mutant grown in Vogels_fungal_media, filtered; 0.8X -0.6 -0.4 -2.1 -4.7 +0.0
r2a control with 0.2x vogels R2A control with 0.2X Vogels -1.2 -0.6 -0.2 -5.4 -0.3
r2a control R2A control -1.6 -0.6 -0.5 -4.3 -0.3
stress R2A with Polymyxin B sulfate 0.002 mg/ml -0.2 -1.5 -1.6 -4.1 +0.2
r2a control with 0.2% methanol R2A control with 0.2% methanol +0.2 -1.3 -0.3 -5.5 -0.3
lb LB -1.7 -2.2 -0.9 -1.8 -0.1
supernatant Supernatant; Trichoderma atroviride IMI dcr22mutant grown in Vogels_fungal_media, filtered; 0.8X -0.0 -1.0 -2.0 -3.9 +0.2
stress R2A with Fusaric 480 ug/mL +0.4 +0.3 -1.7 -5.6 +0.2
r2a control R2A control -0.8 +0.3 -0.1 -5.6 +0.0
nitrogen source NAG (N); with MOPS +0.1 -5.6 -0.4 -0.4 +0.3
stress R2A with Fusaric 480 ug/mL -0.8 +0.6 -2.2 -3.9 +0.4
r2a control with 0.2x vogels R2A control with 0.2X Vogels -0.2 -0.4 +0.4 -5.4 -0.2
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=288_hrs -1.6 -3.4 -1.1 +0.6 -0.2
stress R2A with Fusaric 120 ug/mL +0.5 -0.7 -0.4 -4.9 -0.2
carbon source ferulate (C); with MOPS -3.5 -1.7 -0.3 +0.6 -0.6
stress R2A with Fusaric 240 ug/mL +0.4 +0.8 -0.6 -5.3 -0.2
carbon source 3-methyl-1-butanol 0.1 vol% (C) +1.3 +0.8 +0.3 -1.5 -5.5
supernatant Supernatant; Trichoderma atroviride IMI dcr22mutant grown in Vogels_fungal_media, filtered; 0.8X +1.1 +0.2 -2.2 -3.4 -0.0
supernatant control:fungal media R2A with Vogels_fungal_media 0.8X +1.2 +1.2 +0.9 -4.6 -0.0
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 +3.1 +1.2 +2.2 +1.8 +0.2
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