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.

By the year 2050, there will be at least 9 billion people on Earth to feed using the same amount or less land and water than is available today. Currently, about one-third of all potential agricultural commodities grown worldwide are lost to diseases, weeds, insects and other pests. Farmers will be challenged to produce more, but to do so using sustainable cropping practices and less fertilizer and pesticides. Biological control is an integral part of sustainable agriculture. This chapter provides an overview of the topics of the construction, activity and use of transgenic biocontrol agents (BCAs) and their future potential in 21st century agriculture.

This chapter briefly describes some examples of past and present (next to potential novel) applications of genetically modified micro-organisms to soil, stressing the importance of analysing the putative impacts of such applications to the life support functions (LSF) of a living soil at three levels: i) functioning for soil fertility; ii) functioning for pathogen suppressiveness; iii) functioning for the provision of clean drinking water. To understand the impact of such genetically modified micro-organism applications on the soil, it is important to deepen our understanding of the microbial communities that are responsible for the key LSF of that soil. Moreover, we need to understand how these might be affected mechanistically. It is, therefore, important to further develop databases that contain extensive data on the microbial communities in the soil systems under study. This chapter advocates the application of the currently available powerful methods, which enable the dissection of soil microbial systems into their individual components. Finally, the chapter proposes the definition of a normal operating range (NOR) to fit the dataset obtained into a framework which is quantifiable and may serve to support decision making.