Sustainable agriculture requires replacing agrochemicals with environmentally friendly products. One alternative is bacterial inoculants with plant-growth-promoting (PGP) activity. Bacterial consortia offer advantages over single-strain inoculants, as they possess more PGP traits and allow the exploitation of bacterial synergies. Synthetic bacterial communities (SynComs) can be used as inoculants that are thoroughly characterized and assessed for efficiency and safety. Here, we describe the construction of a SynCom composed of seven bacterial strains isolated from the rhizosphere of tomato plants and other orchard vegetables. The strains were identified by 16S rDNA sequencing as Pseudomonas spp. (two isolates), Rhizobium sp., Ensifer sp., Microbacterium sp., Agromyces sp., and Chryseobacterium sp. The metagenome of the combined strains was sequenced, allowing the identification of PGP traits and the assembly of their individual genomes. These traits included nutrient mobilization, phytostimulation, and biocontrol. When inoculated into tomato plants in an agricultural soil, the SynCom caused minor effects in soil and rhizosphere bacterial communities. However, it had a high impact on the gene expression pattern of tomato plants. These effects were more significant at the systemic than at the local level, indicating a priming effect in the plant, as signaling through jasmonic acid and ethylene appeared to be altered.

The model rhizobacterium Pseudomonas ogarae F113, a relevant plant growth-promoting bacterium, encodes three different Type VI secretion systems (T6SS) in its genome. In silico analysis of its genome revealed the presence of a genetic auxiliary module containing a gene encoding an orphan VgrG protein (VgrG5a) that is not genetically linked to any T6SS structural cluster, but is associated with genes encoding putative T6SS-related proteins: a possible adaptor Tap protein, followed by a putative effector, Tfe8, and its putative cognate immunity protein, Tfi8. The bioinformatic analysis of the VgrG5a auxiliary module has revealed that this cluster is only present in several subgroups of the P. fluorescens complex of species. An analysis of the mutants affecting the vgrG5a and tfe8 genes has shown that the module is involved in bacterial killing. To test whether Tfe8/Tfi8 constitute an effector–immunity pair, the genes encoding Tfe8 and Tfi8 were cloned and expressed in E. coli, showing that the ectopic expression of tfe8 affected growth. The growth defect was suppressed by tfi8 ectopic expression. These results indicate that Tfe8 is a bacterial killing effector, while Tfi8 is its cognate immunity protein. The Tfe8 protein sequence presents homology to the proteins of the MATE family involved in drug extrusion. The Tfe8 effector is a membrane protein with 10 to 12 transmembrane domains that could destabilize the membranes of target cells by the formation of pores, revealing the importance of these effectors for bacterial interaction. Tfe8 represents a novel type of a T6SS effector present in pseudomonads.