The group of Microbiology (initially the project group Fungal Evolution and Biodiversity) was established in 2002, when the first application of molecular biology methods highlighted the urgent need for the study of microbial biodiversity. Since then, our research has focused on the diversity and evolution of filamentous fungi on the molecular level and on the development of the modern bioinformatic tools for their correct identification.

We are deeply interested in understanding the speciation process in mitosporic filamentous fungi and in the development of integrated DNA-based and metabolic species criteria that could be applied to the differentiation of these organisms. The main model organisms for our research are cosmopolitan fungi from the order Hypocreales; the mycoparasitic genus Trichoderma and the plant pathogenic fungus Fusarium.


Currently we are the most challenged by the comparative genomics of filamentous fungi as the genomes of Trichoderma and numerous related fungi have been sequenced. Our group is deeply involved in the sequencing of the several plant-beneficial species of Trichoderma and in genomics of such biotrophic species as mycoparasites (agents of biological control and pathogens of mushrooms), endophytes and pathogens of animals. We are interested in the revealing the ecological genomics of Trichoderma, we aim to understand the biology of this industrially important microorganisms through the function and evolution of its genomes. For this purpose we use the analysis of Trichoderma transcriptomes and apply methods of reverse genetics.

We are also interested in the evolution of Trichoderma mycoparasism as a genus-wide trait of the fungus. For this reason we compare mycoparasitism-associated genes of Trichoderma with those or other known fungicolous fungi such as Clonostachys or Escovopsis.  This knowledge constantly aids the screening various indigenous ecosystems for the best mycoparasitic strains of Trichoderma that can be locally applied for protection of such crops as coffee, cacao or banana.

The availability of numerous genomes opened an opportunity to develop a semi-automated genome annotation pipeline for Trichoderma and other fungi. This project attracts our deepest interest and is performed in cooperation with colleagues from China and the US.


In a course of a decade we were interested in a whole genus screening for the most appropriate biotechnological agents because Trichoderma is an important industrial microorganism used in the production of extracellular enzymes and in agriculture as agents of biological control of plant pathogenic fungi. For this purpose, we have conducted the research on the development of multigene molecular DNA barcode methods for quick in silico identification of Trichoderma. Expertise obtained in this area constantly attracts scientists and farmers world-wide aiming molecular identification of Trichoderma strains. In addition to molecular diversity and evolution, we are interested in the in situ ecology of these organisms and their nutritional preferences and interactions with other microbionts in their ecosystem. For this reason, we direct our research towards the introduction of modern metagenomic and metatranscriptomic methods. In this area our research also includes studies on molecular evolution of human pathogenic bacteria such as Vibrio cholera complex.

TUCIM TU Wien Collection of Industrial microorganisms

  • Since 2011 listed on organogram of the ICE
  • Established by Christian P. Kubicek before 2002 with 500 cultures
  • Financed and maintained by the Microbiology group
  • Powered by the interactive web-based database of gene sequences (MySQL, PHP)
  • Contains biogeographic tags
  • Stand alone local BLAST server
  • Contains ecophysiological profiles and image upload
  • for Oct 5, 2012: 5241 records


The skills in DNA barcoding and microbial ecology allow us to offer the service of mold diagnostics to general public. We have served numerous storage places, libraries and other in-door habitats to detect and identify mold-related damage and to estimate its potential risk for human health and stored materials.


The other focus of our research is the functional biodiversity of filamentous fungi. We developed semi-high-throughput methods of phenotype profiling to study the response of fungi to various abiotic factors (illumination, temperature, carbon and nitrogen nutrition) and their interactions with other microorganisms in the environment. In a course of this project we are now most interested in the newly discovered cross-talks between filamentous fungi and bacteria. For this purpose we now investigate Trichoderma - Burkholderia interaction that has been detected in natural ecosystem of the tropical rain forest.


The new branch of our research is the screening for novel Trichoderma hydrophobins, the small cystein-rich proteins, which have a potential of targeting enzymes to polymers. This project has been initialy developed in collaboration with Austrian Center of Industrial Biotechnology (ACIB) and now is an established area of our research that attracts industrial interest. In particular Trichoderma hydrophobins find their application in facilitating of enzymatic degradation of synthetic polymers such as PET and PLA and have high potential for biomedical applications. We now work on rational design of hydrophobins with improved surface propertiesand advanced biotechnological applications.


Our group holds expertise for heterologous protein production in various microbial cell factories ranging from E. coli to such eukaryotic systems as Pichia pastoris and Trichoderma reesei. These skills constantly attract industrial cooperation for needs of agriculture and biotechnology.


The mechanisms by which organisms compete for territory and resources are key processes in ecology. The carpenter ants in the Camponotus (Colobopsis) cylindricus complex (‘COCY’, or exploding ants), that dominate arboreal habitats in rain forests on Borneo, have evolved a so-far unique and remarkable behaviour: In territorial combat with enemy ants and other arthropods they sacrifice themselves by rupturing (autothysis) and releasing sticky and irritant contents of their hypertrophied mandibular glands to kill rivals. Voluntary self-sacrifice is very rare in nature, undoubtedly due to attendant fitness losses. It is known in termites and honeybees, where effective deployment in defence of the nest may leave self-sacrificing workers with indirect fitness. Contrary to that, workers of COCY ants forage solitarily and explode during one-on-one confrontations far from nests. Thus they are defending the territory against potential competitors probably for continuously renewing food resources such as phyllosphere microbes. The hypothesis of this project is that autothysis of ants far from their nests is a mechanism employed by COCY ants to protect a specific microbiome that co-evolved with them and which they use for nutrition. For this purpose we will study evolution of COCY ants and phyllosphere microbiomes on their foraging grounds. Our project will identify a new and major type of interaction between dominant rainforest insects, their associated microorganisms and plants.