Fig. 3

Metagenomic analyses of rhizobacterial communities and genomic information of four isolates. a Venn diagram showing the gene numbers with differential abundance (measured in TPM [transcripts per million]) and heatmap showing the relative abundance of the differentially enriched functional genes (top 50) among different groups. b Genome features of binned genomes: x-axis denotes the GC content (%) of the genome and y-axis denotes the abundance of the genome in the metagenome. c Pan-genome statistics of four strains: E, Ensifer sesbaniae; Na, Novosphingobium arvoryzae; N, Novosphingobium resinovorum; H, Hydrocarboniphaga effuse. d Functional enrichment of core genomes of strains E and N. The function of each gene was assigned using Clusters of Orthologous Groups (COG) categories. V, defense mechanisms; U, intracellular trafficking, secretion, and vesicular transport; T, signal transduction mechanisms; Q, secondary metabolites biosynthesis, transport, and catabolism; P, inorganic ion transport and metabolism; O, posttranslational modification, protein turnover, chaperones; NA, unannotated; N, cell motility; M, cell wall/membrane/envelope biogenesis; L, replication, recombination, and repair; K, transcription; J, translation, ribosomal structure, and biogenesis; I, lipid transport and metabolism; H, coenzyme transport and metabolism; G, carbohydrate transport and metabolism; F, nucleotide transport and metabolism; E, amino acid transport and metabolism; D, cell cycle control, cell division, chromosome partitioning; C, energy production and conversion; B, chromatin structure and dynamics