Supplementary Figure 4: Comparison of the microbiota structures using the third batch of sequences from pot experiment.

To confirm the results from the first community analysis, Hawaii 7996 and Moneymaker were grown in pots with the field soil from the mesocosm experiment. After 45 days, metagenomic DNA was extracted from tomato rhizosphere at the active growth and first flowering stage. Amplification and pyrosequencing of 16S rRNA gene were performed separately using the metagenomic DNA. (a) Taxonomic comparison at the phylum level. First, active growth and first flowering stage; second, fruiting and senescence stage. (b) Taxonomic comparison at the class level. (c) Taxonomic comparison at the family level. (d) Comparison of the rarefaction curves of the samples. Species richness was calculated at the 3% dissimilarity level. (e) Comparison of the diversity indices of the samples at the 3% dissimilarity level. ACE and Chao indicate the richness diversity indices. Inverse Simpson and Shannon indicate the evenness diversity indices. (f) Correlation of the microbial community at the class level between resulted from the first sequencing data used in Fig. 1 and Supplementary Figs. 2a-f, and the third sequencing data used in Supplementary Fig. 3. A total of 80 bacterial classes are shown in the figure. Each circle represents the bacterial taxon.