Fig. 3

Alpha diversity analysis of the fungal communities of all samples. a Chao index; (b) Ace index; (c) Shannon index; (d) Simpson index. The x-axis indicates the sample groups and the y-axis represents the observed value of different indices based on OTU abundance. n = 3 for each cultivar. Bars with the different letters indicate a significant difference between means by one-way ANOVA and Duncan’s multiple test (p < 0.05). Values represent the mean. Error bars indicate ± standard deviation. Abbreviations: H, L represent fungal communities from “standard rootstocks”, “dwarfing rootstocks”, respectively. Vm, nVm represent fungal communities from “disease”, “health”, respectively. R, RS, RZ represent fungal communities from “root endophyte”, “root rhizosphere soil” and “root zone soil”, respectively