Background Unravel the complex functioning of plant immune system is essential and something in which great effort is being made since its performance is not entirely clear yet. Knowing plant immune system allows strengthening it and therefore developing a more efficient and environmentally friendly agriculture, avoiding the massive use of agrochemicals and making plants the main protagonist in the defense against pathogens.The use of beneficial rhizobacteria (bioeffectors) and its derived metabolic elicitors are biotechnological alternatives in plant immune system elicitation. The present work aimed to check the ability of 25 bacterial strains selected from a group of 175, isolated from the rhizosphere of Nicotiana glauca, to trigger the innate immune system of Arabidopsis thaliana seedlings against the pathogen Pseudomonas syringae DC3000. A study of the signal transduction pathways involved in plant response was made.Results The selected 25 strains were chosen because of their biochemical traits and avoiding phylogenetic redundancy. The 5 strains, of the previous 25, more effective in the prevention of pathogen infection were used to elucidate signal transduction pathways involved in the plant immune response, studying the differential expression of Salicylic acid and Jasmonic acid/Ethylene pathway marker genes. Some strains stimulated the two pathways with no inhibitory effects between them, while others stimulated either one or the other. Metabolic elicitors of two strains, chosen for their taxonomic affiliation and for the results obtained in the differential expression of the genes studied, were extracted using n-hexane, ethyl acetate and n-butanol, and their capacity to mimic bacterial effect to trigger the immune system of the plant was studied. N-hexane and ethyl acetate were the most effective fractions against the pathogen in both strains, achieving similar protection rates although gene expression responses were different from that obtained by the bacteria. Conclusions Beneficial rhizobacteria and its metabolic elicitors have great potential as biotechnological tools since they are able to improve plant immune system through the triggering of either Salicylic acid or Jasmonic acid/Ethylene pathway or both pathways simultaneously. These results open a huge amount of biotechnological possibilities to develop biological products for agriculture in different situations and plant species.