Genomic / transcriptomic approaches to fungus-pest interactions and biological control

The project aims at studying biological control agents and plant growth promoting microorganisms. Their exploitation in sustainable strategies can reduce pressures on ecosystem services and natural resources, on which human societies will increasingly depend. The development of such sustainable strategies is urgently needed. Pesticides use is increasingly regulated in the European Union and the production of fertilizers is ecologically costly and relies on limited natural resources. To this end the genomic and transcriptomic analysis of Clonostachys and a comparison of the underlying molecular mechanisms for biological control in Clonostachys and Trichoderma will be performed. Although they belong to distantly related families of the Hypocreales, both possess traits that include plurivorous life styles such as mycoparasitism/mycotrophy and parasitism on animal pests of plants. On the basis of the proposed research, new biological control agents and plant growth promoters could be discovered. Also, it may lead at better understanding the underlying mechanisms of interactions between beneficial microorganisms and their hosts, which is a prerequisite for their exploitation in sustainable production systems.

Nematodes (roundworms) have established themselves in all ecosystems of earth. Over 25,000 species have been described of which more than half are parasitic on animals or plants. Plant parasitic nematodes cause a total global agricultural damage of more $100 billion USD per year. Due to their broad host range root-rot nematodes cannot be controlled by crop rotation. They are today the most commonly controlled with chemical nematicides. However, the heightened scientific interest on the establishment of integrated pest management strategies in order to reduce the application of chemical pesticides, has raised interest in biological control. The soil filamentous fungus Trichoderma longibrachiatum is a promising candidate for this, as it can effectively infect eggs and worms. However, T. longibrachiatum is also known as a facultative pathogen of immunocompromised vertebrates and humans. In this project we investigated the genetic basis for these traits, by sequencing and annotating the genomes of T. longibrachiatum, and two of its close neighbors T. citrinoviride (also a facultative pathogen but ineffective against nematodes) and T. parareesei (which affects neither humans and vertebrates nor nematodes). An in depth comparison of their genomic inventory that consists of around 10.000 genes revealed that more than 93 % of them are conserved, and the remaining genes that occur only in one or two of them are mostly unknown or orphan genes. The expression of the aforementioned different lifestyles therefore is most likely due to differential gene expression or epigenetic regulation. In order to study this experimentally, we developed a dual cultivation system in which epithelial cells are confronted with Trichoderma, and the cells and fungus be sampled for further analysis.