I started my scientific career in molecular paleontology using antibodies to study the macromolecular remains in fossil shells and dinosaur bones. Inspired by the work of the American scientists Norman Pace and David Stahl, I changed my research interests from dinosaurs to microbes. In 1993, I introduced DGGE (denaturing gradient gel electrophoresis) in microbial ecology as an easy, rapid and cost-effective method to study the structure and dynamics of microbial communities. DGGE changed the field of Microbial Ecology completely; for the first time, it became possible to compare different microbial communities simultaneously, and to monitor population changes over time and after perturbations in a single view. Over the years, DGGE has been used successfully by hundreds of microbiologists from all over the world, including developing countries, to study the diversity of microbial communities. I used the method to study microbial communities from different natural and engineered ecosystems and was astonished by the enormous microbial diversity present in these environments. Although being able to characterize microbial communities with molecular techniques, I strongly believe, as a true representative of the ‘Delft School of Microbiology’, that isolation of microbes in pure culture is required for a comprehensive understanding of their role and behavior in nature.
In 2011, I accepted a position as Full Professor of Microbial Systems Ecology in the Institute for Biodiversity and Ecosystem Dynamics at the University of Amsterdam. By applying a systems biology approach, which includes experimental work, the use of state-of-the-art omics techniques, and mathematical modelling, I am studying the diversity and activity of microbial communities, the interactions (competition/coexistence) between different community members, and the role of diversity in ecosystem functioning. In 2012, I received a prestigious ERC Advanced Grant on a project entitled ‘The Paradox of Sulfur Bacteria in Soda Lakes’ (PARASOL) to study the diversity and ecophysiology of sulfur bacteria in soda lakes, their niche differentiation, and the molecular mechanisms by which they adapt to extreme halo-alkaline conditions.
Currently, I am coordinator of the research priority area ‘Systems Biology’ of the University of Amsterdam. Within this RPA we are focusing on host-microbe interactions in humans, plants and other organisms, such as sponges. I already studied the host-microbe interactions in seagrasses, but recently started to study the host-microbe interactions in the green alga Caulerpa. Within this research I will use a systems biology approach to study both host and microbiome (‘holobiont’) at different levels of organization, i.e., from molecule to ecosystem, and so hope to obtain a comprehensive understanding on the role of the microbiome in growth, development and ecological success of Caulerpa.
algal genomics, Caulerpa, climate change, ecology, evolution, holobiont, hologenome, macroalgae, marine biology, marine microbiology, mathematic modeling, metabolic modeling, meta-omics, microbiology, microbial ecology, molecular biology, seagrasses, seaweed, soda lakes, stable isotope probing, sulfur bacteria, system biology