Rhizosphere-induced genes in Rlv3841 metabolic pathways. Bold lines show reactions encoded by genes induced (by three-fold or more, P ≤ 0.05) and are color coded for the rhizospheres: black, all; green, pea-specific; red, alfalfa-specific; blue, legume-specific; purple, alfalfa and sugar beet. An induced gene is also considered to be elevated in further rhizospheres where expression was elevated by two-fold or more (Additional file 8). Where more than one enzyme carries out a reaction the color reflects the gene elevated in most rhizospheres. Asterisks indicate compounds imported by a transport system whose expression was elevated (Figure 1). aGenes are part of an induced operon and elevated ≥ 1.3-fold; bgenes induced ≥ 3-fold, P ≤ 0.11; cgenes elevated ≥ 2.2-fold, P ≤ 0.05. Dotted lines and boxed genes show those down-regulated (≤ 0.3-fold, P ≤ 0.05) relative to glucose-grown cells. Expression is considered to be down-regulated in all rhizospheres if ≤ 0.5-fold. Reactions carried out by genes slightly down-regulated (0.4- to 0.8-fold; Additional file 8) are shown by a thin grey line. The dichloroethane pathway shown in italics is speculative. Genes underlined have been mutated and results of their competitiveness in the rhizosphere are shown in Additional file 8. DHAP, dihydroxyacetone phosphate; ED, Entner-Doudoroff; TCA, tricarboxylic acid.