The Department of Molecular Ecology directs its work towards understanding the structure and function of microbial communities and their dynamics with regard to biotic and abiotic changes in the environment. The habitats that are under investigation in our group are of different complexity.
Usually the molecular methods developed for pure cultures and enrichments are optimized for environmental use in more defined systems like biofilms or symbiotic associations and finally adapted to the study of more complex systems such as planktonic or benthic bacterial communities.

Focus on cultivation-independent techniques

We identify marine microorganisms on the basis of their genes (DNA). A key player is the gene for the ribosomal RNA (rRNA) – the “backbone” of the ribosome, which is the protein factory of the cell. It is well suited to classify microorganisms, but also to identify them in the environment.

First, we isolate the DNA from the sample and identify the rRNA genes. Via comparative sequence analysis, the identity of the microorganisms can be reconstructed and each sequence is taxonomically affiliated. Thereby, we can estimate the diversity of the entire microbial community.

In a next step, we develop rRNA targeted DNA oligonucleotides (so called probes) for specific, taxonomically well-defined groups of microorganisms. Probes are short fluorescently-labeled DNA fragments, which specifically bind to the rRNA of ribosomes within intact cells (Fluorescence in situ hybridization, FISH).

The advantage of these techniques is that not only diversity, but also abundance of microorganisms can be determined without prior cultivation.

More and more frequently, the whole genomic information of microorganisms is deciphered (whole genome sequencing). Each gene codes for a certain protein, which plays a specific role within the metabolism of the cell, shedding light on the life style of the microorganisms and their relationships to the environment.