Organic acids, amino acids, and carbohydrates were quantified and those which had a concentration of Compound Library >0.1 μmol g-1(dry weight) were included

in the graph. Proline, a known constituent of maize root exudate, was not detected since the derivatization reagent (OPA) used reacts only with primary amino groups. Overall changes in gene expression in response to root exudates In the rhizosphere, root exudates may occur at high concentrations in certain microenvironments, e.g. in vicinity of root tips [26], but their concentration in specific niches of the environment is unknown. Therefore, the choice of a physiologically relevant concentration of exudates to be used for microarray experiments can only be tentative. Based on a previous study on changes in the proteomics of FZB42 [27], three exudate concentrations (0.25 g l-1, 0.5 g l-1 and 1.0 g l-1) were applied to liquid cultures of FZB42, and bacterial cells were harvested for RNA extraction at two growth stages (OD600 = 1.0 and OD600 = 3.0). For simplicity, the two population densities were referred to as OD1.0 and OD3.0 throughout this paper, respectively. A concentration of 0.25 g l-1 was sufficient to result in a significant response of FZB42 transcriptome. When bacteria were cultured at OD3.0 the number of up-regulated Roxadustat ic50 genes gradually decreased with increasing root exudate concentration, suggesting that some compounds

need to occur at lower abundance to induce gene expression, or that gene transcription in general may be suppressed at high concentrations of some exudates components (Figure 2). More transcripts were significantly altered (q ≤ 0.01) at the transition to the stationary growth (OD 3.0) than at the exponential growth (OD1.0) (Figure 2), suggesting that OD 3.0 was a sampling point which reflected more clearly the effect of root exudates on FZB42 than OD1.0. For these reasons, the exudate concentration of 0.25 g l-1 and the OD3.0 for Methisazone harvesting of cells were used for all subsequent microarray experiments.

Figure 2 Number of FZB42 genes altered in transcription in response to root exudates at different exudate concentrations and cell densities. Maize root exudates were supplemented in three concentrations (0.25 mg/ml, 0.5 mg/ml and 1.0 mg/ml) to FZB42 cultures and total RNA was prepared from the bacterial cells harvested at two optical densities (OD600 = 1.0 and OD600 = 3.0). Genes significantly altered in transcription (q ≤ 0.01 and fold change ≥1.5) by presence of root exudates are represented in the figure. Six independent experiments were performed and the genes whose transcription fulfilled the condition of yielding a q value not greater than 0.01 (q ≤ 0.01) and a fold change not less than 1.5 (FCH ≥ 1.5) were regarded as being significantly influenced by root exudates. A total of 302 genes, representing 8.