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Additional file 2: Supplemental Figure S2. RIN values obtained after laser microdissection of rice root sections before a) and after optimization steps (b-f). a) The original protocol of [9] b) The RIN value obtained after replacing the initial fixation step with a 5-min vacuum step, followed by overnight fixation at 4 °C. Cold fixation achieved an RIN value close to three. c) The RIN value after replacing the microwave dehydration steps by additional dehydration steps at a cold temperature (4 °C); the RIN value achieved is approximately 5. d) The RIN value for the complete protocol obtained using a paraffin coating and 3 × 5 minutes in the microwave instead of 3 × 3 hours. e, f) RIN values obtained for two more repetitions of the complete protocol. The red bar shows an RIN value of 7 as the minimum quality threshold selected for RNA extraction after laser microdissection.

Additional file 3: Supplemental Figure S3. Expression profiling of the putative tissue-specific genes extracted from RiceXpro.

Additional file 1: Supplemental Figure S1. Preparation of root tip samples. A) A hydroponic culture system using a floating net. B) Harvesting of 2-cm-long root tips and staining of a root tip with eosin for the positioning of root bundles. C) Embedding cassette (right) of root tips covered with biopsy foam (left). D) Embedding of the whole root bundle in paraffin.

Additional file 5: Supplemental Figure S5. qRT-PCR for OsSHR1 A) and EXP’ B) using serial dilutions of total root RNA. Diagrams showing the correlations between the Ct and pg of RNA per reaction.

Additional file 6: Supplemental File 1. Methods.

Additional file 4: Supplemental Figure S4. Preparation of RNase-free material prior to sample dehydration and embedding. a) Histological cassettes. b) to d) Elements of the water bath for the microwave: b) lid, c) beaker, and d) fixing system for histology cassettes. e) Glass Petri dish. f) Tongs. g) Stirrers.

International audience; Understanding how biotic interactions can improve plant tolerance to drought is a challenging prospect for agronomy and ecology. Plant growth-promoting rhizobacteria (PGPR) are promising candidates but the phenotypic changes induced by PGPR under drought remain to be elucidated. We investigated the effects of Phyllobacterium brassicacearum STM196 strain, a PGPR isolated from the rhizosphere of oilseed rape, on two accessions of Arabidopsis thaliana with contrasting flowering time. We measured multiple morphophysiological traits related to plant growth and development in order to quantify the added value of the bacteria to drought-response strategies of Arabidopsis in soil conditions. A delay in reproductive development induced by the bacteria resulted in a gain of biomass that was independent of the accession and the watering regime. Coordinated changes in transpiration, ABA content, photosynthesis and development resulted in higher water-use efficiency and a better tolerance to drought of inoculated plants. Our findings give new insights into the ecophysiological bases by which PGPR can confer stress tolerance to plants. Rhizobacteria-induced delay in flowering time could represent a valuable strategy for increasing biomass yield, whereas rhizobacteria-induced improvement of water use is of particular interest in multiple scenarios of water availability.

International audience; The Phyllobacterium brassicacearum STM196 strain stimulates Arabidopsis thaliana growth and antagonizes high nitrate inhibition of lateral root development. A previous study identified two STM196-responsive genes, NRT2.5 and NRT2.6 (Mantelin etal., 2006, Planta 223: 591603). We investigated the role of NRT2.5 and NRT2.6 in the plant response to STM196 using single and double Arabidopsis mutants. The single mutants were also crossed with an nrt2.1 mutant, lacking the major nitrate root transporter, to distinguish the effects of NRT2.5 and NRT2.6 from potential indirect effects of nitrate pools. The nrt2.5 and nrt2.6 mutations abolished the plant growth and root system architecture responses to STM196. The determination of nitrate content revealed that NRT2.5 and NRT2.6 do not play an important role in nitrate distribution between plant organs. Conversely, NRT2.5 and NRT2.6 appeared to play a role in the plant response independent of nitrate uptake. Using a nitrate reductase mutant, it was confirmed that the NRT2.5/NRT2.6-dependent plant signalling pathway is independent of nitrate-dependent regulation of root development. Our findings demonstrate that NRT2.5 and NRT2.6, which are preferentially expressed in leaves, play an essential role in plant growth promotion by the rhizospheric bacterium STM196.

The maize abscisic acid (ABA)-responsive gene rab28 has been shown to be ABA-inducible in embryos and vegetative tissues, expression being mostly restricted to vascular elements during late embryogenesis. In the course of an expressed sequence tags (ESTs) programme, we have isolated an Arabidopsis thaliana gene, Atrab28, encoding the orthologue of maize rab28. The Atrab28 cDNA is 1090 bp long, including a poly(A)+ stretch, and encodes a polypeptide of 262 amino acids. Atrab28 antibody against the recombinant protein recognizes a polipeptide of about 30 kDa and pI 6, in close agreement with the predicted molecular mass and pI. As for maize rab28, expression studies with Atrab28 revealed high specificity for embryo tissues, transcription being stimulated by the transcriptional activator abi3. In contrast, Atrab28 was not induced in vegetative tissues by ABA, osmotic stress or dehydration. The expression of Atrab28 mRNA and the accumulation of Atrab28 protein was largely restricted to provascular tissues of mature embryos and in the seed coat outer tegument and embryo and silique epidermis, as revealed by in situ hybridization and immunocytochemistry with anti-Atrab28 antibodies., This work was supported by a joint programme between the CNRS (Centre National de la Recherche Scientifique) and the CSIC (Consejo Superior de Investigaciones Científicas), the European Associated Laboratory between Perpignan and Barcelona in Plant Molecular and Cellular Biology. In addition, both Perpignan and Barcelona groups are members of the European project ‘Characterising and engineering abscisic acid action’ (Biotech BIO4-CT96-0062). Work in Barcelona was supported in part by the European Communities Biotech Programme, as part of the Project of Technological Priority and by grant BIO94-0750 from Plan Nacional de Investigatión Científica y Desarrollo Tecnológico. Work in Perpignan was supported by CNRS grants URA 565 and UMR 5545.