Plant root transcriptome profiling reveals a strain-dependent response during Azospirillum-rice cooperation.

Benoît Drogue,Florence Wisniewski-Dyé,Olivier Panaud,Hervé Sanguin,Claire Prigent-Combaret,Nathalie Picault,Michael Mozar,Amel Chamam,Christel Llauro

doi:10.3389/fpls.2014.00607

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.

Highlights

Rhizodeposition supports growth of a wide range of microorganisms able to establish intimate interactions with plant roots
According to the cultivar of which each strain was originally isolated, Cigalon/A. lipoferum 4B (Cig_4B) and Nip_B510 combinations constitute interactions between a strain and its original host cultivar, which will be hereafter designed as host combinations, while Cig_B510 and Nipponbare/A. lipoferum 4B (Nip_4B) combinations constitute interactions with non-host cultivars, which will be hereafter designed as non-host combinations
Unraveling the molecular basis of host-specific adaptations in Plant Growth-Promoting Rhizobacteria (PGPR)-plant cooperation helps understanding frontiers between the perception of symbiotic, cooperative, and pathogenic microbes hosted by plant roots

Summary

Introduction

Rhizodeposition supports growth of a wide range of microorganisms able to establish intimate interactions with plant roots. In the case of parasitism, nutritional requirements of the microbe partner are supported at the expense of plant development and reproduction (O’Brien et al, 2011; Schumacher and Tudzynski, 2012). Whether engaged in a parasitic or mutualistic interaction, the microbial partner is perceived as an intruder and the success of the adaptation strategy partly depends on the microbe’s ability to bypass defense mechanisms and invade plant tissues (Soto et al, 2009). Cooperation involving Plant Growth-Promoting Rhizobacteria (PGPR) results in improvements of plant growth and health; the invasion of root tissues is not a critical step in successful interaction as several efficient strains are described as root-surface colonizers (Lugtenberg and Kamilova, 2009; Chamam et al, 2013). If mechanisms directly implicated in plant growth-promotion have been extensively studied, most of these works have assessed the impact of PGPR on plant morphological traits and little is known about changes induced at the molecular level (Bashan and de-Bashan, 2010; Galland et al, 2012; van de Mortel et al, 2012; Wisniewski-Dyé et al, 2013)

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