Bacillus subtilis species group is frequently used biological agent for plant protection and growth promotion. To improve their efficiency and persistence in the rhizosphere, we explore the ecology and evolution of Bacilli using experimental evolution on plant roots, testing their influence of plant development, dissecting secondary metabolite production diversity, and probing their presence in natural soil. Here, I will present interaction of Bacilli with other soil microorganisms, testing the prevalence of competition or cooperation and demonstrating the importance of secondary metabolites for establishment in synthetic microbial communities. Finally, I will highlight how we test microbial interactions in simplified plant cultivation systems.