Modern sequencing techniques revealed the existence of a vast majority of microorganisms that are uncultured to date – the “microbial dark matter”. Bacteria belonging to these so-called candidate phyla (CP) often have small, reduced genomes and are likely living in symbiotic or parasitic relationships with other microorganisms. Using an innovative droplet-microfluidics platform, the project DarkMicro will analyze metabolic dependencies of CP bacteria from groundwater samples by co-cultivating them with putative hosts. The ultrahigh-throughput incubation of bacterial cultures in picoliter droplets opens new perspectives for studying the interactions in complex microbial communities and discovering the “microbial dark matter”.

The fraction of photosynthetically active light determines the oxygen and nutrient concentration in deeper waters and leads to physiological adaptations in the plankton microbiome. The project Light into Darkness will use novel materials for spatially and spectrally directed delivery of light into deep water layers. The metabolic regulative processes in microalgae in response to the light exposure will be monitored at the cellular and sub-cellular level. Such system for targeted light delivery will pave the way for controlled manipulative experiments, allowing the study of disturbed microbial communities.

In a combined effort of optical physicists and microbiologists, the project NISUS explores 3D XUV nanoscopy in a lab scale for imaging microbiological samples. Interactions of single cells are the main driving forces behind microbial communities in the environment, and also determine the outcome of human infections. The aim is to develop a “road map” on how to image microorganisms with modern XUV imaging techniques and to make them accessible to a wide range of bio-medical applications.

Cobamides are exclusively produced by a limited number of prokaryotes and are essential cofactors in universal metabolic pathways. The project B-TWELVE will investigate the molecular mechanisms underlying the structural diversity among B₁₂ vitamers. Their selective use by bacteria and microalgae is going to be analyzed. Efforts are made to improve the in situ detection of cobamides via Surface-Enhanced Raman Spectroscopy (SERS) and to establish a discrimination method for cobamides in natural samples. The project aims to develop a strategy for the use of cobamides as chemical tool to fine-adjust the fitness of individual players in a microbial community.

The human pathogen Staphylococcus aureus causes serious invasive infections and may persist as small colony variants in host cells. The incorporation of host fatty acids into the cellular membranes may allow the pathogen to evade the host immune defense during chronic infection. The project Lipstaph will investigate the transfer and potential immunomodulatory function of fatty acids in S. aureus and host cells. Understanding the mechanisms may open up new treatment opportunities for staphylococcal chronic infections in the future.