Gene expression profiling of tomato roots interacting with Pseudomonas fluorescens unravels the molecular reprogramming that occurs during the early phases of colonization

The concerns of people over the wide use of chemicals are determining an increasing attention to more eco-friendly management practices in agriculture. Plant growth promoting rhizobacteria (PGPR) are emerging as important beneficial microbial inoculants because of their capability to promote plant growth and improve plant protection. We performed RNASeq to analyze gene expression profiling at 24, 48 and 72 h post inoculation (hpi) by Pseudomonas fluorescens strain CREA 16 (Pf-16), a PGPR previously isolated from Pisum sativum rhizosphere and with proven growth promotion activity on tomato plants, to unravel the extent of transcriptome reprogramming of tomato roots during the colonization. Pf-16 induces transcriptional reprogramming mainly at 24 and 72 hpi particularly affecting the down-regulation of genes. During the investigated time span, two phases can be clearly distinguished. In the first phase, within the first 48 h, Pf-16 strongly represses R-genes, calcium/calmodulin-mediated signaling and various transcription factors involved in the salicylic and jasmonic acid metabolism. Even more, Pf-16 blocks ethylene biosynthesis/signaling and protease-dependent mechanisms. At a later stage, from 48/72 h onwards, an intimate relationship between tomato roots and Pf-16 is established as a result of cell wall modifications. Finally, Pf-16 triggers the up-regulation of genes associated with plant growth promotion. Based on the main findings derived from this research, a model that gathers and describes the molecular events of outmost importance during tomato roots-Pf-16 interaction is proposed.