Journal of Biosciences

, 44:98 | Cite as

Impact of Pseudomonas putida RRF3 on the root transcriptome of rice plants: Insights into defense response, secondary metabolism and root exudation

  • Rekha Kandaswamy
  • Mohan Kumar Ramasamy
  • Rameshthangam Palanivel
  • Usha BalasundaramEmail author


Pseudomonas putida is widely used as a biocontrol agent, however, mechanisms by which it initiates the plants’ defense response remains obscure. To gain an insight into the molecular changes that occur in plants upon plant growth-promoting rhizobacteria colonization, root transcriptome analysis by using a microarray was performed in rice using P. putida RRF3 (a rice rhizosphere isolate). Data analysis revealed a differential regulation of 61 transcripts (48 h post-treatment), of which, majority corresponded to defense response, cell wall modification and secondary metabolism. Seven genes encoding salicylic acid (SA) responsive pathogenesis-related proteins were up-regulated significantly (fold change ranges from 1 to 4), which suggests that RRF3 has a profound impact on a SA-mediated defense signaling mechanism in rice. Investigations performed at later stages of RRF3 colonization by real-time polymerase chain reaction and high-performance liquid chromatography (HPLC) analysis confirmed the above results, demonstrating RRF3 as a potent biocontrol agent. Further, the impact of RRF3 colonization on root exudation, in particular, exudation of SA was investigated by HPLC. However, analysis revealed RRF3 to have a negative impact on root exudation of SA. Overall, this study shows that P. putida RRF3 immunizes the rice plants by re-organizing the root transcriptome to stimulate plant defense responses (‘priming’), and simultaneously protects itself from the primed plants by altering the rhizosphere chemical constituents.


Defense Pseudomonas putida rice root exudation salicylic acid secondary metabolism 



The authors are very much indebted to the Department of Science and Technology, India for the financial support of the project (SB/FT/LS-137/2012).

Supplementary material

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Supplementary material 1 (DOCX 942 kb)
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Supplementary material 2 (DOCX 20 kb)


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Copyright information

© Indian Academy of Sciences 2019

Authors and Affiliations

  • Rekha Kandaswamy
    • 1
    • 2
  • Mohan Kumar Ramasamy
    • 3
  • Rameshthangam Palanivel
    • 4
  • Usha Balasundaram
    • 2
    Email author
  1. 1.Department of Chemical EngineeringPennsylvania State UniversityState CollegeUSA
  2. 2.Department of Genetic EngineeringSRM Institute of Science and TechnologyKattankulathurIndia
  3. 3.Interdisciplinary Institute of Indian System of Medicine (IIISM)SRM Institute of Science and TechnologyKattankulathurIndia
  4. 4.Department of Biotechnology, Science CampusAlagappa UniversityKaraikudiIndia

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