Fig. 6

Relative number of reads (number of reads/total number of reads) assigned to genes from the category environmental information processing. Rhizosphere samples collected 12 weeks after plantlets were transferred to pots containing virgin (CO = green) and apple replant soils (ARD = red) (DESeq2 analysis to test for differential gene abundance using negative binomial generalized linear models, all genes showed p < 0.05 after adjusted using the Bonferroni correction method for multiple pairwise comparisons). Abbreviations: opuA = osmoprotectant transport system, virD4 = Type secretion system IV, potA = spermidine/putrescine transport system, potH = putrescine transport system, opuBD = osmoprotectant permease, livF = amino acid transport system, cheY = TCS chemotaxis, atoC = TCS NtrC family, gltI = glutamate/aspartate transport system, mcp = chemotaxis protein, potF = putrescine transport system, drrA = antibiotic transport system, dctP = C4-dicarboxylate-binding protein DctP, pleC = TCS sensor kinase, dcuB = anaerobic C4-dicarboxylate transporter DcuB, frcA = fructose transport system, ttrB = tetrathionate reductase subunit B, cheW = purine-binding chemotaxis protein, devR = TCS NarL family, nifA = regulatory protein, barA = TCS NarL family, ctrA = cell cycle response regulator CtrA, rcsC = TCS NarL family, csrA = carbon storage regulator, mtrB = TCS OmpR sensor kinase