title: Plant root transcriptome profiling reveals a strain-dependent response during Azospirillum-rice cooperation.
abstract: Cooperation involving Plant Growth-Promoting Rhizobacteria results in improvements of plant growth and health. While pathogenic and symbiotic interactions are known to induce transcriptional changes for genes related to plant defense and development, little is known about the impact of phytostimulating rhizobacteria on plant gene expression. This study aims at identifying genes significantly regulated in rice roots upon Azospirillum inoculation, considering possible favored interaction between a strain and its original host cultivar. Genome-wide analyzes of Oryza sativa japonica cultivars Cigalon and Nipponbare were performed, by using microarrays, seven days post-inoculation with Azospirillum lipoferum 4B (isolated from Cigalon) or Azospirillum sp. B510 (isolated from Nipponbare) and compared to the respective non-inoculated condition. A total of 7384 genes were significantly regulated, which represent about 16% of total rice genes. A set of 34 genes is regulated by both Azospirillum strains in both cultivars, including a gene orthologous to PR10 of Brachypodium, and these could represent plant markers of Azospirillum-rice interactions. The results highlight a strain-dependent response of rice, with 83% of the differentially expressed genes being classified as combination-specific. Whatever the combination, most of the differentially expressed genes are involved in primary metabolism, transport, regulation of transcription and protein fate. When considering genes involved in response to stress and plant defense, it appears that strain B510, a strain displaying endophytic properties, leads to the repression of a wider set of genes than strain 4B. Individual genotypic variations could be the most important driving force of rice roots gene expression upon Azospirillum inoculation. Strain-dependent transcriptional changes observed for genes related to auxin and ethylene signaling highlight the complexity of hormone signaling networks in the Azospirillum-rice cooperation.
authors.affiliation: Ecologie Microbienne, UMR CNRS 5557/USC INRA 1364, Université Lyon 1 Villeurbanne, France.
authors.forename: Benoît
authors.initials: B
authors.lastname: Drogue
authors.affiliation: Ecologie Microbienne, UMR CNRS 5557/USC INRA 1364, Université Lyon 1 Villeurbanne, France.
authors.forename: Hervé
authors.initials: H
authors.lastname: Sanguin
authors.affiliation: Ecologie Microbienne, UMR CNRS 5557/USC INRA 1364, Université Lyon 1 Villeurbanne, France.
authors.forename: Amel
authors.initials: A
authors.lastname: Chamam
authors.affiliation: Laboratoire de Génome et Développement des Plantes, UMR 5096 CNRS/IRD/Université de Perpignan Via Domitia Perpignan, France.
authors.forename: Michael
authors.initials: M
authors.lastname: Mozar
authors.affiliation: Laboratoire de Génome et Développement des Plantes, UMR 5096 CNRS/IRD/Université de Perpignan Via Domitia Perpignan, France.
authors.forename: Christel
authors.initials: C
authors.lastname: Llauro
authors.affiliation: Laboratoire de Génome et Développement des Plantes, UMR 5096 CNRS/IRD/Université de Perpignan Via Domitia Perpignan, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Panaud
authors.affiliation: Ecologie Microbienne, UMR CNRS 5557/USC INRA 1364, Université Lyon 1 Villeurbanne, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Prigent-Combaret
authors.affiliation: Laboratoire de Génome et Développement des Plantes, UMR 5096 CNRS/IRD/Université de Perpignan Via Domitia Perpignan, France.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Picault
authors.affiliation: Ecologie Microbienne, UMR CNRS 5557/USC INRA 1364, Université Lyon 1 Villeurbanne, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Wisniewski-Dyé
keywords: Azospirillum; hormone signaling; plant defense; plant growth-promoting rhizobacteria; rice; transcriptome