Plants and microbes in the rhizosphere are constantly interacting in a chain, from pathogens (deleterious) to symbionts (beneficial). Relationships between the two sides are very large at various stages of plant development, and signaling molecules play a significant role on both sides. The result of this conversation is that the microbe is absorbed by the plant’s roots and responds to it. Among the microbes that approach the roots of plants during this signal conversation are the plant growthpromoting rhizobacteria (PGPR). In order to emphasize the beneficial effects of PGPR on the plant, it is important for the roots of the plants to be colonized by PGPR. Colonization of plant roots by PGPR induces beneficial effects on the plant, such as increasing the overall growth of the plant, resistance to disease, and increasing tolerance to abiotic stresses. Among the mechanisms used by PGPR to increase plant growth are: eliminating the need for plant nitrogen by fixing the molecular nitrogen of the atmosphere, increasing the bioavailability of nutrients needed by plants such as phosphorus, potassium, and iron producing various growth hormones and regulators such as auxins, cytokinins, and gibberellins, reducing the level of ethylene produced by plant roots under stress conditions, etc. Since PGPR may modulate plant regulatory mechanisms, an important question to be answered is how is the plant–microbe relationship, and what factors play a role in it, and whether or not the microbes can influence the expression of different plant genes at different times? To answer these questions, transcriptomics analysis is an ideal technique that has been addressed in this chapter.
