Fungi in the genus Trichoderma have been known since at least the 1920s for their ability to act as biocontrol agents against plant pathogens. Until recently, the principal mechanisms for control have been assumed to be those primarily acting upon the pathogens and included mycoparasitism, antibiosis, and competition for resources and space. Recent advances demonstrate that the effects of Trichoderma on plants, including induced systemic or localized resistance, are also very important. These fungi colonize the root epidermis and outer cortical layers and release bioactive molecules that cause walling off of the Trichoderma thallus. At the same time, the transcriptome and the proteome of plants are substantially altered. As a consequence, in addition to induction of pathways for resistance in plants, increased plant growth and nutrient uptake occur. However, at least in maize, the increased growth response is genotype specific, and some maize inbreds respond negatively to some strains. Trichoderma spp. are beginning to be used in reasonably large quantities in plant agriculture, both for disease control and yield increases. The studies of mycoparasitism also have demonstrated that these fungi produce a rich mixture of antifungal enzymes, including chitinases and β-1,3 glucanases. These enzymes are synergistic with each other, with other antifungal enzymes, and with other materials. The genes encoding the enzymes appear useful for producing transgenic plants resistant to diseases and the enzymes themselves are beneficial for biological control and other processes.

Structural and functional genomics investigations are making an important impact on the current understanding and application of microbial agents used for plant disease control. Here, we review the case of Trichoderma spp., the most widely applied biocontrol fungi, which have been extensively studied using a variety of research approaches, including genomics, transcriptomics, proteomics, metabolomics, etc. Known for almost a century for their beneficial effects on plants and the soil, these fungi are the subject of investigations that represent a successful case of translational research, in which 'omics-generated novel understanding is directly translated in to new or improved crop treatments and management methods. We present an overview of the latest discoveries on the Trichoderma expressome and metabolome, of the complex and diverse biotic interactions established in nature by these microbes, and of their proven or potential importance to agriculture and industry.

Plants exist in close association with uncountable numbers of microorganisms around, on, and within them. Some of these endophytically colonize plant roots. The colonization of roots by certain symbiotic strains of plant-associated bacteria and fungi results in these plants performing better than plants whose roots are colonized by only the wild populations of microbes. We consider here crop plants whose roots are inhabited by introduced organisms, referring to them as Enhanced Plant Holobionts (EPHs). EPHs frequently exhibit resistance to specific plant diseases and pests (biotic stresses); resistance to abiotic stresses such as drought, cold, salinity, and flooding; enhanced nutrient acquisition and nutrient use efficiency; increased photosynthetic capability; and enhanced ability to maintain efficient internal cellular functioning. The microbes described here generate effects in part through their production of Symbiont-Associated Molecular Patterns (SAMPs) that interact with receptors in plant cell membranes. Such interaction results in the transduction of systemic signals that cause plant-wide changes in the plants’ gene expression and physiology. EPH effects arise not only from plant-microbe interactions, but also from microbe-microbe interactions like competition, mycoparasitism, and antibiotic production. When root and shoot growth are enhanced as a consequence of these root endophytes, this increases the yield from EPH plants. An additional benefit from growing larger root systems and having greater photosynthetic capability is greater sequestration of atmospheric CO₂. This is transferred to roots where sequestered C, through exudation or root decomposition, becomes part of the total soil carbon, which reduces global warming potential in the atmosphere. Forming EPHs requires selection and introduction of appropriate strains of microorganisms, with EPH performance affected also by the delivery and management practices.