Biofertilizers are living microbial preparations which enhance or promote plant growth, relatively to a control without inoculation. A huge amount of research literature has been produced in the last 20 years concerning plant growth-promoting rhizobacteria (PGPR) related subjects, describing different micro-organisms acting on different plants, and proposing different mechanisms to explain the plant growth promotion effect. However, we still do not know which of the different in vitro mechanisms of biofertilizer action are responsible for the positive effects in the field. Biofertilizer technology has significantly developed in the market. The nature of multiple mechanisms discovered for PGPR actions and the possibility of genetically modifying a particular strain concerning a particular plant growth-promoting activity suggest that the use of genetically modified organisms such as biofertilizers will be an area of multiple and diverse possibilities of action in the near future. The study of the microbial ecology of this scenario and its dynamics will certainly improve the development of biofertilizer technology for the future of agriculture.