The use of beneficial microorganisms to suppress plant diseases has become a reliable alternative to reduce the application of pesticides. There is a strong growing market for microbial inoculants worldwide with an annual growth rate of approximately 10%. The use of ‘Omic technologies leads to products with more predictable and consistent effect. The future success of biological control will depend on interdisciplinary researches about the ecological interactions taking place in soil and root environment.Aim of the present research is to gain insight on the interaction between biological control agents (BCAs) and to assess its potential synergistic effect on suppression of the fungal pathogen Verticillium dahliae and on plant growth and health. The protagonists of the research are one of the most important beneficial fungus for agriculture, Trichoderma velutinum G1/8 and one of the most promising candidate for application as a BCA and plant growth promotion, the bacterium Stenotrophomonas rhizophila DSM14405T. Character of absolute innovation is the assessment of the role played by secondary metabolites and volatile organic compounds (VOCs) in the interaction between the BCAs, between the BCAs and the pathogen and between the BCAs and the plant.Controlled lab-based and environmental microcosms will be developed to carry out the molecular ecological interactions. DNA-based methodologies in combination with proteomic and confocal laser scanning microscopy will be used to assess the dynamics of interaction, biocontrol activity and expression of each other’s primary biocontrol genes.This research effort will result in new knowledge of the mode of the interaction between BCAs, BCAs and the pathogen, and BCAs and the plant. This will constitute the basis for the development of innovative biotechnological applications.