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. 2022 Oct 11;23(12):e55380. doi: 10.15252/embr.202255380

Figure 4. Nutrient acquisition systems are associated with bacterial adaptation to the plant environment in a strain‐specific manner.

Figure 4

  1. KEGG enrichment analysis of genes that are plant‐associated (PA) and significantly induced in planta compared with in vitro (rich media) (orange) and genes that are non‐PA and significantly suppressed in planta compared with in vitro (purple). The left panel shows the number of genes involved in each KEGG orthology term.
  2. Expression fold changes (in planta vs. in vitro) of genes with different functions. The top bars indicate the ratio of PA genes in each strain. All individual data points (genes) are overlaid to the box plots with colors for DEGs (red: upregulated, blue: downregulated, black: non‐DEG).
  3. Suflur metabolic pathways. For each step, a strain name was indicated when the strain has at least one gene significantly induced (red) or suppressed (blue) in planta. APS, adenosine 50‐phosphosulfate; PAPS, 30‐phosphoadenosine‐50‐phosphosulfate.
  4. Expression fold changes (in planta vs. in vitro) of genes with different functions. The top bars indicate the ratio of PA genes in each strain. All individual data points (genes) are overlaid to the box plots with colors for DEGs (red: upregulated, blue: downregulated, black: non‐DEG).
  5. Expression of the plant gene (E) AtDUR3 (urea transporter) based on the RNA‐seq data.
  6. Expression fold changes (in planta vs. in vitro) of genes with different functions. The top bars indicate the ratio of PA genes in each strain. All individual data points (genes) are overlaid to the box plots with colors for DEGs (red: upregulated, blue: downregulated, black: non‐DEG).
  7. Expression of the plant gene AtSTP13 (sugar transporter) based on the RNA‐seq data.

Data information: For the full expression data with the orthologous group, KEGG annotation, DEG, and PA information, see Dataset EV3. (B, D, F) For each condition, mean values of three biological replicates were taken. (E, G) Nine and three biological replicates were taken for the mock condition and the other conditions, respectively. Asterisks indicate statistically significant difference (¦log2FC¦ > 1; FDR  < 0.01; two‐tailed Student's t‐test followed by Storey's q‐value) compared with the mock (water‐inoculated) condition. (B, D–G) In the box plots, boxes display the 25th–75th percentiles, the centerline indicating the median, whiskers extending to the minimum, and maximum values no further than 1.5 interquartile range.