A detailed mechanistic understanding about plant-microbe interactions in the rhizosphere is essential for a sustainable production of crops under changing environmental conditions. Mainly the use of plant growth promoting rhizobacteria as inocula to improve plant health, is depending on an improved knowledge of microbial functionality in the root surrounding area.. Microbial activities of rhizosphere soil have been so far determined by classical techniques such as those for determining soil respiration, enzyme activities, N mineralization, adenylate energy charge, etc which do not give any data on gene induction and expression. Methods are now available to determine gene expression at both transcription (extraction and characterization of RNA) and translational (proteomic approach) levels. Phenotypic expression in the rhizosphere soil of specific genes can be determined by a reporter assays, expressed from a constitutive or inducible promoter. Classical determination of microbial diversity in the rhizosphere soil has been criticised for the problem of unculturable microorganisms. The use of molecular techniques has allowed overcoming this problem The microbial gene expression can be also linked directly to plant performance by using stable isotopes. This methods will definitely help to give new insights into plant-microbe interactions and form the basis for a new mechanistic understanding.