Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens

Pseudomonas fluorescens strain SS101 (Pf.SS101) promotes growth of Arabidopsis thaliana, enhances greening and lateral root formation, and induces systemic resistance (ISR) against the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). Here, targeted and untargeted approaches were adopted to identify bacterial determinants and underlying mechanisms involved in plant growth promotion and ISR by Pf.SS101. Based on targeted analyses, no evidence was found for volatiles, lipopeptides and siderophores in plant growth promotion by Pf.SS101. Untargeted, genome-wide analyses of 7,488 random transposon mutants of Pf.SS101 led to the identification of 21 mutants defective in both plant growth promotion and ISR. Many of these mutants, however, were auxotrophic and impaired in root colonization. Genetic analysis of three mutants followed by site-directed mutagenesis, genetic complementation and plant bioassays revealed the involvement of the phosphogluconate dehydratase gene edd, the response regulator gene colR and the adenylsulfate reductase gene cysH in both plant growth promotion and ISR. Subsequent comparative plant transcriptomics analyses strongly suggest that modulation of sulfur assimilation, auxin biosynthesis and transport, steroid biosynthesis and carbohydrate metabolism in Arabidopsis are key mechanisms linked to growth promotion and ISR by Pf.SS101. Comparative transcriptome analysis of Arabidopsis treated with Pf. SS101, a growth and ISR promoting rhizobacteria and plants treated with cysH mutant of Pf.SS101 that fails to induce the afformentioned phenotypes Arabidopsis plants (col-0) were grown in half strenght MS-medium and one week seedlings were inoculated with 2 µl Pf.SS101 cell suspensions, 2 µl of the cysH mutant (20H12) and in the control treatement seedlings were inoculated with 2 µl of 10 mM MgSO4. The shoot of the plants receiving different treatment were harvested after 18 d of growth and imediately frozen in liquid nitrogen and kept at -80 0C until further use. Four biological replicates with 30 plants per replicate were used for each treatment.