Supplementary Figure 2: Structures of the rhizosphere and bulk soil microbiotas based on 16S rDNA-amplicon pyrosequencing.

(a) Comparison of the rarefaction curves of the samples. Species richness was calculated at the 3% dissimilarity level. First, active growth and first flowering stage; second, fruiting and senescence stage. (b) 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. (c) Principal coordinate analysis. Principal coordinate analysis (PCoA) was performed with the representative sequences at the 3% dissimilarity level: bulk soil 5,134/3,981 (active growth/senescence), Korean cabbage 2,791/2,274, Moneymaker 2,265/2,859, and Hawaii 7996 2,425/1,952. PCoA plot shows that there are distinct differences between the microbial communities of bulk and planted soils, and between the first and second sampling stages. (d) Taxonomic comparison at the class level using 16S rDNA reads from amplicon sequencing. Circles indicate the bacterial classes with ≥ 0.1% relative abundance in both samples. Colored circles indicate ≥ 15% abundant taxa with ≥ 0.5% relative abundance in Hawaii 7996 or Moneymaker, as compared with each other. (e) Taxonomic comparison at the class level using the pyrosequencing reads of 16S rDNA amplicons. Taxonomic comparison was conducted with the average relative abundance of 10 subsets, which were randomly sub-sampled from 454 pyrosequencing data of Hawaii 7996 and Moneymaker. Taxa which relative abundance was higher than 0.5% in Hawaii 7996 or Moneymaker were shown as a bar graph. The bar plots indicate the average relative abundance of each sample in 10 subsets and the error bar indicates the standard error of the 10 subsets. Relative abundances of Alphaproteobacteria and Flavobacteriia are shown in the left Y-axis and relative abundances of the other taxa are shown in the right Y-axis. Statistical analysis was performed using one-way ANOVA, Kruskal-Wallis test in SPSS program. A total of 79 bacterial classes were analyzed for the statistical test. Among them, 13 bacterial classes had significant p-values (*, p < 0.05; **, p < 0.005; ***, p < 0.0005): Flavobacteriia 0.0002, Betaproteobacteria 0.0002, Gammaproteobacteria 0.0009, unclassified phylum 0.0015, Anaerolineae 0.0494, unclassified Proteobacteria 0.0002, Acidobacteria Gp4 0.0041, Bacteroidetes incertae sedis 0.0052, Cyanobacteria 0.0002, Acidobacteria Gp6 0.0233, Saccharibacteria genera incertae sedis 0.0002, Cytophagia 0.0041, Chloroflexia 0.0009. The dot plots in the below the bar plot were generated with same data used in the bar plot. Each circle indicates the distribution of relative abundance for each taxon. (f) Taxonomic comparison at the family level. Circles indicate the bacterial families with ≥ 0.1% relative abundance in both samples. Colored circles are the families that have the relative abundant of ≥ 0.5% in either of the samples and abundance difference of ≥ 20% when compared with each other. (g) Comparison of the relative abundances of taxa between Hawaii 7996 and bulk soil in the mesocosm and pot experiments. Bacterial abundance values in Hawaii 7996 relative to bulk soil were log-transformed. The plot shows bacterial families with ≥ 0.1% relative abundance and average relative abundance values in Hawaii 7996 were indicated by circle size. A total of 67 bacterial families are shown in the figure. The families with ≰ 0.05 FDR-adjusted p-value were highlighted by red color. (h) Comparison of the relative abundances of taxa between Moneymaker and bulk soil in the mesocosm and pot experiments. Bacterial abundance values in Moneymaker relative to bulk soil were log-transformed. The plot shows bacterial families with ≥ 0.1% relative abundance and average relative abundance values in Moneymaker were indicated by circle size. A total of 67 bacterial families are shown in the figure. The families with ≰ 0.05 FDR-adjusted p-value were highlighted by blue color.