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Identification of a small set of genes commonly regulated in rice roots in response to beneficial rhizobacteria

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Abstract

Rhizosphere bacteria, whether phytopathogenic or phytobeneficial, are thought to be perceived by the plant as a threat. Plant Growth-Promoting Rhizobacteria (PGPR), such as many strains of the Azospirillum genus known as the main phytostimulator of cereals, cooperate with host plants and favorably affect their growth and health. An earlier study of rice root transcriptome, undertaken with two rice cultivars and two Azospirillum strains, revealed a strain-dependent response during the rice-Azospirillum association and showed that only a few genes, including some implicated in plant defense, were commonly regulated in all tested conditions. Here, a set of genes was selected from previous studies and their expression was monitored by qRT-PCR in rice roots inoculated with ten PGPR strains isolated from various plants and belonging to various genera (Azospirillum, Herbaspirillum, Paraburkholderia). A common expression pattern was highlighted for four genes that are proposed to be markers of the rice-PGPR interaction: two genes involved in diterpenoid phytoalexin biosynthesis (OsDXS3 and OsDTC2) and one coding for an uncharacterized protein (Os02g0582900) were significantly induced by PGPR whereas one defense-related gene encoding a pathogenesis-related protein (PR1b, Os01g0382000) was significantly repressed. Interestingly, exposure to a rice bacterial pathogen also triggered the expression of OsDXS3 while the expression of Os02g0582900 and PR1b was down-regulated, suggesting that these genes might play a key role in rice-bacteria interactions. Integration of these results with previous data led us to propose that the jasmonic acid signaling pathway might be triggered in rice roots upon inoculation with PGPR.

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Abbreviations

IAA:

Indole acetic acid

ISR:

Induced systemic resistance

JA:

Jasmonic acid

MAMP:

Microbe-associated molecular patterns

PGPR:

Plant Growth-Promoting Rhizobacteria

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Acknowledgements

We wish to thank Emmanuel Guiderdoni (AGAP laboratory, CIRAD Montpellier) for gift of Nipponbare seeds and Lisa Sanchez for providing the GFP-tagged P. phytofirmans PsJN strain. We are grateful to Jonathan Gervaix (AME platform of UMR CNRS-5557) for his invaluable help in acetylene reduction assay, to Danis Abrouk (iBio platform of UMR CNRS-5557) and Samuel Barreto for their great help in statistical analyses. The platform “Serre” of FR41 (University Lyon 1) was used to carry out this work. MV receives a fellowship from «Ministère de l’enseignement supérieur et de la recherche».

Funding

This study was supported by reccurent funding from CNRS and University Lyon 1. MV receives a fellowship from « Ministère de l’enseignement supérieur et de la recherche » .

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  1. Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Lyon1, 16 rue Dubois, 69622, Villeurbanne, France

    Marine Valette, Marjolaine Rey, Jeanne Doré, Florence Gerin & Florence Wisniewski-Dyé

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  1. Marine Valette
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  2. Marjolaine Rey
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M.V. conducted experiments and wrote the paper; M.R., J.D. and F.G. conducted experiments; F.W.D. designed experiments and wrote the paper; all authors discussed the data, and read and approved the contents of this manuscript.

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Correspondence to Florence Wisniewski-Dyé.

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Valette, M., Rey, M., Doré, J. et al. Identification of a small set of genes commonly regulated in rice roots in response to beneficial rhizobacteria. Physiol Mol Biol Plants 26, 2537–2551 (2020). https://doi.org/10.1007/s12298-020-00911-1

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