Characterization of Leaf Transcriptome of Grafted Tomato Seedlings after Rhizospheric Inoculation with Azospirillum baldaniorum or Paraburkholderia graminis

Inoculation with plant growth promoting rhizobacteria (PGPR) might be a sustainable practice to increase nutrients use efficiency of crops. In order to elucidate the mechanisms underlying the beneficial interaction, an RNA-Seq transcriptional profiling of tomato leaves was performed after roots' inoculation with Azospirillum baldaniorum (AB) or Paraburkholderia graminis (PG). Overall, 427 and 512 differentially expressed tomato genes were retrieved for AB and PB inoculation, respectively, and in both cases, the number of up-regulated genes exceeded the number of those down-regulated. Expression profiles suggest that the interactions between tomato seedlings and microorganisms are species-specific. The common activated pathways involved genes coding for proteins related to water and nutrients uptake, defense responses to biotic and abiotic stresses and hormonal regulation of fruit-set and ripening. While AB induced genes coding for MYB transcription factors known to be involved in response to biotic and abiotic stresses, PG upregulated 5 genes coding for putative late blight resistance protein homolog. Auxin responsive molecules and gibberellins involved in the fruit-set and early fruit growth in tomato were mainly induced by AB correlating to higher fruit number obtained in a previous field study. On the other hand, ERF transcription factors involved in ripening were induced mainly by PG treatment.

Automated summary

Inoculation with plant growth promoting rhizobacteria can enhance nutrient use efficiency in crops. RNA-Seq analysis revealed species-specific interactions between tomato seedlings and different PGPR strains, activating pathways related to water and nutrient uptake, stress responses, and hormonal regulation.