Fig. 2

Taxonomic variation in the rhizosphere microbiome induced by inocula. A–C Taxonomic differences in rhizosphere microbiomes for comparisons of PGP5-Day 3 vs. CK-Day 3 (A), PGP41-Day 3 vs. CK-Day 3 (B), and CK-Day 30 vs. CK-Day 3 (C). The largest circles represent domains (Bacteria and Archaea) and the inner circles refer to phylum, class, family, and genus. The circle sizes represent the relative abundances of taxa at different taxonomic levels. Blue circles represent significantly enriched genera in CK-Day 3; green circles represent significantly enriched genera in PGP5-Day 3, PGP41-Day 3, and CK-Day 30 in panels A, B and C respectively; and yellow circles represent non-significantly enriched (Non-S) genera. D Co-occurrence networks of the non-inoculated microbiome in early (top) and late (bottom) phases. E Co-occurrence networks of the PGP41-inoculated microbiome in early (top) and late (bottom) phases. Nodes refer to OTUs; edges refer to significant correlations. The color of each node indicates the phylum; the size of each node is proportional to the degree. The OTUs represent strains PGP5 and PGP41 (with 100% identity) are labeled in the networks. F, G Differences in node-level properties of the co-occurrence networks for comparisons of non-inoculated vs. PGP5-inoculated microbiomes (F), and non-inoculated vs. PGP41-inoculated microbiomes (G) in the early phase. Significant differences were detected between samples in the early phase (Wilcoxon test, ***P < 0.001; **P < 0.01; *P < 0.05) while no significant differences were detected between samples in the late phase