Fungal Genes and Metabolites Associated with the Biocontrol of Soil-borne Plant Pathogenic Fungi

The biocontrol of plant pathogenic fungi includes two complementary approaches depending on whether the aim is to control soil-borne or air-borne pathogenic fungi. In the first case, natural biotic interactions within the indigenous microflora should be stimulated to regulate inoculum density and the infectious activity of pathogen populations. This strategy can be enhanced by inoculating one or more previously selected biocontrol agents. In the second case, one or more previously selected biocontrol agents can be sprayed on plant foliage to interfere with the development of the targeted pathogen through different mechanisms involving particular enzymes or metabolites. Selecting the most effective biological control agents implies (i) knowing the mechanisms of their interactions with the pathogens and (ii) checking that the environment in which the biocontrol agent is introduced will permit the expression of these mechanisms. The common thread of this chapter is the impressive diversity of metabolites and proteins produced by fungi and involved in interactions between pathogenic and nonpathogenic fungi. Many metabolites and proteins were discovered empirically or by chance a few decades ago, and what we knew about them was they inhibited the growth of pathogenic models on agar medium. Fungi producing these metabolites were not well-known fungal species and were not used as biocontrol agents. However, the demonstration of their intense metabolic activity paved the way for more investigations in this area and led to deciphering the mechanisms of interactions between fungal strains. Thus, in recent years a large number of enzymes, signal molecules, secondary metabolites, large-size proteins, as well as new metabolic pathways have been revealed by genomics, and it is now possible to understand why some strains can control a given pathogen more than others or stimulate plant defense reactions. To date, the most studied fungi include many strains of the genus Trichoderma but also the species Chlonostachys rosea, Coniothyrium minitans, Verticillium biguttatum, and the oomycete Pythium oligandrum. All of them are successfully used as biocontrol agents. This chapter does not aim to provide a comprehensive catalog, but rather to associate these metabolites and proteins to the modes of action involved in pathogen control. The state of the art presented in this review suggests promising prospects for rational, appropriate, and effective use of the biocontrol potential offered by the huge diversity of fungal metabolites and proteins.