Rowth in the rhizosphereAs (-)-Blebbistatin web useful information about how micro-organisms respond to
Rowth in the rhizosphereAs useful information about how micro-organisms respond to the rhizosphere can PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/28859980 be obtained by incubating bacteria in root secretions [6], bacterial responses to constituent components were measured (Table 1). Pea root exudate was added to liquid-grown cells and microarray analysis showed 21 genes elevated by 3-fold (P 0.05), 18 of which were also elevated by growth in medium containing the flavonoid hesperetin (27 genes elevated 3-fold, P 0.05) (Additional file 6). Common induced genes, in addition to the nod and rhi gene clusters on pRL10 (nodABCEFIJLMNO and rhiIABC), include RL2418, encoding a CUT1 ABC transporter (and also induced three-fold or more in all rhizospheres and in the presence of acetoacetate, hydroxybenzoate and protocatechuate) (Additional files 6 and 9). Expression of RL2418 is clearly important for pea rhizosphere growth as a mutant showed much reduced competitiveness with Rlv3841 in the pea rhizosphere (RCI 0.43; Additional file 8). Genes elevated under these two conditions (root exudate and hesperetin) form only a small proportion of those elevated in plant rhizospheres. One reason is that root secretions are very dilute and only induce genes responsive to low concentrations of bioactive compounds (for example, nod genes). Furthermore, growth in the rhizosphere involves a far more complex series of interactions, including attachment to roots, biofilm formation, contact with a complex array of plant macromolecules and cell-cell competition.Comparative analysis reveals that the sugar beet rhizosphere is N-limited. Expression of genes encoding glutamine synthetase II (GlnII, RL3549), the NH 4 + transporter AmtB (RL4564) (Figure 1) and PAAT (polar amino acid transporter) family importer pRL120079 (Figure 1) was elevated, as they were in all N-limited microarrays (Additional files 7 and 9). As these experiments were deliberately conducted in N-free plant growth medium, it is not surprising that the sugar beet rhizosphere was N-limited. However, legume rhizospheres were not N-limited, indicating release ofConclusions Overall, the comparative transcriptome approach used here has revealed bacterial responses common to different plant rhizospheres, as well as mapping key general responses such as organic acid, C1-C2 and aromatic amino acid metabolism. In addition, it has highlighted specific bacterial adaptations to individual plants species and enabled identification of specific detoxification systems, such as that for canavanine in the alfalfa rhizosphere. Mutation of two genes (RL0680 and pRL80021) specifically induced in the pea rhizosphere only reduced competitiveness in the pea and not the alfalfa rhizosphere. A dramatic observation is the large number of genes located on plasmid pRL8 that are specifically induced in the pea rhizosphere. This is particularly exciting and suggests there may be a wealth of plant rhizosphere-specific plasmids or chromosomal islands to be revealed by emerging high-throughput sequencing projects.Ramachandran et al. Genome Biology 2011, 12:R106 http://genomebiology.com/2011/12/10/RPage 10 ofMaterials and methodsBacterial and plant growthR. leguminosarum strains were grown either in tryptone yeast [30] or acid minimal salts as described [31]. Strains, plasmids and oligonucleotide primers are described in Additional file 11. Seeds of pea (Pisum sativa cv Avola), alfalfa (Medicago sativa) or sugar beet (Beta vulgaris) were surface sterilized and grown in 50 ml Falcon.