PhD Projects

Research projects

  • Giant viruses as symbionts in amoeba

    The discovery of giant viruses changed our perception of the viral world. With genome and particle sizes comparable to those of bacteria and a number of cellular features, such as nearly complete sets of translation-related genes, giant viruses sparked a [...]


    Many ants live in symbiotic relationships with plants (myrmecophytes) that provide nesting space (domatia) and plant-derived food sources in the form of extrafloral nectar and/or specialised food bodies. Importantly, recent studies have shown that also other groups of organisms are [...]

  • Chromosome segregation in animal associated bacteria

    Bacterial chromosome segregation has been only studied in free-living organisms under controlled culturing conditions. In the course of my PhD, I investigate this fundamental process in Gammaproteobacteria that thrive attached to animal surfaces and cannot be reared in the laboratory. [...]

  • Genome evolution and metabolic characterization of Lucinid symbionts and close relatives

    Aims: Expand our knowledge of the metabolic capabilities of Lucinid symbiont and compare the genome structure and functions to free-living relatives. This will allow for A) determining the evolutionary origin of Lucinid symbionts (Deep or shallow sea) and B) determining [...]


    Knowledge of the identity of the partners in mutualism, their taxonomic placement and their potential functional repertoire is crucial basic information in mutualism research. The mutualism between the giant ciliate Zoothamnium niveum and its chemoautotrophic ectosymbiont Cand. Thiobios zoothamnicoli from [...]

  • Characterization of natural chlamydial communities

    Chlamydiae, such as Chlamydia trachomatis or C. pneumoniae, are well known bacterial pathogens of humans and animals. Only in the past 20 years closely related bacteria have been found in diverse environments where they thrive as symbionts in protists or [...]

  • Biology and evolution of the intracellular lifestyle in protists

    Bacteria infecting protists are diverse and often share conserved virulence mechanisms. Yet, they may differ fundamentally with respect to their intracellular niche and strategies for host-interaction. These symbionts often share a common ancestry with bacterial pathogens of humans, suggesting an [...]

  • Genome-metabolome modeling and metabolome predictions in microbial symbioses

    Metabolites are central for host-microbe and microbe-microbe interactions. Whole genome or metagenomic bin-based predictions of bacterial metabolism could not yet reasonably predict metabolites, which are central for host-microbe and microbe-microbe interactions.

    Aims: We propose that lack of predicted proteins in [...]


    Dinaric karst caves are unique ecosystems that host an extraordinarily high biodiversity. Recently, centimeter-long “sprout-like” microbial consortia that grow on karst cave stream bed rocks were structurally and phylogenetically described. The major organism forming these consortia is an uncultured novel [...]

  • Effects and dynamics of the root-microbiome of halophytic plants under changing environmental conditions

    Plant-microbe associations harbor multiple beneficial effects for both the plants and associated microbiota. Such associations are also recognized for halophytic plants and suggested to help the plants to sustain the stressful environment. However, much in this association is still unknown [...]

  • Chlamydiae in woodlice: Studying microbe-host interaction in the natural environment

    Chlamydia are well-known pathogens of humans and animals but are also ubiquitous in the environment. Rhabdochlamydia porcellionis infecting the rough woodlouse Porcellio scaber represents a good model system for studying natural chlamydial populations, their genetic heterogeneity, infection and developmental cycle [...]

  • The role of the virome in the metabolic landscape of the neonate gut microbiome

    Though bacteriophages are abundant in the gut, an understanding of their importance to the microbiome is lacking. Phages may control populations, contribute to dysbiosis, and facilitate horizontal gene transfer. They also offer a targeted means to modulate the microbiota (i.e. [...]

  • Interactions of members of the Candidate Phyla Radiation (CPR) with prokaryotic and eukaryotic hosts in a WWTP

    Members of the Candidate Phyla Radiation (CPR) represent a significant fraction (>15%) of the total bacterial diversity of Earth. Almost all members of the CPR are uncultured and their reduced genomes encode very limited biosynthetic capabilities, strongly suggesting a lifestyle [...]

  • Physiological determinants of microbial sulfidogenesis in the intestinal environment

    H2S is an ambivalent molecule produced by commensal gut bacteria but also by the human host. It has detrimental impact on gut epithelial barrier during intestinal inflammation but also manifold beneficial functions. Intestinal H2S production by the microbiota is dependent on [...]

  • Host-microbe interactions in marine lucinid clams

    The symbiosis between lucinid clams and their chemosynthetic endosymbionts is ideal for understanding effects of seasonality; the symbionts rely on energy sources such as hydrogen sulfide from the environment, thus symbiont activity is intimately linked to environmental conditions. Lucinids experience [...]

  • Compaction and organization of animal symbiont chromosomes

    The bacterial nucleoid is highly condensed and forms compartment-like structures within the cell. Although its dynamic organisation is being investigated, we ignore the importance of chromosome structure for adaptation to changing environments and, in particular, for symbiosis maintenance. In this PhD project, [...]

  • Giant ciliate mutualism response to variable abiotic environment

    H2S plays a central role in the nutritional interactions of thiotrophic Cand. Thiobios zoothamnicoli and the colonial ciliate Zoothamnium niveum. Fitness is coupled between mutualistic partners according to H2S concentration (i.e. all forms of dissolved sulfide). H2S is notoriously instable [...]