Fitness for 5 genes in Pseudomonas putida KT2440

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500 ntPP_4013 and PP_4014 are separated by 59 nucleotidesPP_4014 and PP_4015 overlap by 4 nucleotidesPP_4015 and PP_4016 are separated by 137 nucleotidesPP_4016 and PP_4017 are separated by 75 nucleotides PP_4013: PP_4013 - MutT/nudix family protein, at 4,524,570 to 4,525,010 _4013 PP_4014: PP_4014 - tRNA-specific 2-thiouridylase MnmA, at 4,525,070 to 4,526,194 _4014 PP_4015: PP_4015 - HflD-like high frequency lysogenization protein, at 4,526,191 to 4,526,817 _4015 PP_4016: PP_4016 - 5'-phosphoribosyl-4-(N-succinocarboxamide)-5- aminoimidazole lyase (adenylosuccinate lyase), at 4,526,955 to 4,528,325 _4016 PP_4017: PP_4017 - conserved protein of unknown function, at 4,528,401 to 4,529,573 _4017
Group Condition PP_4013 PP_4014 PP_4015 PP_4016 PP_4017
nitrogen source Propiolactam (N) -1.1 N.D. -0.4 N.D. N.D.
pH Growth at pH8 and (C) D-Glucose -0.7 N.D. -0.7 N.D. N.D.
phage P. putida Sci small MOI 0.1 -1.4 N.D. -0.0 N.D. N.D.
reactor 24hr timepoint from 1L M9/1% dextrose BATCH fermentation in 2L Sartorius Biostat reactor kept at 10% DO. -0.3 N.D. -1.0 N.D. N.D.
micoeukaryotes Tetrahymena sp., Mixed culture-2 -1.3 N.D. +0.0 N.D. N.D.
nitrogen source nitrogen source nitrate 5mM -0.8 N.D. -0.5 N.D. N.D.
carbon source D-Glucose (C) -0.2 N.D. -1.0 N.D. N.D.
in planta Plant=Zea_mays; PlantTreatment=34_degrees_celsius; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16_outgrowth_LB; Time=7_days -0.7 N.D. -0.5 N.D. N.D.
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs -0.7 N.D. -0.5 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 -0.3 N.D. -0.8 N.D. N.D.
nitrogen source Ammonium chloride (N); with MOPS -0.1 N.D. -1.0 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 -0.9 N.D. -0.2 N.D. N.D.
temperature Growth at 30C; with MOPS +0.2 N.D. -1.3 N.D. N.D.
temperature shift Temperature shift 30_to_4; with MOPS +0.2 N.D. -1.0 N.D. N.D.
in planta Plant=Zea_mays; PlantTreatment=25mM_NaCl; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16_outgrowth_LB; Time=7_days +0.4 N.D. -0.9 N.D. N.D.
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI ago3mutant +0.4 N.D. -1.0 N.D. N.D.
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI +0.4 N.D. -0.8 N.D. N.D.
nitrogen source Urea (N) +0.4 N.D. -0.8 N.D. N.D.
temperature shift Temperature shift 30_to_34; with MOPS +0.4 N.D. -0.7 N.D. N.D.
phage P. put South MOI 0.1 -0.7 N.D. +0.5 N.D. N.D.
nitrogen source Ammonium chloride (N) -0.6 N.D. +0.6 N.D. N.D.
temperature shift Temperature shift 10_to_30 +0.6 N.D. -0.5 N.D. N.D.
nitrogen source 2,6-diaminopimelic (N) +1.0 N.D. -0.8 N.D. N.D.
pH Growth at pH7 and (C) D-Glucose +0.8 N.D. -0.5 N.D. N.D.
agar plate interaction control Parafilmed volatile agar plate with no fungus +0.8 N.D. -0.4 N.D. N.D.
nitrogen source Ammonium chloride and TNT (N) +0.2 N.D. +0.9 N.D. N.D.
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 +1.2 N.D. -0.0 N.D. N.D.
nitrogen source DL-2-Aminobutyric (N) +0.3 N.D. +0.9 N.D. N.D.
in planta Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=20h_outgrowth_LB; Time=7_days +0.6 N.D. +0.9 N.D. N.D.
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs +1.0 N.D. +0.8 N.D. N.D.
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