Fitness for 5 genes in Pseudomonas putida KT2440

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500 ntPP_2112 and PP_2113 are separated by 224 nucleotidesPP_2113 and PP_2114 are separated by 420 nucleotidesPP_2114 and PP_2115 are separated by 344 nucleotidesPP_2115 and PP_2116 are separated by 21 nucleotides PP_2112: PP_2112 - aconitate hydratase 1, at 2,408,706 to 2,411,447 _2112 PP_2113: PP_2113 - Ribosomal RNA large subunit methyltransferase M, at 2,411,672 to 2,412,736 _2113 PP_2114: PP_2114 - transposase, at 2,413,157 to 2,414,458 _2114 PP_2115: PP_2115 - conserved protein of unknown function, at 2,414,803 to 2,415,000 _2115 PP_2116: PP_2116 - sulfurtransferase, at 2,415,022 to 2,415,264 _2116
Group Condition PP_2112 PP_2113 PP_2114 PP_2115 PP_2116
phage P. putida Sci small MOI 0.1 -0.2 -1.9 N.D. N.D. N.D.
nitrogen source nitrogen source nitrite 1mM -0.5 -0.3 N.D. N.D. N.D.
temperature shift Temperature shift 30_to_21; with MOPS -0.1 -0.7 N.D. N.D. N.D.
temperature shift Temperature shift 30_to_21; with MOPS -0.1 -0.7 N.D. N.D. N.D.
reactor 24hr timepoint from 1L M9/1% dextrose BATCH fermentation in 2L Sartorius Biostat reactor kept at 30% DO with 20% v/v dodecane overlay -0.2 -0.5 N.D. 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 -0.4 -0.3 N.D. N.D. N.D.
soil Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB; SoilTreatment=coldshock; SoilTreatmentTime=0_hrs +0.2 -0.9 N.D. N.D. N.D.
supernatant Supernatant; Trichoderma atroviride IMI dcr22mutant grown in Vogels_fungal_media, filtered; 0.8X -0.3 -0.4 N.D. N.D. N.D.
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI dcr2mutant -0.2 -0.4 N.D. N.D. N.D.
phage PUT8 MOI 0.1 -0.3 -0.4 N.D. 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 -0.5 -0.1 N.D. N.D. N.D.
nitrogen source NAG (N) -0.2 -0.5 N.D. N.D. N.D.
pH Growth at pH6 and (C) Trisodium citrate -0.0 -0.6 N.D. N.D. N.D.
carbon source D-Glucose (C); with MOPS -0.1 -0.6 N.D. N.D. N.D.
pH Growth at pH7 and (C) D-Glucose +0.1 -0.7 N.D. N.D. N.D.
carbon source L-Leucine (C) +0.1 -0.5 N.D. N.D. N.D.
temperature shift Temperature shift 30_to_34 +0.1 -0.5 N.D. N.D. N.D.
carbon source Crotonic (C) +0.2 -0.5 N.D. N.D. N.D.
carbon source D-Lysine 10 mM (C) +0.2 -0.4 N.D. N.D. N.D.
nitrogen source NAG (N); with MOPS +0.3 -0.4 N.D. N.D. N.D.
micoeukaryotes Tetrahymena sp., Mixed culture-2 +0.4 -0.3 N.D. N.D. N.D.
temperature shift Temperature shift 10_to_30; with MOPS -0.3 +0.4 N.D. 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 -0.4 +0.6 N.D. 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 -0.3 +0.5 N.D. N.D. N.D.
pH pH 4 -0.2 +0.5 N.D. N.D. N.D.
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI tmk3mutant -0.2 +0.5 N.D. N.D. N.D.
phage P. putida Sci Big MOI 0.1 -0.2 +0.6 N.D. N.D. N.D.
in planta Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=sand_vermiculite_perlite_mix; Collection=16h_outgrowth_LB; Time=7_days -0.1 +0.6 N.D. N.D. N.D.
carbon source BC Lignin Sorghum 10 vol% (C) +0.2 +0.4 N.D. N.D. N.D.
nitrogen source D-2-Aminobutyric (N) +0.2 +0.7 N.D. N.D. N.D.
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