Fig. 6: Effects of Ammoniphilus sp. on root transcriptomic profiles.
Two-week-old tomato plants were transferred to hydroponic systems and subjected to -Fe (0 μM Fe) treatment with the presence of heat-killed (control) or living (+AS27) bacterial strains at a final concentration of 5 × 107 CFU mL−1 for indicated times. Then, root samples were harvested for comparative transcriptome analysis. a Principal component analysis (PCA) of all the samples. b The number of DEGs (FDR-adjusted p value < 0.05, fold-change ≥ |2 | ). c Hierarchical clustering of DEGs in at least one pairwise comparison. The median expression values of genes from three biological replicates were z-score normalized to achieve a mean of 0 and a standard deviation of 1 across different samples (white: mean, blue: downregulated, red: upregulated). KEGG analysis of shared DEGs responsive to d Fe deficiency and e AS27. f Venn diagram and g Heatmap analysis of 12 shared core genes among different treatments. h Measurement of SA levels and i qPCR analysis of PR1 expression in both the control and AS27-inoculated plants subjected to –Fe treatment at 36 and 72 h, respectively. Different lowercase letters indicated significant differences among the different treatments using Duncan’s multiple range tests at p < 0.05 (n = 15 plants per group). Error bars indicate standard deviation of the mean. j AS27 was cultured on minimal media agar with 0.5 mM SA and/or glucose as the carbon source, and a SA-degrading bacterial strain (Peudomonas putida ND6) carrying the NahG gene was used as the control.
