Fig. 3

Functional variation in the rhizosphere microbiome. A PCA showing variation in the microbiome induced by inoculation in the early phase rather than the late phase. B Distributions of coefficients of variation for KEGG categories detected in metagenomes for all samples in the early (day 3) and late (day 30) phases; (left) all KEGG categories; (middle) KEGG categories related to carbohydrate metabolism; (right) KEGG categories related to amino acid metabolism. C Abundance of significantly changed COG categories in PGP41- and PGP5-inoculated microbiomes compared to CK at day 3. D, E Heatmaps depicting the average abundances of significantly changed COG categories in D PGP41- and E PGP5-inoculated microbiomes compared to CK. COG categories are abbreviated as follows: E, amino acid transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; K, transcription; L, replication, recombination, and repair; M, cell wall/membrane/envelope biogenesis; N, cell motility; O, posttranslational modification, protein turnover, and chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport, and catabolism; R, general function prediction only; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking, secretion, and vesicular transport; and V, defense mechanisms