Fitness for 5 genes in Herbaspirillum seropedicae SmR1

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500 ntHSERO_RS19925 and HSERO_RS19930 are separated by 100 nucleotidesHSERO_RS19930 and HSERO_RS19935 are separated by 52 nucleotidesHSERO_RS19935 and HSERO_RS19940 are separated by 864 nucleotidesHSERO_RS19940 and HSERO_RS19945 are separated by 50 nucleotides HSERO_RS19925: HSERO_RS19925 - protocatechuate 3,4-dioxygenase, at 4,572,853 to 4,573,365 _RS19925 HSERO_RS19930: HSERO_RS19930 - 3-carboxy-cis,cis-muconate cycloisomerase, at 4,573,466 to 4,574,833 _RS19930 HSERO_RS19935: HSERO_RS19935 - hydrolase, at 4,574,886 to 4,576,148 _RS19935 HSERO_RS19940: HSERO_RS19940 - ABC transporter substrate-binding protein, at 4,577,013 to 4,578,200 _RS19940 HSERO_RS19945: HSERO_RS19945 - vanillate O-demethylase (vanillate degradation ferredoxin-like) oxidoreductase, at 4,578,251 to 4,579,207 _RS19945
Group Condition HSERO_RS19925 HSERO_RS19930 HSERO_RS19935 HSERO_RS19940 HSERO_RS19945
nitrogen fixation control D-Glucose (C) with ammonium chloride; anaerobic; 3 days N.D. -0.3 -0.4 -0.1 -0.3
carbon source L-Lactate (C) N.D. +0.2 -0.1 -1.1 -0.0
carbon source D-Galactose (C) N.D. +0.2 -0.6 -0.2 -0.3
carbon source L-Arabinose (C) N.D. +0.4 -0.2 -0.3 -0.5
supernatant Supernatant; Trichoderma atroviride IMI grown in Vogels_fungal_media, filtered; 0.8X; growth supplemented with 0.4X LB N.D. +0.3 -0.4 -0.6 +0.1
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI N.D. -0.4 +0.3 +0.3 -0.5
carbon source L-Rhamnose (C) N.D. +0.4 -0.2 -0.4 -0.1
stress Thallium(I) acetate 0.001 mg/ml N.D. -0.1 +0.0 +0.5 -0.6
plant Plant assay with Setaria viridis; 10 days of inoculation with plant; outgrowth in LB N.D. -0.5 -0.1 -0.1 +0.6
carbon source succinate (C) N.D. +0.6 -0.0 -0.6 -0.0
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI N.D. +0.3 -0.1 +0.4 -0.4
carbon source L-Lactate (C) N.D. +0.6 -0.3 -0.3 +0.2
carbon source D-Xylose (C) N.D. +0.6 -0.0 -0.4 +0.1
plant Plant assay with Setaria viridis; 10 days of inoculation with plant; outgrowth in LB N.D. -0.5 +0.5 +0.1 +0.3
plant Plant assay with Setaria viridis; 10 days of inoculation with plant; outgrowth in LB N.D. +0.1 -0.2 +0.7 -0.2
stress Dimethyl Sulfoxide 5 vol% N.D. -0.3 -0.1 +0.5 +0.4
stress Fusidic 0.025 mg/ml N.D. -0.4 +0.1 +0.9 -0.1
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI dcr2mutant N.D. +0.3 +0.6 -0.3 -0.1
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI tmk3mutant N.D. +0.9 -0.3 +0.0 +0.1
agar plate interaction control Parafilmed volatile agar plate with no fungus N.D. +0.4 +0.1 +0.5 -0.2
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI tmk3mutant N.D. +0.6 -0.3 +0.5 -0.0
agar plate interaction control Parafilmed volatile agar plate with no fungus N.D. -0.1 +0.6 +0.3 +0.2
supernatant control Vogels_fungal_media 0.2X; growth supplemented with 0.4X LB N.D. +0.5 +0.3 +0.4 -0.1
plant Plant assay with Setaria viridis; 10 days of inoculation with plant; outgrowth in LB N.D. -0.2 +0.3 +0.8 +0.2
agar plate interaction control Parafilmed volatile agar plate with no fungus N.D. +0.3 +0.2 +0.3 +0.5
agar plate interaction control Taped volatile agar plate with no fungus N.D. +0.5 +0.3 +0.1 +0.4
supernatant Supernatant; Trichoderma atroviride IMI grown in Vogels_fungal_media, non-filtered; 1X N.D. +0.4 +0.3 +0.5 +0.1
supernatant Supernatant; Trichoderma atroviride IMI grown in Vogels_fungal_media, non-filtered; 0.5X; growth supplemented with 0.4X LB N.D. +0.4 +0.4 +0.7 +0.2
agar plate interaction control Parafilmed volatile agar plate with no fungus N.D. +0.1 +0.5 +0.5 +1.3
agar plate interaction Parafilmed volatile agar plate with Trichoderma atroviridae IMI tmk3mutant N.D. +0.2 +0.3 +1.7 +0.4
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