The Department of Microbial Ecology at the NIOO Centre for Limnology (shortname: KNAW.NIOO.CL) investigates the structure and function of microbial communities in freshwater. The work concentrates thematically on the microbial loop and its members, with emphasis on heterotrophic bacteria and cyanobacteria, but also including protists and bacterial viruses. In addition to classical microbiological techniques, the benefits of three advanced methodologies are combined to shift the limits of observation. Flowcytometry and cell sorting are used to characterize community structure and separate different functional compartments of the microbial loop. Isotope ratio mass spectrometry is used to investigate the routing of different carbon sources into different compartments. Molecular biological techniques are employed to investigate the composition and dynamics of the community by means of marker genes.

The group was among the first to take stock of freshwater bacterial diversity using molecular techniques. Together with collaborating groups abroad, they have shown the ubiquity of specific narrow clusters of alpha and beta proteobacteria in diverse freshwater bodies around the globe. The growing number of similar in-depth molecular studies of bacterial diversity confirm the cosmopolitan nature of these clusters and reveal yet other clusters of bacteria specific for the freshwater habitat. This work shows which bacterial groups are really abundant in freshwater bodies and consequently determine much of the properties of the microbial community. The Department of Microbial Ecology now investigates these groups as to their ecology and meaning for the functioning and state of the ecosystems they inhabit.