Molecular ecology of Trichoderma in European forest soil

Trichoderma spp. are cosmopolitan soil fungi, remarkable for their rapid growth, capability of utilizing diverse substrates, and resistance to noxious chemicals. They are often predominant components of the mycoflora in various soils, such as agricultural, prairie, forest, salt marsh and desert soils in all climatic zones, where they are significant decomposers of woody and herbaceous materials, and are also necrotrophic against the primary wood decomposers. There have also been reports that some taxa (i.e. T. viride) would actually be harmful to plant roots. Several of the now established species of Trichoderma are also of economic importance because of their production of enzymes and antibiotics, or use as biocontrol agents. The occurrence of Trichoderma spp. in soil has been the subject of several investigations, most of them having been performed on ecosystems of the temperate regions of the Northern American Continent but they all suffer from the fact that species identification had been performed exclusively by morphological analysis and according to the key of RIFAI, both of which are now known to lead to ambiguous results. Consequently, while there is already a lot of information about the ecology of Trichoderma in soil, it is not known for which species this information is valid. Such an information would be important to understand the beneficial effects of Trichoderma on the plant rhizosphere and help to predict the behaviour of biocontrol strains in the environment. To this end, we propose here to study the occurrence of Trichoderma in primeval forest systems of Europe (boreal forests of middle taiga` subzones of the Komi Republic; virgin spruce forest at the Central Forest State Biosphere Reserve, Tverskaya district) which differ in climatic and ecological properties, and which have not been influenced by mankind, and to attempt to correlate their occurrence with physical and chemical properties of the soil and meterological data. To this end, we will isolate Trichoderma from soil, and identify strains at the species level by a previously established Trichoderma barcode. In addition - in order to overcome the bias odf this approach for fast growing species - we will construct a "Trichoderma-chip", which will enable us to simultaneously detect several taxa in the same soil sample. The data will not only shed light on the ecology of Trichoderma in forest soil, but also be an example for handling of similar studies on other fungal species.

Trichoderma is a genus of common filamentous fungi that display a remarkable range of life styles and interactions with plants, animals and other fungi. Because of their ability to stimulate plant growth and defence, some Trichoderma strains are used for biological control of plant diseases. However, the real Trichoderma diversity and compositions of infrageneric communities have not been investigated in details so far. In this project a comprehensive study of in situ molecular ecology of the genus has been performed. The most important achievement of the project was the demonstration that there is no hidden diversity of Trichoderma at least in temperate soils and that most of the spores distributed by the air also belong to the known species. On the other hand, less studied undisturbed ecosystems still serve as a depository for novel taxa. These findings in combination with genome inventory of the three species from the genus allowed us to propose a changed concept of Trichoderma ecology. We have shown that the previously widely accepted concept of Trichoderma being a predominantly a soil fungus has to be abandoned in favour of the vision that, irrespective to soil, this fungus as primarily mycotrophic (saprotrophically or biotrophically associated with other fungi). The latter property may have driven the evolution of Trichoderma towards environmental opportunism via such secondary nutritional strategies as efficient saprotrophy in soil and other substrata and towards interactions with plants (endophytism) and animals (opportunistic pathogenesity on humans). We also shown that several opportunistic Trichoderma species may coexist in one microecological niche of soil but also a biased distribution of some species in a vertical soil profile was noted. In vitro modelling of infrageneric communities disclosed a complex interaction network ranging from strong competition to synergism even between close genetic relatives. These results are to be considered for the selection of Trichoderma as agents of biological protection of crops against plant pathogenic fungi. The project provided data for several taxonomic and ecophysiological studies on the genus Trichoderma. Importantly, when combined with current achievements in genomics of Trichoderma, results obtained in a course of this project allowed to establish ecological genomics of the fungus, - a paradigm that is used to understand the nature of the fungus by looking at gene inventory and functions. This knowledge facilitates screening for novel traits in domestication of Trichoderma for biotechnology and agriculture.