Fig. 5. Importance ranking of microbial functional features in random forest analysis.

a Alpha diversity of the rhizosphere soil bacterial communities across different treatments. Richness was calculated using the normalized ASV table. Horizontal bars within boxes represent the median. The tops and bottoms of boxes represent 75th and 25th quartiles, respectively. The upper and lower whiskers represent the range of non-outlier data values. Outliers were plotted as individual points. Different lowercase letters indicated significant differences among respective groups based on two-sided tests by Wilcoxon rank-sum test followed by Dunn’s multiple comparison test (adjusted p < 0.05, n = 9 biologically independent samples); b Principal coordinate analysis (PCoA) with Bray–Curtis dissimilarity performed on the functional profile of the eggplant, pepper and tomato microbiome at different treatment. The p-values were evaluated via the MRPP test; c Ranking of functional pathways driven by commensal microbes (not positively correlated with R. solanacearum) in prebiotic treatment; d: Ranking of functional pathways driven by microbes (positively correlated with R. solanacearum) in non-prebiotic treatment. *** indicated that the pathway was presented simultaneously in Fig. 5c, and Fig. 4c, or in Fig. 5d and Fig. 4c. Pep_NPRS pepper, non-prebiotic treatment, Pep_PRS pepper, prebiotic treatment, Egg_NPRS eggplant, non-prebiotic treatment, Egg_PRS eggplant, prebiotic treatment, Tom_NPRS tomato, non-prebiotic treatment.