Fig. 2

Alpha diversity and assembly of microbial communities. (A) Bacterial Chao 1, (B) bacterial Shannon, (C) fungal Chao 1, and (D) fungal Shannon indices. Stars within the boxplot define the mean value, and outliers are plotted as circles if present. BS, bulk soils; RS, rhizosphere; RP, rhizoplane; ES, endosphere; D, diseased tobacco plants; H, healthy tobacco plants. The asterisks (*) indicate significant differences between healthy and diseased tobacco plants within same niche. *, P < 0.05, **, P < 0.01, or ***, P < 0.001. Lowercase letters over the boxplot indicate statistically significant differences (t-test, P < 0.05) across niches within diseased (letters in regular) or healthy groups (letters in italics). NMDS plot showing the ordination of bacterial (E) and fungal (F) communities among all samples. Samples in different groups are color-coded. Deterministic and stochastic processes in bacterial (G) and fungal (H) communities of diseased and healthy tobacco plants among four niches