Fitness for 5 genes in Pseudomonas putida KT2440

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500 ntPP_1979 and PP_1980 are separated by 104 nucleotidesPP_1980 and PP_1981 are separated by 51 nucleotidesPP_1981 and PP_1982 are separated by 335 nucleotidesPP_1982 and PP_1983 are separated by 90 nucleotides PP_1979: PP_1979 - putative Hydrolase, at 2,242,983 to 2,243,864 _1979 PP_1980: PP_1980 - conserved protein of unknown function, at 2,243,969 to 2,244,403 _1980 PP_1981: PP_1981 - tRNA-dihydrouridine synthase C, at 2,244,455 to 2,245,426 _1981 PP_1982: PP_1982 - small heat shock protein IbpA, at 2,245,762 to 2,246,211 _1982 PP_1983: PP_1983 - PAS/PAC/GAF sensor-containing diguanylate cyclase/phosphodiesterase, at 2,246,302 to 2,249,598 _1983
Group Condition PP_1979 PP_1980 PP_1981 PP_1982 PP_1983
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI tmk3mutant -4.4 N.D. +0.3 +0.2 +0.1
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=144_hrs -1.9 N.D. -0.4 -0.2 -0.5
nitrogen source nitrate (N) -1.7 N.D. -0.7 -0.2 +0.0
carbon source carbon source 4-vinylphenol 0.01 mM -0.3 N.D. -1.5 -0.4 -0.3
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI ago3mutant -1.4 N.D. +0.1 -0.5 -0.3
carbon source Myristic (C) -1.4 N.D. +0.5 -1.0 -0.3
reactor 24hr timepoint from 1L M9/1% dextrose BATCH fermentation in 2L Sartorius Biostat reactor kept at 30% DO. -1.3 N.D. -0.7 -0.2 +0.1
stress MOPS minimal media_Glucose20mM with Carbenicillin 100 .g/mL -1.3 N.D. -0.4 -0.1 -0.2
temperature shift Temperature shift 10_to_30; with MOPS -2.0 N.D. +0.0 +0.2 -0.1
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=0_hrs -1.5 N.D. -0.5 +0.3 -0.1
carbon source acetate (C) -1.9 N.D. +0.5 -0.2 -0.1
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs -2.2 N.D. +0.1 +0.7 +0.0
mixed carbon source mixed (C)s Trisodium citrate 10 mM and L-Phenylalanine 5 mM -1.1 N.D. -0.4 +0.1 +0.3
dilutelb LB 0.1x with 55.5 mM D-Glucose -1.2 N.D. -0.5 +0.1 +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 +0.8 N.D. -1.1 -0.3 -0.1
carbon source Trisodium citrate (C) -1.7 N.D. +0.7 +0.2 +0.2
temperature Growth at 25C; with MOPS -1.2 N.D. +0.5 +0.3 -0.1
phage P. putida Sci small MOI 0.1 +0.3 N.D. +0.5 -0.9 -0.3
nitrogen source 2,6-diaminopimelic (N) -1.9 N.D. +0.8 +0.4 +0.1
phage P. put PUT 10 MOI 10 -1.1 N.D. +0.4 -0.2 +0.4
carbon source L-Lysine (C) +0.5 N.D. +0.2 -0.6 -0.4
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=288_hrs -0.4 N.D. +0.9 -0.5 +0.3
pH Growth at pH6 and (C) D-Glucose -1.0 N.D. +0.5 +0.7 +0.1
nitrogen source Propiolactam (N) +1.0 N.D. -0.6 +0.2 +0.1
nitrogen source D-2-Aminobutyric (N) +0.7 N.D. -0.3 +0.6 -0.4
temperature Growth at 25C -0.5 N.D. +1.0 +0.3 +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 +1.4 N.D. -0.5 +0.3 +0.2
carbon source Valerolactone (C) +0.6 N.D. +0.0 +1.1 -0.3
nitrogen source D-2-Aminobutyric (N) -0.5 N.D. +0.7 +1.2 +0.3
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 +1.0 N.D. +0.3 +0.5 +0.1
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